1
|
Functional identification of the proximal promoter region of human pyridoxine 5′-phosphate oxidase gene. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
2
|
de Oliveira Viana J, Scotti MT, Scotti L. Molecular Docking Studies in Multitarget Antitubercular Drug Discovery. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2018. [DOI: 10.1007/7653_2018_28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
3
|
Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions. Microbiol Mol Biol Rev 2016; 80:451-93. [PMID: 27122598 DOI: 10.1128/mmbr.00070-15] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420 is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420 in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420 in methanogenic archaea in processes such as substrate oxidation, C1 pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid by Mycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Fo and F420 are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.
Collapse
|
4
|
Ankisettypalli K, Cheng JJY, Baker EN, Bashiri G. PdxH proteins of mycobacteria are typical members of the classical pyridoxine/pyridoxamine 5'-phosphate oxidase family. FEBS Lett 2016; 590:453-60. [PMID: 26823273 DOI: 10.1002/1873-3468.12080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 11/08/2022]
Abstract
Pyridoxal 5'-phosphate (PLP) biosynthesis is essential for the survival and virulence of Mycobacterium tuberculosis (Mtb). PLP functions as a cofactor for 58 putative PLP-binding proteins encoded by the Mtb genome and could also act as a potential antioxidant. De novo biosynthesis of PLP in Mtb takes place through the 'deoxyxylulose 5'-phosphate (DXP)-independent' pathway, whereas PdxH enzymes, possessing pyridoxine/pyridoxamine 5'-phosphate oxidase (PNPOx) activity, are involved in the PLP salvage pathway. In this study, we demonstrate that the annotated PdxH enzymes from various mycobacterial species are bona fide members of the classical PNPOx enzyme family, capable of producing PLP using both pyridoxine 5'-phosphate (PNP) and pyridoxamine 5'-phosphate (PMP) substrates.
Collapse
Affiliation(s)
- Karthik Ankisettypalli
- Structural Biology Laboratory and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, New Zealand
| | - Jasmin Jo-Yu Cheng
- Structural Biology Laboratory and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, New Zealand
| | - Edward N Baker
- Structural Biology Laboratory and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, New Zealand
| | - Ghader Bashiri
- Structural Biology Laboratory and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, New Zealand
| |
Collapse
|
5
|
Li W, Liu M, Xie J. Rv3369 Induces Cytokine Interleukin-1β Production and Enhances Mycobacterium smegmatis Intracellular Survival. J Interferon Cytokine Res 2015; 36:140-7. [PMID: 26588672 DOI: 10.1089/jir.2015.0090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The pathogenesis of tuberculosis, caused by Mycobacterium tuberculosis, is largely because of the pathogen's successful entry and survival within macrophages. We predicted that rv3369, a gene encoding a conserved protein, might play a role in the interactions with host cells. To test this, rv3369 gene was heterologously expressed in a nonpathogenic fast-growing Mycobacterium smegmatis strain. The recombinant strain survives better than the control within macrophages, accompanied by more host cell death and a marked higher secretion of interleukin-1β (IL-1β). Furthermore, pharmacological inhibition experiments showed that the NF-κB and ERK pathways were involved in the Rv3369-triggered IL-1β changes. These results provided evidence for the engagement of Rv3369 in the interaction between mycobacteria and host.
Collapse
Affiliation(s)
- Wu Li
- 1 Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University , Chongqing, China .,2 College of Life Sciences, Neijiang Normal University , Neijiang, China
| | - Minqiang Liu
- 1 Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University , Chongqing, China
| | - Jianping Xie
- 1 Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University , Chongqing, China
| |
Collapse
|
6
|
Ahmed FH, Carr PD, Lee BM, Afriat-Jurnou L, Mohamed AE, Hong NS, Flanagan J, Taylor MC, Greening C, Jackson CJ. Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria. J Mol Biol 2015; 427:3554-3571. [PMID: 26434506 DOI: 10.1016/j.jmb.2015.09.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 12/11/2022]
Abstract
The deazaflavin cofactor F420 enhances the persistence of mycobacteria during hypoxia, oxidative stress, and antibiotic treatment. However, the identities and functions of the mycobacterial enzymes that utilize F420 under these conditions have yet to be resolved. In this work, we used sequence similarity networks to analyze the distribution of the largest F420-dependent protein family in mycobacteria. We show that these enzymes are part of a larger split β-barrel enzyme superfamily (flavin/deazaflavin oxidoreductases, FDORs) that include previously characterized pyridoxamine/pyridoxine-5'-phosphate oxidases and heme oxygenases. We show that these proteins variously utilize F420, flavin mononucleotide, flavin adenine dinucleotide, and heme cofactors. Functional annotation using phylogenetic, structural, and spectroscopic methods revealed their involvement in heme degradation, biliverdin reduction, fatty acid modification, and quinone reduction. Four novel crystal structures show that plasticity in substrate binding pockets and modifications to cofactor binding motifs enabled FDORs to carry out a variety of functions. This systematic classification and analysis provides a framework for further functional analysis of the roles of FDORs in mycobacterial pathogenesis and persistence.
