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Jacobi T, Kratzer DA, Plapp BV. Substitution of both histidines in the active site of yeast alcohol dehydrogenase 1 exposes underlying pH dependencies. Chem Biol Interact 2024; 394:110992. [PMID: 38579923 DOI: 10.1016/j.cbi.2024.110992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/13/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Histidine residues 44 and 48 in yeast alcohol dehydrogenase (ADH) bind to the coenzymes NAD(H) and contribute to catalysis. The individual H44R and H48Q substitutions alter the kinetics and pH dependencies, and now the roles of other ionizable groups in the enzyme were studied in the doubly substituted H44R/H48Q ADH. The substitutions make the enzyme more resistant to inactivation by diethyl pyrocarbonate, modestly improve affinity for coenzymes, and substantially decrease catalytic efficiencies for ethanol oxidation and acetaldehyde reduction. The pH dependencies for several kinetic parameters are shifted from pK values for wild-type ADH of 7.3-8.1 to values for H44R/H48Q ADH of 8.0-9.6, and are assigned to the water or alcohol bound to the catalytic zinc. It appears that the rate of binding of NAD+ is electrostatically favored with zinc-hydroxide whereas binding of NADH is faster with neutral zinc-water. The pH dependencies of catalytic efficiencies (V/EtKm) for ethanol oxidation and acetaldehyde reduction are similarly controlled by deprotonation and protonation, respectively. The substitutions make an enzyme that resembles the homologous horse liver H51Q ADH, which has Arg-47 and Gln-51 and exhibits similar pK values. In the wild-type ADHs, it appears that His-48 (or His-51) in the proton relay systems linked to the catalytic zinc ligands modulate catalytic efficiencies.
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Affiliation(s)
- Tobias Jacobi
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Darla Ann Kratzer
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA.
| | - Bryce V Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA.
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2
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Ushimaru R. Functions and mechanisms of enzymes assembling lignans and norlignans. Curr Opin Chem Biol 2024; 80:102462. [PMID: 38692182 DOI: 10.1016/j.cbpa.2024.102462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 05/03/2024]
Abstract
Lignans and norlignans are distributed throughout the plant kingdom and exhibit diverse chemical structures and biological properties that offer potential for therapeutic use. Originating from the phenylpropanoid biosynthesis pathway, their characteristic carbon architectures are formed through unique enzyme catalysis, featuring regio- and stereoselective C-C bond forming processes. Despite extensive research on these plant natural products, their biosynthetic pathways, and enzyme mechanisms remain enigmatic. This review highlights recent advancements in elucidating the functions and mechanisms of the biosynthetic enzymes responsible for constructing the distinct carbon frameworks of lignans and norlignans.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan.
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3
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Mealka M, Sierra NA, Matteo DA, Albekioni E, Khoury R, Mai T, Conley BM, Coleman NJ, Sabo KA, Komives EA, Bobkov AA, Cooksy AL, Silletti S, Schiffer JM, Huxford T, Sohl CD. Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms. Res Sq 2024:rs.3.rs-3889456. [PMID: 38464189 PMCID: PMC10925425 DOI: 10.21203/rs.3.rs-3889456/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant uniquely preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employed static and dynamic structural methods and found that, compared to R132H, the R132Q active site adopted a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling revealed a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.
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Affiliation(s)
- Matthew Mealka
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nicole A. Sierra
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | | | - Elene Albekioni
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Rachel Khoury
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Timothy Mai
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Brittany M. Conley
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nalani J. Coleman
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Kaitlyn A. Sabo
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Elizabeth A. Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Andrey A. Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA USA
| | - Andrew L. Cooksy
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Steve Silletti
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | | | - Tom Huxford
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Christal D. Sohl
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
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4
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Mealka M, Sierra NA, Matteo DA, Albekioni E, Khoury R, Mai T, Conley BM, Coleman NJ, Sabo KA, Komives EA, Bobkov AA, Cooksy AL, Silletti S, Schiffer JM, Huxford T, Sohl CD. Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms. bioRxiv 2024:2024.01.10.574970. [PMID: 38260668 PMCID: PMC10802581 DOI: 10.1101/2024.01.10.574970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant uniquely preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employed static and dynamic structural methods and found that, compared to R132H, the R132Q active site adopted a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling revealed a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.
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Affiliation(s)
- Matthew Mealka
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nicole A Sierra
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | | | - Elene Albekioni
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Rachel Khoury
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Timothy Mai
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Brittany M Conley
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nalani J Coleman
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Kaitlyn A Sabo
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Elizabeth A Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA USA
| | - Andrew L Cooksy
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Steve Silletti
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | | | - Tom Huxford
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Christal D Sohl
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
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5
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Mogensen LS, Mikkelsen SA, Tadini-Buoninsegni F, Holm R, Matsell E, Vilsen B, Molday RS, Andersen JP. On the track of the lipid transport pathway of the phospholipid flippase ATP8A2 - Mutation analysis of residues of the transmembrane segments M1, M2, M3 and M4. Biochim Biophys Acta Mol Cell Res 2024; 1871:119570. [PMID: 37678495 DOI: 10.1016/j.bbamcr.2023.119570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
P4-ATPases, also known as flippases, translocate specific lipids from the exoplasmic leaflet to the cytoplasmic leaflet of biological membranes, thereby generating an asymmetric lipid distribution essential for numerous cellular functions. A debated issue is which pathway within the protein the lipid substrate follows during the translocation. Here we present a comprehensive mutational screening of all amino acid residues in the transmembrane segments M1, M2, M3, and M4 of the flippase ATP8A2, thus allowing the functionally important residues in these transmembrane segments to be highlighted on a background of less important residues. Kinetic analysis of ATPase activity of 130 new ATP8A2 mutants, providing Vmax values as well as apparent affinities of the mutants for the lipid substrate, support a translocation pathway between M2 and M4 ("M2-M4 path"), extending from the entry site, where the lipid substrate binds from the exoplasmic leaflet, to a putative exit site at the cytoplasmic surface, formed by the divergence of M2 and M4. The effects of mutations in the M2-M4 path on the function of the entry site, including loss of lipid specificity in some mutants, suggest that the M2-M4 path and the entry site are conformationally coupled. Many of the residues of the M2-M4 path possess side chains with a potential for interacting with each other in a zipper-like mode, as well as with the head group of the lipid substrate, by ionic/hydrogen bonds. Thus, the translocation of the lipid substrate toward the cytoplasmic bilayer leaflet is comparable to unzipping a zipper of salt bridges/hydrogen bonds.
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Affiliation(s)
| | | | | | - Rikke Holm
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Eli Matsell
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bente Vilsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, Canada
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6
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Plapp BV, Kratzer DA, Souhrada SK, Warth E, Jacobi T. Specific base catalysis by yeast alcohol dehydrogenase I with substitutions of histidine-48 by glutamate or serine residues in the proton relay system. Chem Biol Interact 2023; 382:110558. [PMID: 37247811 PMCID: PMC10527620 DOI: 10.1016/j.cbi.2023.110558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/31/2023]
Abstract
His-48 in yeast alcohol dehydrogenase I (His 51 in horse liver alcohol dehydrogenase) is a highly conserved residue in the active sites of many alcohol dehydrogenases. The imidazole group of His-48 may participate in base catalysis of proton transfer as it is linked by hydrogen bonds through the 2'-hydroxyl group of the nicotinamide ribose and the hydroxyl group of Thr-45 to the hydroxyl group of the alcohol bound to the catalytic zinc. In this study, His-48 was substituted with a glutamic acid residue to determine if a carboxylate could replace imidazole or to a serine residue to determine if the exposure of the 2'-hydroxyl group of the ribose to solvent would allow proton transfer to water without base catalysis. At pH 7.3, the H48E substitution increases affinity for NAD+ and NADH 17- or 2.6-fold, but decreases catalytic efficiency (V/Km) on ethanol by 70-fold and on acetaldehyde by 6-fold relative to wild-type enzyme. The H48S substitution increases affinity for coenzymes by 2-fold and decreases (V/Km) on ethanol and acetaldehyde only by ∼3-fold. The substituted enzymes show substrate deuterium isotope (H/D) effects of 3-4 for turnover number (V1) and catalytic efficiency (V1/Kb) for ethanol oxidation, indicating that hydrogen transfer is partially rate-limiting and suggesting a somewhat more random mechanism for binding of ethanol and NAD+. For reduction of acetaldehyde, the deuterium isotope effects are small, and the kinetic mechanism appears to be ordered for binding of NADH first and acetaldehyde next. The pH dependencies for H48E and H48S ADHs can be described by a mechanism with pK values of about 6-7 and 9. However, the pH dependencies for oxidation of ethanol and butanol by the H48S enzyme are also simply described by a straight line, with slopes of log V1/Kb against pH of 0.37 or 0.43, respectively. The linear dependence apparently represents catalysis by hydroxide that has a low activity coefficient due to the protein environment, or to a kinetically complex proton transfer. The effects of the substitutions of His-48 show that this residue contributes to catalysis, although many dehydrogenases also have other residues.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Darla Ann Kratzer
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Susan K Souhrada
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Edda Warth
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Tobias Jacobi
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
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7
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Zhang S, Zhang L, Greule A, Tailhades J, Marschall E, Prasongpholchai P, Leng DJ, Zhang J, Zhu J, Kaczmarski JA, Schittenhelm RB, Einsle O, Jackson CJ, Alberti F, Bechthold A, Zhang Y, Tosin M, Si T, Cryle MJ. P450-mediated dehydrotyrosine formation during WS9326 biosynthesis proceeds via dehydrogenation of a specific acylated dipeptide substrate. Acta Pharm Sin B 2023; 13:3561-3574. [PMID: 37655329 PMCID: PMC10465960 DOI: 10.1016/j.apsb.2023.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
WS9326A is a peptide antibiotic containing a highly unusual N-methyl-E-2-3-dehydrotyrosine (NMet-Dht) residue that is incorporated during peptide assembly on a non-ribosomal peptide synthetase (NRPS). The cytochrome P450 encoded by sas16 (P450Sas) has been shown to be essential for the formation of the alkene moiety in NMet-Dht, but the timing and mechanism of the P450Sas-mediated α,β-dehydrogenation of Dht remained unclear. Here, we show that the substrate of P450Sas is the NRPS-associated peptidyl carrier protein (PCP)-bound dipeptide intermediate (Z)-2-pent-1'-enyl-cinnamoyl-Thr-N-Me-Tyr. We demonstrate that P450Sas-mediated incorporation of the double bond follows N-methylation of the Tyr by the N-methyl transferase domain found within the NRPS, and further that P450Sas appears to be specific for substrates containing the (Z)-2-pent-1'-enyl-cinnamoyl group. A crystal structure of P450Sas reveals differences between P450Sas and other P450s involved in the modification of NRPS-associated substrates, including the substitution of the canonical active site alcohol residue with a phenylalanine (F250), which in turn is critical to P450Sas activity and WS9326A biosynthesis. Together, our results suggest that P450Sas catalyses the direct dehydrogenation of the NRPS-bound dipeptide substrate, thus expanding the repertoire of P450 enzymes that can be used to produce biologically active peptides.
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Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg 79104, Germany
| | - Anja Greule
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- EMBL Australia, Monash University, Clayton 3800, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
| | - Edward Marschall
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- EMBL Australia, Monash University, Clayton 3800, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
| | | | - Daniel J. Leng
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jingfan Zhang
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Joe A. Kaczmarski
- Research School of Chemistry, the Australian National University, Acton 2601, ACT, Australia
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton 3800, VIC, Australia
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg 79104, Germany
| | - Colin J. Jackson
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
- Research School of Chemistry, the Australian National University, Acton 2601, ACT, Australia
| | - Fabrizio Alberti
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Andreas Bechthold
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg 79104, Germany
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Manuela Tosin
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Max J. Cryle
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- EMBL Australia, Monash University, Clayton 3800, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
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8
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de Magalhães MTQ, de Araújo TS, Silva BM, Icart LP, Scapin SMN, da Silva Almeida M, Lima LMTR. Mutations in asparaginase II from E. coli and implications for inactivation and PEGylation. Biophys Chem 2023; 299:107041. [PMID: 37257341 DOI: 10.1016/j.bpc.2023.107041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023]
Abstract
All clinically-used asparaginases convert L-asparagine (L-Asn) to l-aspartate (L-Asp) and l-glutamine (L-Gln) to L-glutamate (L-Glu), which has been useful in reducing bioavailable asparagine and glutamine in patients under treatment for acute lymphoblastic leukemia. The E. coli type 2 L-asparaginase (EcA2) can present different sequences among varying bacterial strains, which we hypothesized that might affect their biological function, stability and interchangeability. Here we report the analysis of two EcA2 provided by the public health system of a middle-income country. These enzymes were reported to have similar specific activity in vitro, whereas they differ in vivo. Protein sequencing by LC-MS-MS and peptide mapping by MALDI-ToF-MS of their tryptic digests revealed that Aginasa™ share similar sequence to EcA2 from E. coli strain BL21(DE3), while Leuginase™ has sequence equivalent to EcA2 from E. coli strain AS1.357. The two amino acid differences between Aginasa™ (64D and 252 T) and Leuginase™ (64 N and 252S) resulted in structural divergences in solution as accessed by small-angle X-ray scattering and molecular dynamics simulation trajectories. The conformational variability further results in dissimilar surface accessibility with major consequences for PEGylation, as well as different susceptibility to degradation by limited proteolysis. The present results reveal that the sequence variations between these two EcA2 variants results in conformational changes associated with differential conformational plasticity, potentially affecting physico-chemical and biological properties, including proteolytic and immunogenic silent inactivation.
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Affiliation(s)
- Mariana T Q de Magalhães
- Laboratório de Biofísica de Macromoléculas - LBM, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biomédicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil.
| | - Talita Stelling de Araújo
- Protein Advanced Biochemistry - PAB, Centro Nacional de Biologia Estrutural e Bioimagem - CENABIO, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto de Bioquímica Médica Leopoldo De Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Bruno Marques Silva
- Laboratório de Biofísica de Macromoléculas - LBM, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biomédicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Luis Peña Icart
- Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Sandra M N Scapin
- Laboratório de Macromoléculas e Bioquímica (LAMAC), Coordenação-Geral de Metrologia em Biologia (COBIO), Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Duque de Caxias, RJ 25250-020, Brazil.
| | - Marcius da Silva Almeida
- Protein Advanced Biochemistry - PAB, Centro Nacional de Biologia Estrutural e Bioimagem - CENABIO, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Luís Maurício T R Lima
- Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Laboratório de Macromoléculas e Bioquímica (LAMAC), Coordenação-Geral de Metrologia em Biologia (COBIO), Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Duque de Caxias, RJ 25250-020, Brazil; Programa de Pós-Graduação em Quimica Biologica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil.
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9
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Giger S, Buller R. Advances in Noncanonical Amino Acid Incorporation for Enzyme Engineering Applications. Chimia (Aarau) 2023; 77:395-402. [PMID: 38047779 DOI: 10.2533/chimia.2023.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 05/17/2023] [Indexed: 12/05/2023] Open
Abstract
Incorporation of noncanonical amino acids (ncAAs) via genetic code expansion (GCE) opens up new possibilities for chemical biology. The technology has led to the development of novel xenobiotic enzymes with tailored properties which can serve as entry points into a multitude of applications, including protein conjugation, immobilization, or labeling. In this review, we discuss recent progress in the use of GCE to create biocatalysts possessing reaction repertoires that lie beyond what is achievable with canonical amino acids (cAAs). Furthermore, we highlight how GCE enables to gain mechanistic insights into protein function by the incorporation of judiciously selected ncAAs. As the amino acid alphabet continues to grow and improved tools for ncAA incorporation are being developed, we anticipate the creation of additional powerful biological catalysts for synthetic application which merge the chemical versatility of anthropogenic building blocks with the exquisite selectivities of enzymes.
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Affiliation(s)
- Sandro Giger
- Zurich University of Applied Sciences, School of Life Sciences and Facility Management, Institute of Chemistry and Biotechnology, Einsiedlerstrasse 31, CH-8820 Wädenswil.
- Vienna University of Technology, Faculty of Technical Chemistry, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 1060 Vienna, Austria
| | - Rebecca Buller
- Zurich University of Applied Sciences, School of Life Sciences and Facility Management, Institute of Chemistry and Biotechnology, Einsiedlerstrasse 31, CH-8820 Wädenswil,.
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10
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Coleman T, Podgorski MN, Doyle ML, Scaffidi-Muta JM, Campbell EC, Bruning JB, De Voss JJ, Bell SG. Cytochrome P450-catalyzed oxidation of halogen-containing substrates. J Inorg Biochem 2023; 244:112234. [PMID: 37116269 DOI: 10.1016/j.jinorgbio.2023.112234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/15/2023] [Accepted: 04/15/2023] [Indexed: 04/30/2023]
Abstract
Cytochrome P450 (CYP) enzymes are heme-thiolate monooxygenases which catalyze the oxidation of aliphatic and aromatic C-H bonds and other reactions. The oxidation of halogens by cytochrome P450 enzymes has also been reported. Here we use CYP199A4, from the bacterium Rhodopseudomonas palustris strain HaA2, with a range of para-substituted benzoic acid ligands, which contain halogens, to assess if this enzyme can oxidize these species or if the presence of these electronegative atoms can alter the outcome of P450-catalyzed reactions. Despite binding to the enzyme, there was no detectable oxidation of any of the 4-halobenzoic acids. CYP199A4 was, however, able to efficiently catalyze the oxidation of both 4-chloromethyl- and 4-bromomethyl-benzoic acid to 4-formylbenzoic acid via hydroxylation of the α‑carbon. The 4-chloromethyl substrate bound in the enzyme active site in a similar manner to 4-ethylbenzoic acid. This places the benzylic α‑carbon hydrogens in an unfavorable position for abstraction indicating a degree of substrate mobility must be possible within the active site. CYP199A4 catalyzed oxidations of 4-(2'-haloethyl)benzoic acids yielding α-hydroxylation and desaturation metabolites. The α-hydroxylation product was the major metabolite. The desaturation pathway is significantly disfavored compared to 4-ethylbenzoic acid. This may be due to the electron-withdrawing halogen atom or a different positioning of the substrate within the active site. The latter was demonstrated by the X-ray crystal structures of CYP199A4 with these substrates. Overall, the presence of a halogen atom positioned close to the heme iron can alter the binding orientation and outcomes of enzyme-catalyzed oxidation.
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Affiliation(s)
- Tom Coleman
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia
| | | | - Maya L Doyle
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia
| | | | - Eleanor C Campbell
- Australian Synchrotron, 800 Blackburn Rd, Clayton, Melbourne, VIC 3168. Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia.
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11
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Machado TFG, da Silva RG. Employing deuterium kinetic isotope effects to uncover the mechanism of (R)-3-hydroxybutyrate dehydrogenase. Methods Enzymol 2023; 685:225-240. [PMID: 37245903 DOI: 10.1016/bs.mie.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Short-chain dehydrogenases/reductases (SDR) form a large enzyme superfamily playing important roles in health and disease. Furthermore, they are useful tools in biocatalysis. Unveiling the nature of the transition state for hydride transfer is a crucial undertaking toward defining the physicochemical underpinnings of catalysis by SDR enzymes, including possible contributions from quantum mechanical tunneling. Primary deuterium kinetic isotope effects can uncover the contribution from chemistry to the rate-limiting step and potentially provide detailed information on the hydride-transfer transition state in SDR-catalyzed reactions. For the latter, however, one needs to determine the intrinsic isotope effect: that which would be measured if hydride transfer were rate determining. Alas, as is the case for many other enzymatic reactions, those catalyzed by SDRs are often limited by the rate of isotope-insensitive steps, such as product release and conformational changes, which masks the expression of the intrinsic isotope effect. This can be overcome by the powerful yet underexplored method of Palfey and Fagan via which intrinsic kinetic isotope effects can be extracted from pre-steady-state kinetics data. SDRs are ideal systems to which this method can be applied. We have employed this approach to elucidate the transition states for hydride transfer catalyzed by NADH-dependent cold- and warm-adapted (R)-3-hydroxybutyrate dehydrogenase. Experimental conditions which simplify the analysis are discussed.
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Affiliation(s)
- Teresa F G Machado
- School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, Fife, United Kingdom
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, Fife, United Kingdom.
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12
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Lee SG, Kim V, Lee GH, Kim C, Jeong E, Guengerich FP, Kim D. Hydroxylation and lyase reactions of steroids catalyzed by mouse cytochrome P450 17A1 (Cyp17a1). J Inorg Biochem 2023; 240:112085. [PMID: 36640554 PMCID: PMC9892303 DOI: 10.1016/j.jinorgbio.2022.112085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 01/12/2023]
Abstract
Cytochrome P450 17A1 (CYP17A1) catalyzes 17α-hydroxylation and 17,20-lyase reactions with steroid hormones. Mice contain an orthologous Cyp17a1 enzyme in the genome, and its amino acid sequence has high similarity with human CYP17A1. We purified recombinant mouse Cyp17a1 and characterized its oxidation reactions with progesterone and pregnenolone. The open reading frame of the mouse Cyp17a1 gene was inserted and successfully expressed in Escherichia coli and then purified using Ni2+-nitrilotriacetic acid (NTA) affinity column chromatography. Purified mouse Cyp17a1 displayed typical Type I binding titration spectral changes upon the addition of progesterone, 17α-OH progesterone, pregnenolone, and 17α-OH pregnenolone, with similar binding affinities to those of human CYP17A1. Catalytic activities for 17α-hydroxylation and 17,20-lyase reactions were studied using ultra-performance liquid chromatography (UPLC)-mass spectrometry analysis. Mouse Cyp17a1 showed cytochrome b5 stimulation in catalysis. In comparison to human enzyme, much higher specificity constants (kcat/Km) were observed with mouse Cyp17a1. In the reactions of Δ4-steroids (progesterone and 17α-OH progesterone), the specificity constants were 2100 times higher than the human enzyme. The addition of cytochrome b5 produced significant stimulation of 17,20-lyase activities of mouse Cyp17a1. Two Arg mutants of mouse Cyp17a1 (R347H and R358Q) displayed a larger decrease in 17,20-lyase reaction (from 17α-OH pregnenolone to dehydroepiandrosterone, DHEA) than 17α-hydroxylation, indicating that -as in human CYP17A1-these basic residues in mouse Cyp17a1 are important in interacting with the cytochrome b5 protein in the lyase reactions.