Collapse
Affiliation(s)
- F Hafna Ahmed
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Paul D Carr
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Brendon M Lee
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Livnat Afriat-Jurnou
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - A Elaaf Mohamed
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Nan-Sook Hong
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Jack Flanagan
- University of Auckland Faculty of Medical and Health Sciences, 85 Park Road, Grafton, Auckland 2013, New Zealand
| | - Matthew C Taylor
- Commonwealth Scientific and Industrial Research Organisation Land and Water Flagship, Clunies Ross Street, Acton, ACT 2060, Australia
| | - Chris Greening
- Commonwealth Scientific and Industrial Research Organisation Land and Water Flagship, Clunies Ross Street, Acton, ACT 2060, Australia
| | - Colin J Jackson
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia.
| |
Collapse
|
7
|
Experimental Evidence for a Revision in the Annotation of Putative Pyridoxamine 5'-Phosphate Oxidases P(N/M)P from Fungi. PLoS One 2015; 10:e0136761. [PMID: 26327315 PMCID: PMC4556617 DOI: 10.1371/journal.pone.0136761] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 08/08/2015] [Indexed: 11/19/2022] Open
Abstract
Pyridoxinamine 5'-phosphate oxidases (P(N/M)P oxidases) that bind flavin mononucleotide (FMN) and oxidize pyridoxine 5'-phosphate or pyridoxamine 5'-phosphate to form pyridoxal 5'-phosphate (PLP) are an important class of enzymes that play a central role in cell metabolism. Failure to generate an adequate supply of PLP is very detrimental to most organisms and is often clinically manifested as a neurological disorder in mammals. In this study, we analyzed the function of YLR456W and YPR172W, two homologous genes of unknown function from S. cerevisiae that have been annotated as putative P(N/M)P oxidases based on sequence homology. Different experimental approaches indicated that neither protein catalyzes PLP formation nor binds FMN. On the other hand, our analysis confirmed the enzymatic activity of Pdx3, the S. cerevisiae protein previously implicated in PLP biosynthesis by genetic and structural characterization. After a careful sequence analysis comparing the putative and confirmed P(N/M)P oxidases, we found that the protein domain (PF01243) that led to the YLR456W and YPR172W annotation is a poor indicator of P(N/M)P oxidase activity. We suggest that a combination of two Pfam domains (PF01243 and PF10590) present in Pdx3 and other confirmed P(N/M)P oxidases would be a stronger predictor of this molecular function. This work exemplifies the importance of experimental validation to rectify genome annotation and proposes a revision in the annotation of at least 400 sequences from a wide variety of fungal species that are homologous to YLR456W and are currently misrepresented as putative P(N/M)P oxidases.
Collapse
|
8
|
Yang Y, Hu B, Lill MA. Analysis of factors influencing hydration site prediction based on molecular dynamics simulations. J Chem Inf Model 2014; 54:2987-95. [PMID: 25252619 PMCID: PMC4210176 DOI: 10.1021/ci500426q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Water
contributes significantly to the binding of small molecules
to proteins in biochemical systems. Molecular dynamics (MD) simulation
based programs such as WaterMap and WATsite have been used to probe
the locations and thermodynamic properties of hydration sites at the
surface or in the binding site of proteins generating important information
for structure-based drug design. However, questions associated with
the influence of the simulation protocol on hydration site analysis
remain. In this study, we use WATsite to investigate the influence
of factors such as simulation length and variations in initial protein
conformations on hydration site prediction. We find that 4 ns MD simulation
is appropriate to obtain a reliable prediction of the locations and
thermodynamic properties of hydration sites. In addition, hydration
site prediction can be largely affected by the initial protein conformations
used for MD simulations. Here, we provide a first quantification of
this effect and further indicate that similar conformations of binding
site residues (RMSD < 0.5 Å) are required to obtain consistent
hydration site predictions.