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Affiliation(s)
- Sung-Gyu Lee
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Vitchan Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Gyu-Hyeong Lee
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Changmin Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Eunseo Jeong
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - F. Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea.
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13
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Tran AD, Cho K, Han O. Rice peroxygenase catalyzes lipoxygenase-dependent regiospecific epoxidation of lipid peroxides in the response to abiotic stressors. Bioorg Chem 2023; 131:106285. [PMID: 36450198 DOI: 10.1016/j.bioorg.2022.106285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022]
Abstract
The peroxygenase pathway plays pivotal roles in plant responses to oxidative stress and other environmental stressors. Analysis of a network of co-expressed stress-regulated rice genes demonstrated that expression of OsPXG9 is negatively correlated with expression of genes involved in jasmonic acid biosynthesis. DNA sequence analysis and structure/function studies reveal that OsPXG9 is a caleosin-like peroxygenase with amphipathic α-helices that localizes to lipid droplets in rice cells. Enzymatic studies demonstrate that 12-epoxidation is slightly more favorable with 9(S)-hydroperoxyoctadecatrienoic acid than with 9(S)-hydroperoxyoctadecadienoic acid as substrate. The products of 12-epoxidation are labile, and the epoxide ring is hydrolytically cleaved into corresponding trihydroxy compounds. On the other hand, OsPXG9 catalyzed 15-epoxidation of 13(S)-hydroperoxyoctadecatrienoic acid generates a relatively stable epoxide product. Therefore, the regiospecific 12- or 15-epoxidation catalyzed by OsPXG9 strongly depends on activation of the 9- or 13- peroxygenase reaction pathways, with their respective preferred substrates. The relative abundance of products in the 9-PXG and 13-PXG pathways suggest that the 12-epoxidation involves intramolecular oxygen transfer while the 15-epoxidation can proceed via intramolecular or intermolecular oxygen transfer. Expression of OsPXG9 is up-regulated by abiotic stimuli such as drought and salt stress, but it is down-regulated by biotic stimuli such as flagellin 22 and salicylic acid. The results suggest that the primary function of OsPXG9 is to modulate the level of lipid peroxides to facilitate effective defense responses to abiotic and biotic stressors.
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Affiliation(s)
- Anh Duc Tran
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Kyoungwon Cho
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Oksoo Han
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea.
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14
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Kunert S, Emperle M, Adam S, Bräcker J, Brockmeyer J, Rajavelu A, Jeltsch A. The R736H cancer mutation in DNMT3A modulates the properties of the FF-subunit interface. Biochimie 2022:S0300-9084(22)00329-7. [PMID: 36528185 DOI: 10.1016/j.biochi.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
The DNMT3A DNA methyltransferase is an important epigenetic enzyme that is frequently mutated in cancers, particularly in AML. The heterozygous R736H mutation in the FF-interface of the tetrameric enzyme is the second most frequently observed DNMT3A cancer mutation, but its pathogenic mechanism is unclear. We show here that R736H leads to a moderate reduction in catalytic activity of 20-40% depending on the substrate, but no changes in CpG specificity, flanking sequence preferences and subnuclear localization. Strikingly, R736H showed a very strong stimulation by DNMT3L and the R736H/DNMT3L complex was 3-fold more active than WT/DNMT3L. Similarly, formation of mixed R736H/DNMT3A WT FF-interfaces led to an increased activity. R736H/DNMT3L and mixed R736H/DNMT3A WT FF-interfaces were less stable than interfaces not involving R736H, suggesting that an increased flexibility of the mixed interfaces stimulates catalytic activity. Our data suggest that aberrant activity of DNMT3A R736H may lead to DNA hypermethylation in cancer cells which could cause changes in gene expression.
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15
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Toraya T, Tobimatsu T, Mori K, Yamanishi M, Shibata N. Coenzyme B 12-dependent eliminases: Diol and glycerol dehydratases and ethanolamine ammonia-lyase. Methods Enzymol 2022; 668:181-242. [PMID: 35589194 DOI: 10.1016/bs.mie.2021.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Adenosylcobalamin (AdoCbl) or coenzyme B12-dependent enzymes catalyze intramolecular group-transfer reactions and ribonucleotide reduction in a wide variety of organisms from bacteria to animals. They use a super-reactive primary-carbon radical formed by the homolysis of the coenzyme's Co-C bond for catalysis and thus belong to the larger class of "radical enzymes." For understanding the general mechanisms of radical enzymes, it is of great importance to establish the general mechanism of AdoCbl-dependent catalysis using enzymes that catalyze the simplest reactions-such as diol dehydratase, glycerol dehydratase and ethanolamine ammonia-lyase. These enzymes are often called "eliminases." We have studied AdoCbl and eliminases for more than a half century. Progress has always been driven by the development of new experimental methodologies. In this chapter, we describe our investigations on these enzymes, including their metabolic roles, gene cloning, preparation, characterization, activity assays, and mechanistic studies, that have been conducted using a wide range of biochemical and structural methodologies we have developed.
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Affiliation(s)
- Tetsuo Toraya
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan.
| | - Takamasa Tobimatsu
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Koichi Mori
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Mamoru Yamanishi
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Naoki Shibata
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, Japan
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16
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Zhong Y, Gao Y, Zhou D, Ma X, Chen H, Xu Y, Yang W, Yu X. Structural basis for the activity and regulation of human α-ketoglutarate dehydrogenase revealed by Cryo-EM. Biochem Biophys Res Commun 2022; 602:120-6. [PMID: 35272141 DOI: 10.1016/j.bbrc.2022.02.093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 02/23/2022] [Indexed: 11/21/2022]
Abstract
The human mitochondrial alpha-ketoglutarate (α-KG) dehydrogenase complex (hKGDHc) is a well-studied macromolecular enzyme that converts α-KG to succinyl-CoA and NADH. Abnormalities of the complex lead to several diseases, including neurodegenerative disorders. Despite its importance in human metabolism and diseases, structural information on hKGDHc is not well defined. Here, we report the 2.92 Å resolution cryo-electron microscopy (EM) structure of its E1 component 2-oxoglutarate dehydrogenase (OGDH). The density map comprised residues 129-1,023, which is nearly the full length of OGDH. The structure clearly shows the active site and Ca2+ binding site of OGDH. This structural information will improve our understanding of the structure and function of hKGDHc and benefit pharmaceutical and basic science targeting this enzyme complex.
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17
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Lorenzi M, Ceccaldi P, Rodríguez-Maciá P, Redman HJ, Zamader A, Birrell JA, Mészáros LS, Berggren G. Stability of the H-cluster under whole-cell conditions-formation of an H trans-like state and its reactivity towards oxygen. J Biol Inorg Chem 2022; 27:345-355. [PMID: 35258679 PMCID: PMC8960641 DOI: 10.1007/s00775-022-01928-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/03/2022] [Indexed: 11/29/2022]
Abstract
Hydrogenases are metalloenzymes that catalyze the reversible oxidation of molecular hydrogen into protons and electrons. For this purpose, [FeFe]-hydrogenases utilize a hexanuclear iron cofactor, the H-cluster. This biologically unique cofactor provides the enzyme with outstanding catalytic activities, but it is also highly oxygen sensitive. Under in vitro conditions, oxygen stable forms of the H-cluster denoted Htrans and Hinact can be generated via treatment with sulfide under oxidizing conditions. Herein, we show that an Htrans-like species forms spontaneously under intracellular conditions on a time scale of hours, concurrent with the cells ceasing H2 production. Addition of cysteine or sulfide during the maturation promotes the formation of this H-cluster state. Moreover, it is found that formation of the observed Htrans-like species is influenced by both steric factors and proton transfer, underscoring the importance of outer coordination sphere effects on H-cluster reactivity.
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Affiliation(s)
- Marco Lorenzi
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Pierre Ceccaldi
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
- Present Address: Current Address: R&I Consultant, Home Office, Marseille, France
| | - Patricia Rodríguez-Maciá
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
- Present Address: Current address: Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QR UK
| | - Holly Jayne Redman
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Afridi Zamader
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, 38054 Grenoble, France
| | - James A. Birrell
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Livia S. Mészáros
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
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18
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Placenti MA, Roman EA, González Flecha FL, González-Lebrero RM. Functional characterization of Legionella pneumophila Cu + transport ATPase. The activation by Cu + and ATP. Biochim Biophys Acta Biomembr 2022; 1864:183822. [PMID: 34826402 DOI: 10.1016/j.bbamem.2021.183822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/08/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Cu+-ATPases are integral membrane proteins belonging to the IB subfamily of the P-type ATPases that couple Cu+ transport to the hydrolysis of ATP. As some structural and functional particularities arise for Cu+-ATPases, several authors suggest that some of the reaction steps of the Albers-Post model postulated for other P-ATPases may be different. In this work we describe a functional characterization of Legionella pneumophila Cu+-ATPase (LpCopA), the first PIB-ATPase whose structure was determined by X-ray crystallography. Cu+-ATPase activity of the enzyme presents a maximum at ∼37 °C and pH 6.6-6.8. Phospholipids enhance LpCopA Cu+-ATPase activity in a non-essential mode where optimal activity is achieved at an asolectin molar fraction of 0.15 and an amphiphile-protein ratio of ~30,000. As described for other P-ATPases, Mg2+ acts as an essential activator. Furthermore, Cu+-ATPase activity dependence on [Cu+] and [ATP] can both be described by a sum of two hyperbolic functions. Based on that, and the [Cu+] and [ATP] dependencies of the best fitting parameters of the hyperbolae pointed above, we propose a minimal reaction scheme for the catalytic mechanism that shares the basic reaction steps of the Albers-Post model for P-type ATPases. The reaction scheme postulated contemplates two different binding affinities for a single ATP (apparent affinities of 0.66 and 550 μM at [Cu+] → ∞) and binding of at least 2 Cu+ with different affinities as well (apparent affinities of 1.4 and 102.5 μM at [ATP] → ∞).
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Affiliation(s)
- M Agueda Placenti
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - Ernesto A Roman
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Buenos Aires, Argentina
| | - F Luis González Flecha
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina.
| | - Rodolfo M González-Lebrero
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina.
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19
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Oakley AJ. Proposed mechanism for monomethylarsonate reductase activity of human omega-class glutathione transferase GSTO1-1. Biochem Biophys Res Commun 2021; 590:7-13. [PMID: 34959192 DOI: 10.1016/j.bbrc.2021.12.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/20/2021] [Indexed: 11/02/2022]
Abstract
Contamination of drinking water with toxic inorganic arsenic is a major public health issue. The mechanisms of enzymes and transporters in arsenic elimination are therefore of interest. The human omega-class glutathione transferases have been previously shown to possess monomethylarsonate (V) reductase activity. To further understanding of this activity, molecular dynamics of human GSTO1-1 bound to glutathione with a monomethylarsonate isostere were simulated to reveal putative monomethylarsonate binding sites on the enzyme. The major binding site is in the active site, adjacent to the glutathione binding site. Based on this and previously reported biochemical data, a reaction mechanism for this enzyme is proposed. Further insights were gained from comparison of the human omega-class GSTs to homologs from a range of animals.
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Affiliation(s)
- Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia.
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20
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Venkatachalam K, Ettrich RH. Role of aspartic acid residues D87 and D89 in APS kinase domain of human 3'-phosphoadenosine 5'-phosphosulfate synthase 1 and 2b: A commonality with phosphatases/kinases. Biochem Biophys Rep 2021; 28:101155. [PMID: 34712849 PMCID: PMC8528679 DOI: 10.1016/j.bbrep.2021.101155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/06/2021] [Accepted: 10/15/2021] [Indexed: 11/26/2022] Open
Abstract
3'-phosphoadenosine 5'-phosphosulfate (PAPS) is synthesized in two steps by PAPS synthase (PAPSS). PAPSS is comprised of ATP sulfurylase (ATPS) and APS kinase (APSK) domain activities. ATPS combines inorganic sulfate with α-phosphoryl of ATP to form adenosine 5'-phosphosulfate (APS) and PPi. In the second step APS is phosphorylated at 3'-OH using another mole of ATP to form PAPS and ADP catalyzed by APSK. The transfer of gamma-phosphoryl from ATP onto 3'-OH requires Mg2 + and purported to involve residues D87GD89N. We report that mutation of either aspartic residue to alanine completely abolishes APSK activity in PAPS formation. PAPSS is an, unique enzyme that binds to four different nucleotides: ATP and APS on both ATPS and APSK domains and ADP and PAPS exclusively on the APSK domain. The thermodynamic binding and the catalytic interplay must be very tightly controlled to form the end-product PAPS in the forward direction. Though APS binds to ATPS and APSK, in ATPS domain, the APS is a product and for APSK it is a substrate. DGDN motif is absent in ATPS and present in APSK. Mutation of D87 and D89 did not hamper ATPS activity however abolished APSK activity severely. Thus, D87GD89N region is required for stabilization of Mg2+-ATP, in the process of splitting the γ-phosphoryl from ATP and transfer of γ-phosphoryl onto 3'-OH of APS to form PAPS a process that cannot be achieved by ATPS domain. In addition, gamma32P-ATP, trapped phosphoryl enzyme intermediate more with PAPSS2 than with PAPSS1. This suggests inherent active site residues could control novel catalytic differences. Molecular docking studies of hPAPSS1with ATP + Mg2+ and APS of wild type and mutants supports the experimental results.
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Affiliation(s)
- K.V. Venkatachalam
- College of Allopathic Medicine, Nova Southeastern University, Ft. Lauderdale, FL, 33328, USA
| | - Rudiger H. Ettrich
- College of Biomedical Sciences, Larkin University, Miami, FL, 33169, USA
- Faculty of Mathematics and Physics, Charles University, 121 16, Prague, Czech Republic
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21
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Miyahara I. The crystal structure of D-amino acid oxidase with a substrate analogue, o-aminobenzoate. J Biochem 2021; 171:27-29. [PMID: 34750609 DOI: 10.1093/jb/mvab122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/12/2022] Open
Abstract
Since the discovery of D-Amino acid oxidase (DAO) in 1935, many studies have been conducted without clarifying its three-dimensional structure for a long time. In 1996, the crystal structure of DAO was determined, and it was shown that the catalytic bases required for the two catalytic mechanisms were not present in the active site. The crystal structure of DAO in complex with o-aminobenzoate was solved and is used for modeling Michaelis complex. The Michaelis complex model provided structural information leading to a new mechanism for reductive half-reaction of DAO. Currently, DAO is being researched for medical and applied purposes.
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Affiliation(s)
- Ikuko Miyahara
- Graduate School of Science, Osaka City University, Osaka 558-8585, Japan
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22
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Pal S, Plapp BV. The Thr45Gly substitution in yeast alcohol dehydrogenase substantially decreases catalysis, alters pH dependencies, and disrupts the proton relay system. Chem Biol Interact 2021; 349:109650. [PMID: 34529977 PMCID: PMC8530938 DOI: 10.1016/j.cbi.2021.109650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/19/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
X-Ray crystallography shows that the hydroxyl group of Thr-45 in the fermentative alcohol dehydrogenase (ADH1) from Saccharomyces cerevisiae is hydrogen-bonded to the hydroxyl group of the alcohol bound to the catalytic zinc and is part of a proton relay system linked to His-48. The contribution of Thr-45 to catalysis was studied with steady state kinetics of the enzyme with the T45G substitution. Affinities for coenzymes decrease by only 2-4-fold, but the turnover numbers (V/Et) and catalytic efficiencies (V/KmEt) decrease 480-fold and 2900-fold for the oxidation of ethanol and 450-fold and 8400-fold for acetaldehyde reduction, respectively, relative to wild-type enzyme. Binding of NADH appears to require protonation of a group with a pK value of ∼7.4 in wild-type ADH1, but the pK value for T45G ADH1 appears to be less than 5. For wild-type enzyme, the pH dependencies for ethanol oxidation (V1/Et and V1/KbEt) are maximal above pK values of 7.0-7.7 and are attributed to the ionization of the alcohol or water bound to the catalytic zinc facilitated by His-48 in the enzyme-NAD+ complexes. For T45G ADH1, these pK values are shifted to 6.3. The reduction of acetaldehyde (V2/Et and V2/KpEt) modestly increases as the pH increases for wild-type and T45G enzymes. The removal of the hydroxyethyl group of Thr-45 disrupts the connection of the oxygen of ligands bound to the catalytic zinc with the proton relay system and formation of productive catalytic states. The conformational change of the enzyme and the exchange of ligands on the catalytic zinc can also be affected. Assignments of groups responsible for the pK values are discussed in the context of studies on other forms of horse liver and yeast ADHs. The substitutions with Ala-45 and Cys-45 in yeast ADH1 and the homologous substitutions with Ala-48 in horse and human liver ADHs also significantly decrease catalytic efficiency. Threonine or serine residues at this position in alcohol dehydrogenases are highly conserved and contribute substantially to catalysis.
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Affiliation(s)
- Suresh Pal
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52246, USA
| | - Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52246, USA.
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Trasviña-Arenas CH, Demir M, Lin WJ, David SS. Structure, function and evolution of the Helix-hairpin-Helix DNA glycosylase superfamily: Piecing together the evolutionary puzzle of DNA base damage repair mechanisms. DNA Repair (Amst) 2021; 108:103231. [PMID: 34649144 DOI: 10.1016/j.dnarep.2021.103231] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
The Base Excision Repair (BER) pathway is a highly conserved DNA repair system targeting chemical base modifications that arise from oxidation, deamination and alkylation reactions. BER features lesion-specific DNA glycosylases (DGs) which recognize and excise modified or inappropriate DNA bases to produce apurinic/apyrimidinic (AP) sites and coordinate AP-site hand-off to subsequent BER pathway enzymes. The DG superfamilies identified have evolved independently to cope with a wide variety of nucleobase chemical modifications. Most DG superfamilies recognize a distinct set of structurally related lesions. In contrast, the Helix-hairpin-Helix (HhH) DG superfamily has the remarkable ability to act upon structurally diverse sets of base modifications. The versatility in substrate recognition of the HhH-DG superfamily has been shaped by motif and domain acquisitions during evolution. In this paper, we review the structural features and catalytic mechanisms of the HhH-DG superfamily and draw a hypothetical reconstruction of the evolutionary path where these DGs developed diverse and unique enzymatic features.
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Affiliation(s)
| | - Merve Demir
- Department of Chemistry, University of California, Davis, CA 95616, U.S.A
| | - Wen-Jen Lin
- Department of Chemistry, University of California, Davis, CA 95616, U.S.A
| | - Sheila S David
- Department of Chemistry, University of California, Davis, CA 95616, U.S.A..
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24
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Arif T, Currie MJ, Dobson RCJ, Newson HL, Poonthiyil V, Fairbanks AJ, North RA, Rendle PM. Synthesis of N-acetylmannosamine-6-phosphate derivatives to investigate the mechanism of N-acetylmannosamine-6-phosphate 2-epimerase. Carbohydr Res 2021; 510:108445. [PMID: 34607125 DOI: 10.1016/j.carres.2021.108445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/14/2021] [Accepted: 09/21/2021] [Indexed: 11/19/2022]
Abstract
The synthesis of analogues of natural enzyme substrates can be used to help deduce enzymatic mechanisms. N-Acetylmannosamine-6-phosphate 2-epimerase is an enzyme in the bacterial sialic acid catabolic pathway. To investigate whether the mechanism of this enzyme involves a re-protonation mechanism by the same neighbouring lysine that performed the deprotonation or a unique substrate-assisted proton displacement mechanism involving the substrate C5 hydroxyl, the syntheses of two analogues of the natural substrate, N-acetylmannosamine-6-phosphate, are described. In these novel analogues, the C5 hydroxyl has been replaced with a proton and a methyl ether respectively. As recently reported, Staphylococcus aureus N-acetylmannosamine-6-phosphate 2-epimerase was co-crystallized with these two compounds. The 5-deoxy variant bound to the enzyme active site in a different orientation to the natural substrate, while the 5-methoxy variant did not bind, adding to the evidence that this enzyme uses a substrate-assisted proton displacement mechanism. This mechanistic information may help in the design of potential antibacterial drug candidates.
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Affiliation(s)
- Tanzeel Arif
- Ferrier Research Institute, Victoria University of Wellington, PO Box 33-436, Lower Hutt, 5046, New Zealand
| | - Michael J Currie
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Renwick C J Dobson
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Harriet L Newson
- Ferrier Research Institute, Victoria University of Wellington, PO Box 33-436, Lower Hutt, 5046, New Zealand
| | - Vivek Poonthiyil
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Antony J Fairbanks
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Rachel A North
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Phillip M Rendle
- Ferrier Research Institute, Victoria University of Wellington, PO Box 33-436, Lower Hutt, 5046, New Zealand.
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25
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Furubayashi N, Inaka K, Kamo M, Umena Y, Matsuoka T, Morimoto Y. Dynamic interactions in the l-lactate oxidase active site facilitate substrate binding at pH4.5. Biochem Biophys Res Commun 2021; 568:131-5. [PMID: 34214876 DOI: 10.1016/j.bbrc.2021.06.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 11/23/2022]
Abstract
The crystal structure of l-lactate oxidase in complex with l-lactate was solved at a 1.33 Å resolution. The electron density of the bound l-lactate was clearly shown and comparisons of the free form and substrate bound complexes demonstrated that l-lactate was bound to the FMN and an additional active site within the enzyme complex. l-lactate interacted with the related side chains, which play an important role in enzymatic catalysis and especially the coupled movement of H265 and D174, which may be essential to activity. These observations not only reveal the enzymatic mechanism for l-lactate binding but also demonstrate the dynamic motion of these enzyme structures in response to substrate binding and enzymatic reaction progression.
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26
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Kunzelmann S. Measurement of Nucleotide Hydrolysis Using Fluorescent Biosensors for Phosphate. Methods Mol Biol 2021; 2263:289-318. [PMID: 33877604 DOI: 10.1007/978-1-0716-1197-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Assays for the detection of inorganic phosphate (Pi) are widely used to measure the activity of nucleotide hydrolyzing enzymes, such as ATPases and GTPases. The fluorescent biosensors for Pi, described here, are based on fluorescently labeled versions of E. coli phosphate-binding protein (PBP), which translates Pi binding into a large change in fluorescence intensity. In comparison with other Pi-detection systems, these biosensors are characterized by a high sensitivity (sub-micromolar Pi concentrations) and high time resolution (tens of milliseconds), and they are therefore particularly well suited for measurements of phosphate ester hydrolysis in real time. In this chapter, it is described how the Pi biosensors can be used to measure kinetics of ATPase and GTPase reactions, both under steady state and pre-steady state conditions. An example protocol is given for determining steady state kinetic parameters, Km and kcat, of the ATP-dependent chromatin remodeler Chd1, in a plate reader format. In addition, the measurement of Pi release kinetics under pre-steady state conditions is described, including a detailed experimental procedure for a single turnover measurement of ATP hydrolysis by the ABC-type ATPase SufBC using rapid mixing.
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27
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de Araújo TS, Scapin SMN, de Andrade W, Fasciotti M, de Magalhães MTQ, Almeida MS, Lima LMTR. Biophysical characterization of two commercially available preparations of the drug containing Escherichia coli L-Asparaginase 2. Biophys Chem 2021; 271:106554. [PMID: 33607531 DOI: 10.1016/j.bpc.2021.106554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 01/05/2023]
Abstract
The hydrolysis of asparagine and glutamine by L-asparaginase has been used to treat acute lymphoblastic leukemia for over four decades. Each L-asparaginase monomer has a long loop that closes over the active site upon substrate binding, acting as a lid. Here we present a comparative study of two commercially available preparations of the drug containing Escherichia coli L-Asparaginase 2 (EcA2), performed by a comprehensive array of biophysical and biochemical approaches. We report the oligomeric landscape and conformational and dynamic plasticity of E. coli type 2 L-asparaginase present in two different formulations, and its relationship with L-aspartic acid, which is present in Aginasa, but not in Leuginase. The L-Asp present in Aginasa formulation was found to provide to EcA2 a resistance to in vitro proteolysis. EcA2 shows a composition of monomers and oligomers up to tetramers, which is mostly not altered in the presence of L-Asp. Ion-mobility spectrometry-mass spectrometry reveals two conformers for the monomeric EcA2, and that monomeric species has sufficient capacity for selective binding to L-Asp and L-Glu. The N-terminal loop of the EcA2 present in Leuginase, which is part of the active site is disordered, but it gets ordered in the presence of L-Asp, while L-Glu only does so to a limited extent. These data provide new insights on the mechanistic of ligand recognition by EcA2, and the impact of formulation in its conformational diversity landscape.
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Affiliation(s)
- Talita Stelling de Araújo
- Pharmaceutical Biotechnology Laboratory - pbiotech, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Protein Advanced Biochemistry - PAB, National Center for Structural Biology and Bioimaging - CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil; Institute for Medical Biochemistry Leopoldo DeMeis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Sandra M N Scapin
- National Institute of Metrology, Quality and Technology - INMETRO, Duque de Caxias, RJ 25250-020, Brazil
| | - William de Andrade
- Pharmaceutical Biotechnology Laboratory - pbiotech, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Maíra Fasciotti
- National Institute of Metrology, Quality and Technology - INMETRO, Duque de Caxias, RJ 25250-020, Brazil
| | - Mariana T Q de Magalhães
- Macromolecular Biophysics Laboratory (LBM), Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Marcius S Almeida
- Protein Advanced Biochemistry - PAB, National Center for Structural Biology and Bioimaging - CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil; Institute for Medical Biochemistry Leopoldo DeMeis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil.
| | - Luís Maurício T R Lima
- Pharmaceutical Biotechnology Laboratory - pbiotech, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; National Institute of Metrology, Quality and Technology - INMETRO, Duque de Caxias, RJ 25250-020, Brazil.
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Peskin AV, Meotti FC, de Souza LF, Anderson RF, Winterbourn CC, Salvador A. Intra-dimer cooperativity between the active site cysteines during the oxidation of peroxiredoxin 2. Free Radic Biol Med 2020; 158:115-125. [PMID: 32702382 DOI: 10.1016/j.freeradbiomed.2020.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 01/02/2023]
Abstract
Peroxiredoxin 2 (Prdx2) and other typical 2-Cys Prdxs function as homodimers in which hydrogen peroxide oxidizes each active site cysteine to a sulfenic acid which then condenses with the resolving cysteine on the alternate chain. Previous kinetic studies have considered both sites as equally reactive. Here we have studied Prdx2 using a combination of non-reducing SDS-PAGE to separate reduced monomers and dimers with one and two disulfide bonds, and stopped flow analysis of tryptophan fluorescence, to investigate whether there is cooperativity between the sites. We have observed positive cooperativity when H2O2 is added as a bolus and oxidation of the second site occurs while the first site is present as a sulfenic acid. Modelling of this reaction showed that the second site reacts 2.2 ± 0.1 times faster. In contrast, when H2O2 was generated slowly and the first active site condensed to a disulfide before the second site reacted, no cooperativity was evident. Conversion of the sulfenic acid to the disulfide showed negative cooperativity, with modelling of the exponential rise in tryptophan fluorescence yielding a rate constant of 0.75 ± 0.08 s-1 when the alternate active site was present as a sulfenic acid and 2.29 ± 0.08-fold lower when it was a disulfide. No difference in the rate of hyperoxidation at the two sites was detected. Our findings imply that oxidation of one active site affects the conformation of the second site and influences which intermediate forms of the protein are favored under different cellular conditions.
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Affiliation(s)
- Alexander V Peskin
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Flávia C Meotti
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo-SP, Brazil
| | - Luiz F de Souza
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo-SP, Brazil
| | - Robert F Anderson
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Christine C Winterbourn
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand.
| | - Armindo Salvador
- CNC - Centre for Neuroscience Cell Biology, University of Coimbra, Coimbra, Portugal; CQC, Department of Chemistry, And University of Coimbra, Coimbra, Portugal; Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.
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29
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Faraj SE, Valsecchi WM, Cerf NT, Fedosova NU, Rossi RC, Montes MR. The interaction of Na +, K +, and phosphate with the gastric H,K-ATPase. Kinetics of E1-E2 conformational changes assessed by eosin fluorescence measurements. Biochim Biophys Acta Biomembr 2020; 1863:183477. [PMID: 32949561 DOI: 10.1016/j.bbamem.2020.183477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022]
Abstract
H,K-ATPase and Na,K-ATPase show the highest degree of sequence similarity among all other members of the P-type ATPases family. To explore their common features in terms of ligand binding, we evaluated conformational transitions due to the binding of Na+, K+ and Pi in the H,K-ATPase, and compared the results with those obtained for the Na,K-ATPase. This work shows that eosin fluorescence time courses provide a reasonably precise method to study the kinetics of the E1-E2 conformational changes in the H,K-ATPase. We found that, although Na+ shifts the equilibrium toward the E1 conformation and seems to compete with H+ in ATPase activity assays, it was neither possible to isolate a Na+-occluded state, nor to reveal an influx of Na+ related to H,K-ATPase activity. The high rate of the E2K → E1 transition found for the H,K-ATPase, which is not compatible with the presence of a K+-occluded form, agrees with the negligible level of occluded Rb+ (used as a K+ congener) found in the absence of added ligands. The use of vanadate and fluorinated metals to induce E2P-like states increased the level of occluded Rb+ and suggests that-during dephosphorylation-the probability of K+ to remain occluded increases from the E2P-ground to the E2P-product state. From kinetic experiments we found an unexpected increase in the values of kobs for E2P formation with [Pi]; consequently, to obey the Albers-Post model, the binding of Pi to the E2 state cannot be a rapid-equilibrium reaction.
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Affiliation(s)
- S E Faraj
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina
| | - W M Valsecchi
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina
| | - N T Cerf
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina
| | - N U Fedosova
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - R C Rossi
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina
| | - M R Montes
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina.
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30
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Harrington L, Alexander LT, Knapp S, Bayley H. Nanopore Enzymology to Study Protein Kinases and Their Inhibition by Small Molecules. Methods Mol Biol 2021; 2186:95-114. [PMID: 32918732 DOI: 10.1007/978-1-0716-0806-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Nanopore enzymology is a powerful single-molecule technique for the label-free study of enzymes using engineered protein nanopore sensors. The technique has been applied to protein kinases, where it has enabled the full repertoire of kinase function to be observed, including: kinetics of substrate binding and dissociation, product binding and dissociation, nucleotide binding, and reversible phosphorylation. Further, minor modifications enable the screening of type I kinase inhibitors and the determination of inhibition constants in a facile and label-free manner. Here, we describe the design and production of suitably engineered protein nanopores and their use for the determination of key mechanistic parameters of kinases. We also provide procedures for the determination of inhibition constants of protein kinase inhibitors.
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31
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Kerber T, Vrielink A. The role of hydrogen atoms in redox catalysis by the flavoenzyme cholesterol oxidase. Methods Enzymol 2020; 634:361-377. [PMID: 32093840 DOI: 10.1016/bs.mie.2019.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Flavoenzymes comprise a large class of proteins that carry out a diverse range of important redox chemistry. Although X-ray crystal structures of many flavoenzymes have been determined, there are still unresolved questions regarding the actual oxidation state of the flavin cofactors in these structures due to photoreduction by the ionizing radiation of the X-ray beam during the diffraction experiment. Additionally, the ability to visualize hydrogen atoms in X-ray structures is difficult due to the weak scattering capability of these atoms. Since hydrogen atoms affect the electrostatic nature of enzyme active sites and play important roles in the chemistry of key amino acid residues, visualizing the precise positions of these atoms provides a more detailed understanding of their role in enzyme catalysis. Single crystal neutron diffraction is an alternative method to structure determination, circumventing problems associated with photoreduction of the sample thus providing a clearer view of the structural features of a flavoenzyme in different redox states. Additionally, the larger neutron scattering factors for hydrogen and deuterium atoms enables one to visualize these atoms much more easily than from X-ray scattering measurements. In this chapter we give an overview of neutron and X-ray crystallography studies on the flavoenzyme, cholesterol oxidase and how the observations of unusual hydrogen atom positions provide insight into the redox chemistry of the flavin cofactor.
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Affiliation(s)
- Tatiana Kerber
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia.
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32
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Pierce J, Cuneo MJ, Jennings A, Li L, Meilleur F, Zhao J, Myles DAA. Dynamic nuclear polarization enhanced neutron crystallography: Amplifying hydrogen in biological crystals. Methods Enzymol 2020; 634:153-75. [PMID: 32093831 DOI: 10.1016/bs.mie.2019.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Dynamic nuclear polarization (DNP) can provide a powerful means to amplify neutron diffraction from biological crystals by 10-100-fold, while simultaneously enhancing the visibility of hydrogen by an order of magnitude. Polarizing the neutron beam and aligning the proton spins in a polarized sample modulates the coherent and incoherent neutron scattering cross-sections of hydrogen, in ideal cases amplifying the coherent scattering by almost an order of magnitude and suppressing the incoherent background to zero. This chapter describes current efforts to develop and apply DNP techniques for spin polarized neutron protein crystallography, highlighting concepts, experimental design, labeling strategies and recent results, as well as considering new strategies for data collection and analysis that these techniques could enable.
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Abstract
The paradigm that protein structure determines protein function has been clearly established. What is less clear is whether a specific protein structure is always required to carry out a specific function. Numerous cases are now known where there is no apparent connection between the biological function of a protein and the other members of its structural class, and where functionally related proteins can have quite diverse structures. A set of enzymes with these diverse properties, the ammonia-lyases, will be examined in this review. These are a class of enzymes that catalyze a relatively straightforward deamination reaction. However, the individual enzymes of this class possess a wide variety of different structures, utilize a diverse set of cofactors, and appear to catalyze this related reaction through a range of different mechanisms. This review aims to address a basic question: if there is not a specific protein structure and active site architecture that is both required and sufficient to define a catalyst for a given chemical reaction, then what factor(s) determine the structure and the mechanism that is selected to catalyze a particular reaction?
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Affiliation(s)
- Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, USA
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34
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Wilkinson IVL, Reynolds JK, Galan SRG, Vuorinen A, Sills AJ, Pires E, Wynne GM, Wilson FX, Russell AJ. Characterisation of utrophin modulator SMT C1100 as a non-competitive inhibitor of firefly luciferase. Bioorg Chem 2019; 94:103395. [PMID: 31733898 DOI: 10.1016/j.bioorg.2019.103395] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
Firefly luciferase (FLuc) is a powerful tool for molecular and cellular biology, and popular in high-throughput screening and drug discovery. However, FLuc assays have been plagued with positive and negative artefacts due to stabilisation and inhibition by small molecules from a range of chemical classes. Here we disclose Phase II clinical compound SMT C1100 for the treatment of Duchenne muscular dystrophy as an FLuc inhibitor (KD of 0.40 ± 0.15 µM). Enzyme kinetic studies using SMT C1100 and other non-competitive inhibitors including resveratrol and NFκBAI4 identified previously undescribed modes of inhibition with respect to FLuc's luciferyl adenylate intermediate. Employing a photoaffinity strategy to identify SMT C1100's binding site, a photolabelled SMT C1100 probe instead underwent FLuc-dependent photooxidation. Our findings support novel binding sites on FLuc for non-competitive inhibitors.
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Affiliation(s)
- Isabel V L Wilkinson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Jessica K Reynolds
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Sébastien R G Galan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Aini Vuorinen
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Adam J Sills
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Elisabete Pires
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Graham M Wynne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Francis X Wilson
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, Oxfordshire OX14 4SB, UK
| | - Angela J Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3PQ, UK.
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Wanninayake US, Subedi B, Fitzpatrick PF. pH and deuterium isotope effects on the reaction of trimethylamine dehydrogenase with dimethylamine. Arch Biochem Biophys 2019; 676:108136. [PMID: 31604072 DOI: 10.1016/j.abb.2019.108136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 11/24/2022]
Abstract
The flavoprotein trimethylamine dehydrogenase is a member of a small class of flavoproteins that catalyze amine oxidation and transfer the electrons through an Fe/S center to an external oxidant. The mechanism of amine oxidation by this family of enzymes has not been established. Here, we describe the use of pH and kinetic isotope effects with the slow substrate dimethylamine to study the mechanism. The data are consistent with the neutral amine being the form of the substrate that binds productively at the pH optimum, since the pKa seen in the kcat/Kamine pH profile for a group that must be unprotonated matches the pKa of dimethylamine. The D(kcat/Kamine) value decreases to unity as the pH decreases. This suggests the presence of an alternative pathway at low pH, in which the protonated substrate binds and is then deprotonated by an active-site residue prior to oxidation. The kcat and Dkcat values both decrease to limiting values at low pH with similar pKa values. This is consistent with a step other than amine oxidation becoming rate-limiting for turnover.
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Affiliation(s)
- Udayanga S Wanninayake
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Bishnu Subedi
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA.
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Camponeschi F, Muzzioli R, Ciofi-Baffoni S, Piccioli M, Banci L. Paramagnetic 1H NMR Spectroscopy to Investigate the Catalytic Mechanism of Radical S-Adenosylmethionine Enzymes. J Mol Biol 2019; 431:4514-4522. [PMID: 31493409 DOI: 10.1016/j.jmb.2019.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 10/26/2022]
Abstract
Iron-sulfur clusters in radical S-adenosylmethionine (SAM) enzymes catalyze an astonishing array of complex and chemically challenging reactions across all domains of life. Here we showed that 1H NMR spectroscopy experiments tailored to reveal hyperfine-shifted signals of metal-ligands is a powerful tool to monitor the binding of SAM and of the octanoyl-peptide substrate to the two [4Fe-4S] clusters of human lipoyl synthase. The paramagnetically shifted signals of the iron-ligands were specifically assigned to each of the two bound [4Fe-4S] clusters, and then used to examine the interaction of SAM and substrate molecules with each of the two [4Fe-4S] clusters of human lipoyl synthase. 1H NMR spectroscopy can therefore contribute to the description of the catalityc mechanism of radical SAM enzymes.
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Affiliation(s)
- Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Riccardo Muzzioli
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Mario Piccioli
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
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Phillips RS, Crocker M, Lin R, Idowu OE, McCannon DK, Lima S. The roles of Ser-36, Asp-132 and Asp-201 in the reaction of Pseudomonas fluorescens Kynureninase. Biochim Biophys Acta Proteins Proteom 2019; 1867:722-731. [PMID: 31100408 DOI: 10.1016/j.bbapap.2019.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
Kynureninase from Pseudomonas fluorescens (Pfkynase) catalyzes the pyridoxal-5'-phosphate (PLP) dependent hydrolytic cleavage of L-kynurenine to give anthranilate and L-alanine. Asp-132 and Asp-201 are located in the structure near the pyridine NH of the PLP, with Asp-201 forming a hydrogen bond. Mutation of Asp-132 to alanine and glutamate and Asp-201 to glutamate results in reduced catalytic activity with L-kynurenine and β-benzoyl-L-alanine, but not O-benzoyl-l-serine. D132A, D132E D201E and S36A mutant Pfkynases all can form quinonoid and vinylogous amide intermediates with β-benzoyl-L-alanine, similar to wild-type enzyme. D132A, D132E, and D201E Pfkynase react more slowly with β-benzoyl-L-alanine and benzaldehyde to form an aldol product absorbing at 490 nm than wild-type, with D132E reacting the slowest. The 1H NMR spectra of wild-type and D201E Pfkynase are very similar in the low field region from 10 to 18 ppm, but that of D132A Pfkynase is missing a resonance at 13.1 ppm. These results show that these residues modulate the reactivity of the PLP at different stages during the reaction cycle. Ser-36 is located near the expected location of the carbonyl oxygen of the substrate. Mutation of Ser-36 to alanine results in a 230-fold reduction of kcat and 30-fold reduction in kcat/Km with L-kynurenine, but very little effect on the reaction of O-benzoyl-l-serine. Thus, the rate-determining step in the reaction of S36A Pfkynase is the Cβ-Cγ bond cleavage. These results support the hypothesis that Ser-36 together with Tyr-226 is part of an oxyanion hole that polarizes the carbonyl of the substrate in the catalytic mechanism of Pfkynase.
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Affiliation(s)
- Robert S Phillips
- Department of Chemistry, University of Georgia, Athens, GA 30602, United States of America; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States of America.
| | - Mori Crocker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States of America
| | - Richard Lin
- Department of Chemistry, University of Georgia, Athens, GA 30602, United States of America
| | - O Elijah Idowu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States of America
| | - David K McCannon
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States of America
| | - Santiago Lima
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States of America
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Rohman A, Dijkstra BW. The role and mechanism of microbial 3-ketosteroid Δ 1-dehydrogenases in steroid breakdown. J Steroid Biochem Mol Biol 2019; 191:105366. [PMID: 30991094 DOI: 10.1016/j.jsbmb.2019.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/26/2019] [Accepted: 04/12/2019] [Indexed: 02/08/2023]
Abstract
3-Ketosteroid Δ1-dehydrogenases are FAD-dependent enzymes that catalyze the introduction of a double bond between the C1 and C2 atoms of the A-ring of 3-ketosteroid substrates. These enzymes are found in a large variety of microorganisms, especially in bacteria belonging to the phylum Actinobacteria. They play a critical role in the early steps of the degradation of the steroid core. 3-Ketosteroid Δ1-dehydrogenases are of particular interest for the etiology of some infectious diseases, for the production of starting materials for the pharmaceutical industry, and for environmental bioremediation applications. Here we summarize and discuss the biochemical and enzymological properties of these enzymes, their microbial sources, and their natural diversity. The three-dimensional structure of a 3-ketosteroid Δ1-dehydrogenase in connection with the enzyme mechanism is highlighted.
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Affiliation(s)
- Ali Rohman
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia; The Laboratory of Proteomics, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; The Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Bauke W Dijkstra
- The Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands.
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Zeb N, Rashid MH, Mubarak MQE, Ghafoor S, de Visser SP. Flavonol biosynthesis by nonheme iron dioxygenases: A computational study into the structure and mechanism. J Inorg Biochem 2019; 198:110728. [PMID: 31203088 DOI: 10.1016/j.jinorgbio.2019.110728] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022]
Abstract
Plants produce flavonol compounds for vital functions regarding plant growth, fruit and flower colouring as well as fruit ripening processes. Several of these biosynthesis steps are stereo- and regioselective and are being carried out by nonheme iron enzymes. Using density functional theory calculations on a large active site model complex of flavanone-3β-hydroxylase (FHT), we established the mechanism for conversion of naringenin to its dihydroflavonol, which is a key step in the mechanism of flavonol biosynthesis. The reaction starts with dioxygen binding to the iron(II) centre and a reaction with α-ketoglutarate co-substrate gives succinate, an iron(IV)-oxo species and CO2 with large exothermicity and small reaction barriers. The rate-determining reaction step in the mechanism; however, is hydrogen atom abstraction of an aliphatic CH bond by the iron(IV)-oxo species. We identify a large kinetic isotope effect for the replacement of the transferring hydrogen atom by deuterium. In a final step the OH and substrate radicals combine to form the alcohol product with a barrier of several kcal mol-1. We show that the latter is the result of geometric constraints in the active site pocket. Furthermore, the calculations show that a weak tertiary CH bond is shielded from the iron(IV)-oxo species in the substrate binding position and therefore the enzyme is able to activate a stronger CH bond. As such, the flavanone-3β-hydroxylase enzyme reacts regioselectively with one specific CH bond of naringenin by avoiding activation of weaker bonds through tight substrate and oxidant positioning.
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Affiliation(s)
- Neelam Zeb
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom; National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad H Rashid
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - M Qadri E Mubarak
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sidra Ghafoor
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom; Department of Chemistry, Government College University Faisalabad, Jhang Road, 3800 Faisalabad, Pakistan
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.
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Kim K, Plapp BV. Substitution of cysteine-153 ligated to the catalytic zinc in yeast alcohol dehydrogenase with aspartic acid and analysis of mechanisms of related medium chain dehydrogenases. Chem Biol Interact 2019; 302:172-182. [PMID: 30721696 DOI: 10.1016/j.cbi.2019.01.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 01/14/2019] [Accepted: 01/31/2019] [Indexed: 11/28/2022]
Abstract
The catalytic zincs in complexes of horse liver and yeast alcohol dehydrogenases (ADH) with NAD+ and the substrate analogue, 2,2,2-trifluoroethanol, are ligated to two cysteine residues and one histidine residue from the protein and the oxygen from the alcohol. The zinc facilitates deprotonation of the alcohol and is essential for catalysis. In the yeast apoenzyme, the zinc is coordinated to a nearby glutamic acid, which is displaced by the alcohol in the complex with NAD+. Some homologous medium chain dehydrogenases have a cysteine replaced by aspartic or glutamic acid residues. How an aspartic acid would affect catalysis was studied by replacing Cys-153 in Saccharomyces cerevisiae ADH1 by using site-directed mutagenesis. The C153D enzyme was about as stable as the wild-type enzyme, if EDTA was not included in the buffers. The substitution increased affinity for NAD+ by 3-fold, but did not affect NADH binding. At pH 7.3, the turnover number for ethanol oxidation (V1/Et) decreased by 7-fold and catalytic efficiency decreased 18-fold (V1/EtKb), but turnover for acetaldehyde reduction (V2/Et) was the same as for wild-type enzyme and catalytic efficiency decreased 8-fold (V2/EtKp). Deuterium isotope effects of 3.0 on V1/Et and 3.8 on V1/EtKb for ethanol oxidation suggest that hydride transfer is more rate-limiting for turnover for the C153D enzyme than by wild-type enzyme. The patterns of pH dependence for V1/EtKb for ethanol oxidation were similar for both enzymes in the pH range from 7 to 9. The C153D substitution decreased binding of trifluoroethanol by 5-fold and of pyrazole by 65-fold. Substrate specificities for C153D and wild-type ADHs for primary alcohols have similar patterns. Efficiency for secondary alcohols decreased only about 4-fold, and efficiencies for 1,2-propanediol and acetone were about the same as for wild-type enzyme. The C153D substitution modestly affects catalysis by altering ligand exchange on the zinc or local structure. Structures and mechanisms for acid-base catalysis in related medium chain dehydrogenases with substitutions of the homologous cysteine are reviewed and analyzed.
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Affiliation(s)
- Keehyuk Kim
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242, USA.
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Wolters V, Rosche A, Bauche A, Kulow F, Harneit A, Fliegert R, Guse AH. NAD binding by human CD38 analyzed by Trp189 fluorescence. Biochim Biophys Acta Mol Cell Res 2019; 1866:1189-96. [PMID: 30472140 DOI: 10.1016/j.bbamcr.2018.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 11/23/2022]
Abstract
The NAD-glycohydrolase/ADP-ribosyl cyclase CD38 catalyzes the metabolism of nicotinamide adenine dinucleotide (NAD) to the Ca2+ mobilizing second messengers ADP-ribose (ADPR), 2'-deoxy-ADPR, and cyclic ADP-ribose (cADPR). In the present study, we investigated binding and metabolism of NAD by a soluble fragment of human CD38, sCD38, and its catalytically inactive mutant by monitoring changes in endogenous tryptophan (Trp) fluorescence. Addition of NAD resulted in a concentration-dependent decrease in sCD38 fluorescence that is mainly caused by the Trp residue W189. Amplitude of the fluorescence decrease was fitted as one-site binding curve revealing a dissociation constant for NAD of 29 μM. A comparable dissociation constant was found with the catalytically inactive sCD38 mutant (KD 37 μM NAD) indicating that binding of NAD is not significantly affected by the mutation. The NAD-induced decrease in Trp fluorescence completely recovered in case of sCD38. Kinetics of recovery was slowed down with decreasing temperature and sCD38 concentration and increasing NAD concentration demonstrating that recovery in fluorescence is proportional to the enzymatic activity of sCD38. Accordingly, recovery in fluorescence was not observed with the catalytically inactive mutant. This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech.
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Pluta P, Roversi P, Bernardo-Seisdedos G, Rojas AL, Cooper JB, Gu S, Pickersgill RW, Millet O. Structural basis of pyrrole polymerization in human porphobilinogen deaminase. Biochim Biophys Acta Gen Subj 2018; 1862:1948-1955. [PMID: 29908816 DOI: 10.1016/j.bbagen.2018.06.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/17/2018] [Accepted: 06/13/2018] [Indexed: 01/27/2023]
Abstract
Human porphobilinogen deaminase (PBGD), the third enzyme in the heme pathway, catalyzes four times a single reaction to convert porphobilinogen into hydroxymethylbilane. Remarkably, PBGD employs a single active site during the process, with a distinct yet chemically equivalent bond formed each time. The four intermediate complexes of the enzyme have been biochemically validated and they can be isolated but they have never been structurally characterized other than the apo- and holo-enzyme bound to the cofactor. We present crystal structures for two human PBGD intermediates: PBGD loaded with the cofactor and with the reaction intermediate containing two additional substrate pyrrole rings. These results, combined with SAXS and NMR experiments, allow us to propose a mechanism for the reaction progression that requires less structural rearrangements than previously suggested: the enzyme slides a flexible loop over the growing-product active site cavity. The structures and the mechanism proposed for this essential reaction explain how a set of missense mutations result in acute intermittent porphyria.
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Affiliation(s)
- Paula Pluta
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Derio, Bizkaia 48160, Spain
| | - Pietro Roversi
- Oxford Glycobiology Institute, Dept. of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, England, UK
| | | | - Adriana L Rojas
- Structural Biology Unit, CIC bioGUNE, Derio, Bizkaia 48160, Spain
| | - Jonathan B Cooper
- Department of Biological Sciences, Birkbeck, London WC1E 7HX, UK; Division of Medicine, University College London, London WC1E 6BT, UK
| | - Shuang Gu
- School of Biological and Chemical Sciences, Chemistry & Biochemistry Department, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Richard W Pickersgill
- School of Biological and Chemical Sciences, Chemistry & Biochemistry Department, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Oscar Millet
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Derio, Bizkaia 48160, Spain.
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Gillam ME, Hunter GA, Ferreira GC. Ferrochelatase π-helix: Implications from examining the role of the conserved π-helix glutamates in porphyrin metalation and product release. Arch Biochem Biophys 2018; 644:37-46. [PMID: 29481781 DOI: 10.1016/j.abb.2018.02.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/17/2018] [Accepted: 02/20/2018] [Indexed: 11/23/2022]
Abstract
Protoporphyrin ferrochelatase catalyzes the insertion of Fe2+ into protoporphyrin IX to form heme. To determine whether a conserved, active site π-helix contributes to the translocation of the metal ion substrate to the ferrochelatase-bound porphyrin substrate, the invariant π-helix glutamates were replaced with amino acids with non-negatively charged side chains, and the kinetic mechanisms of the generated variants were examined. Analysis of yeast wild-type ferrochelatase-, E314Q- and E318Q-catalyzed reactions, under multi- and single-turnover conditions, demonstrated that the mutations of the π-helix glutamates hindered both protoporphyrin metalation and release of the metalated porphyrin, by slowing each step by approximately 30-50%. Protoporphyrin metalation occurred with an apparent pKa of 7.3 ± 0.1, which was assigned to binding of Fe2+ by deprotonated Glu-314 and Glu-314-assisted Fe2+ insertion into the porphyrin ring. We propose that unwinding of the π-helix concomitant with the adoption of a protein open conformation positions the deprotonated Glu-314 to bind Fe2+ from the surface of the enzyme. Transition to the closed conformation, with π-helix winding, brings Glu-314-bound Fe2+ to the active site for incorporation into protoporphyrin.
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Young CJ, Richard K, Beruar A, Lo SY, Siemann S. An investigation of the pH dependence of copper-substituted anthrax lethal factor and its mechanistic implications. J Inorg Biochem 2018; 182:1-8. [PMID: 29407865 DOI: 10.1016/j.jinorgbio.2018.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/18/2017] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
Abstract
Anthrax lethal factor (LF) is a zinc-dependent endopeptidase involved in the cleavage of proteins critical to the maintenance of host signaling pathways during anthrax infections. Although zinc is typically regarded as the native metal ion in vivo, LF is highly tolerant to metal substitution, with its replacement by copper yielding an enzyme (CuLF) 4.5-fold more active than the native zinc protein (at pH 7). The current study demonstrates that by careful choice of the buffer, ionic strength, pH and substrate, the activity ratio of CuLF and native LF can be increased to >40-fold. Using a fluorogenic LF substrate, such optimized assay conditions can be exploited to detect LF concentrations as low as 2 pM. In contrast to the zinc form, CuLF was found to be inhibited by bromide and iodide ions, to be resistant to metal loss under acidic conditions, and to display a sharp pH dependence with significantly shifted alkaline limb towards more acidic conditions. The alkaline limb in the enzyme's pH profile is suggested to originate from changes in the protonation state of the metal-bound water molecule which serves as the nucleophile in the catalytic mechanism. Based on these observations and studies on other zinc proteases, a minimal mechanism for LF is proposed.
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Affiliation(s)
- Calvin J Young
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Kaitlin Richard
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Ananya Beruar
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Suet Y Lo
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Stefan Siemann
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada.
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Grzela R, Nusbaum J, Fieulaine S, Lavecchia F, Desmadril M, Nhiri N, Van Dorsselaer A, Cianferani S, Jacquet E, Meinnel T, Giglione C. Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts. Biochim Biophys Acta Proteins Proteom 2017; 1866:348-355. [PMID: 29101077 DOI: 10.1016/j.bbapap.2017.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 01/06/2023]
Abstract
Unexpected peptide deformylase (PDF) genes were recently retrieved in numerous marine phage genomes. While various hypotheses dealing with the occurrence of these intriguing sequences have been made, no further characterization and functional studies have been described thus far. In this study, we characterize the bacteriophage Vp16 PDF enzyme, as representative member of the newly identified C-terminally truncated viral PDFs. We show here that conditions classically used for bacterial PDFs lead to an enzyme exhibiting weak activity. Nonetheless, our integrated biophysical and biochemical approaches reveal specific effects of pH and metals on Vp16 PDF stability and activity. A novel purification protocol taking in account these data allowed strong improvement of Vp16 PDF specific activity to values similar to those of bacterial PDFs. We next show that Vp16 PDF is as sensitive to the natural inhibitor compound of PDFs, actinonin, as bacterial PDFs. Comparison of the 3D structures of Vp16 and E. coli PDFs bound to actinonin also reveals that both PDFs display identical substrate binding mode. We conclude that bacteriophage Vp16 PDF protein has functional peptide deformylase activity and we suggest that encoded phage PDFs might be important for viral fitness.
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Affiliation(s)
- Renata Grzela
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Julien Nusbaum
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Sonia Fieulaine
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Francesco Lavecchia
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Michel Desmadril
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, UPR2301, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, UPR2301, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
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Cristaldi JC, Gómez MC, González PJ, Ferroni FM, Dalosto SD, Rizzi AC, Rivas MG, Brondino CD. Study of the Cys-His bridge electron transfer pathway in a copper-containing nitrite reductase by site-directed mutagenesis, spectroscopic, and computational methods. Biochim Biophys Acta Gen Subj 2018; 1862:752-60. [PMID: 29051066 DOI: 10.1016/j.bbagen.2017.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 09/06/2017] [Accepted: 10/12/2017] [Indexed: 11/22/2022]
Abstract
The Cys-His bridge as electron transfer conduit in the enzymatic catalysis of nitrite to nitric oxide by nitrite reductase from Sinorhizobium meliloti 2011 (SmNir) was evaluated by site-directed mutagenesis, steady state kinetic studies, UV-vis and EPR spectroscopic measurements as well as computational calculations. The kinetic, structural and spectroscopic properties of the His171Asp (H171D) and Cys172Asp (C172D) SmNir variants were compared with the wild type enzyme. Molecular properties of H171D and C172D indicate that these point mutations have not visible effects on the quaternary structure of SmNir. Both variants are catalytically incompetent using the physiological electron donor pseudoazurin, though C172D presents catalytic activity with the artificial electron donor methyl viologen (kcat=3.9(4) s-1) lower than that of wt SmNir (kcat=240(50) s-1). QM/MM calculations indicate that the lack of activity of H171D may be ascribed to the Nδ1H…OC hydrogen bond that partially shortcuts the T1-T2 bridging Cys-His covalent pathway. The role of the Nδ1H…OC hydrogen bond in the pH-dependent catalytic activity of wt SmNir is also analyzed by monitoring the T1 and T2 oxidation states at the end of the catalytic reaction of wt SmNir at pH6 and 10 by UV-vis and EPR spectroscopies. These data provide insight into how changes in Cys-His bridge interrupts the electron transfer between T1 and T2 and how the pH-dependent catalytic activity of the enzyme are related to pH-dependent structural modifications of the T1-T2 bridging chemical pathway.
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Mbenza NM, Vadakkedath PG, McGillivray DJ, Leung IKH. NMR studies of the non-haem Fe(II) and 2-oxoglutarate-dependent oxygenases. J Inorg Biochem 2017; 177:384-394. [PMID: 28893416 DOI: 10.1016/j.jinorgbio.2017.08.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/21/2017] [Accepted: 08/30/2017] [Indexed: 01/13/2023]
Abstract
The non-haem Fe(II) and 2-oxoglutarate (2OG)-dependent oxygenases belong to a superfamily of structurally-related enzymes that play important biological roles in plants, microorganisms and animals. Structural, mechanistic and functional studies of 2OG oxygenases require efficient and effective biophysical tools. Nuclear magnetic resonance (NMR) spectroscopy is a useful tool to study this enzyme superfamily. It has been applied to obtain information about enzyme kinetics, identify and characterise 2OG oxygenase-catalysed oxidation products, elucidate the catalytic mechanism, monitor ligand binding and study protein dynamics. This review summarises the types of information that NMR spectroscopy can provide in the studies of 2OG oxygenases, highlights the advantages of the technique and describes its drawbacks.
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Affiliation(s)
- Naasson M Mbenza
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Praveen G Vadakkedath
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.; MacDiarmid Institute for Advanced Materials and Nanotechnology, PO Box 600, Wellington 6140, New Zealand
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.; MacDiarmid Institute for Advanced Materials and Nanotechnology, PO Box 600, Wellington 6140, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand..
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Balogun EO, Inaoka DK, Shiba T, Tokuoka SM, Tokumasu F, Sakamoto K, Kido Y, Michels PAM, Watanabe YI, Harada S, Kita K. Glycerol kinase of African trypanosomes possesses an intrinsic phosphatase activity. Biochim Biophys Acta Gen Subj 2017; 1861:2830-2842. [PMID: 28778484 DOI: 10.1016/j.bbagen.2017.07.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/28/2017] [Accepted: 07/29/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND In general, glycerol kinases (GKs) are transferases that catalyze phospho group transfer from ATP to glycerol, and the mechanism was suggested to be random bi-bi. The reverse reaction i.e. phospho transfer from glycerol 3-phosphate (G3P) to ADP is only physiologically feasible by the African trypanosome GK. In contrast to other GKs the mechanism of Trypanosoma brucei gambiense glycerol kinase (TbgGK) was shown to be in an ordered fashion, and proceeding via autophosphorylation. From the unique reaction mechanism of TbgGK, we envisaged its potential to possess phosphatase activity in addition to being a kinase. METHODS Our hypothesis was tested by spectrophotometric and LC-MS/MS analyses using paranitrophenyl phosphate (pNPP) and TbgGK's natural substrate, G3P respectively. Furthermore, protein X-ray crystallography and site-directed mutagenesis were performed to examine pNPP binding, catalytic residues, and the possible reaction mechanism. RESULTS In addition to its widely known and expected phosphotransferase (class II) activity, TbgGK can efficiently facilitate the hydrolytic cleavage of phosphoric anhydride bonds (a class III property). This phosphatase activity followed the classical Michaelis-Menten pattern and was competitively inhibited by ADP and G3P, suggesting a common catalytic site for both activities (phosphatase and kinase). The structure of the TGK-pNPP complex, and structure-guided mutagenesis implicated T276 to be important for the catalysis. Remarkably, we captured a crystallographic molecular snapshot of the phosphorylated T276 reaction intermediate. CONCLUSION We conclude that TbgGK has both kinase and phosphatase activities. GENERAL SIGNIFICANCE This is the first report on a bifunctional kinase/phosphatase enzyme among members of the sugar kinase family.
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Affiliation(s)
- Emmanuel Oluwadare Balogun
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Biochemistry, Ahmadu Bello University, Zaria 2222, Nigeria.
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; School of Tropical Medicine and Global Health, Nagasaki University 1-12-4, Sakamoto, Nagasaki 852-8523, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Suzumi M Tokuoka
- Department of Lipidomics, Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, Japan
| | - Fuyuki Tokumasu
- Department of Lipidomics, Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, Japan
| | - Kimitoshi Sakamoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Yasutoshi Kido
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Paul A M Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Yoh-Ichi Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; School of Tropical Medicine and Global Health, Nagasaki University 1-12-4, Sakamoto, Nagasaki 852-8523, Japan.
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Abstract
Enzymes in the α-d-phosphohexomutases superfamily catalyze the reversible conversion of phosphosugars, such as glucose 1-phosphate and glucose 6-phosphate. These reactions are fundamental to primary metabolism across the kingdoms of life and are required for a myriad of cellular processes, ranging from exopolysaccharide production to protein glycosylation. The subject of extensive mechanistic characterization during the latter half of the 20th century, these enzymes have recently benefitted from biophysical characterization, including X-ray crystallography, NMR, and hydrogen-deuterium exchange studies. This work has provided new insights into the unique catalytic mechanism of the superfamily, shed light on the molecular determinants of ligand recognition, and revealed the evolutionary conservation of conformational flexibility. Novel associations with inherited metabolic disease and the pathogenesis of bacterial infections have emerged, spurring renewed interest in the long-appreciated functional roles of these enzymes.
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Affiliation(s)
| | | | - Lesa J Beamer
- University of Missouri, Columbia, MO, United States.
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Yang X. Conformational dynamics play important roles upon the function of N-acetylglutamate kinase. Appl Microbiol Biotechnol 2017; 101:3485-3492. [PMID: 28341883 DOI: 10.1007/s00253-017-8237-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/04/2017] [Accepted: 03/09/2017] [Indexed: 12/14/2022]
Abstract
N-acetylglutamate kinase (NAGK) catalyzes the phosphorylation of N-acetylglutamate. In many bacteria, NAGK catalysis is the rate controlling step in the L-arginine biosynthesis pathway from glutamate to L-arginine and is allosterically inhibited by L-arginine. Many data show that conformational dynamics of NAGKs are essential for their function. The demonstration of the conformational mechanism provides a potential way to improve the yield of arginine. Due to the lack of NAGK catalysis step in arginine synthesis route of mammals, the elucidation of the dynamic mechanism can also provide a way to design a new antivirus drug. This paper reviews how the dynamics affect the activity of NAGKs and are controlled by the effectors. X-ray crystallography and modeling data have shown that in NAGKs, the structural elements required for inhibitor and substrate binding, catalysis and product release, are highly mobile. It is possible to eliminate the inhibition of the arginine and/or block the synthesis of arginine by disturbing the flexibility of the NAGKs. Amino acid kinase family is thought to share some common dynamic features; the flexible structural elements of NAGKs have been identified, but the details of the dynamics and the signal transfer pathways are yet to be elucidated.
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Affiliation(s)
- Xiaorong Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, People's Republic of China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, People's Republic of China. .,Key Laboratory of Renewable Energy, Chinese Academy of Sciences, Guangzhou, 510640, People's Republic of China.
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