Collapse
Affiliation(s)
- Ying Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University , 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | | | | |
Collapse
|
9
|
Bánky D, Iván G, Grolmusz V. Equal opportunity for low-degree network nodes: a PageRank-based method for protein target identification in metabolic graphs. PLoS One 2013; 8:e54204. [PMID: 23382878 PMCID: PMC3558500 DOI: 10.1371/journal.pone.0054204] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 12/11/2012] [Indexed: 11/19/2022] Open
Abstract
Biological network data, such as metabolic-, signaling- or physical interaction graphs of proteins are increasingly available in public repositories for important species. Tools for the quantitative analysis of these networks are being developed today. Protein network-based drug target identification methods usually return protein hubs with large degrees in the networks as potentially important targets. Some known, important protein targets, however, are not hubs at all, and perturbing protein hubs in these networks may have several unwanted physiological effects, due to their interaction with numerous partners. Here, we show a novel method applicable in networks with directed edges (such as metabolic networks) that compensates for the low degree (non-hub) vertices in the network, and identifies important nodes, regardless of their hub properties. Our method computes the PageRank for the nodes of the network, and divides the PageRank by the in-degree (i.e., the number of incoming edges) of the node. This quotient is the same in all nodes in an undirected graph (even for large- and low-degree nodes, that is, for hubs and non-hubs as well), but may differ significantly from node to node in directed graphs. We suggest to assign importance to non-hub nodes with large PageRank/in-degree quotient. Consequently, our method gives high scores to nodes with large PageRank, relative to their degrees: therefore non-hub important nodes can easily be identified in large networks. We demonstrate that these relatively high PageRank scores have biological relevance: the method correctly finds numerous already validated drug targets in distinct organisms (Mycobacterium tuberculosis, Plasmodium falciparum and MRSA Staphylococcus aureus), and consequently, it may suggest new possible protein targets as well. Additionally, our scoring method was not chosen arbitrarily: its value for all nodes of all undirected graphs is constant; therefore its high value captures importance in the directed edge structure of the graph.
Collapse
Affiliation(s)
- Dániel Bánky
- Protein Information Technology Group, Eötvös University, Pázmány Péter stny. 1/C, Budapest, Hungary
- Uratim Ltd., Budapest, Hungary
| | - Gábor Iván
- Protein Information Technology Group, Eötvös University, Pázmány Péter stny. 1/C, Budapest, Hungary
- Uratim Ltd., Budapest, Hungary
| | - Vince Grolmusz
- Protein Information Technology Group, Eötvös University, Pázmány Péter stny. 1/C, Budapest, Hungary
- Uratim Ltd., Budapest, Hungary
- * E-mail:
| |
Collapse
|
10
|
Hilario E, Li Y, Niks D, Fan L. The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:846-53. [PMID: 22751670 DOI: 10.1107/s0907444912014126] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 03/31/2012] [Indexed: 11/11/2022]
Abstract
Xanthomonas citri pv. citri (Xac) causes citrus canker and affects citrus agriculture worldwide. Functional genetic analysis has indicated that a putative general stress protein (XacGSP) encoded by the Xac2369 gene is involved in the bacterial infection. In this report, the crystal structure of XacGSP was determined to 2.5 Å resolution. There are four XacGSP molecules in the crystal asymmetric unit. Each XacGSP monomer folds into a six-stranded antiparallel β-barrel flanked by five α-helices. A C-terminal extension protrudes from the sixth β-strand of the β-barrel and pairs with its counterpart from another monomer to form a bridge between the two subunits of an XacGSP dimer. Two XacGSP dimers cross over each other to form a tetramer; the β-barrels from one dimer contact the β-barrels of the other, while the two bridges are distant from each other and do not make contacts. The three-dimensional structure of the XacGSP monomer is very similar to those of pyridoxine 5-phosphate oxidases, a group of enzymes that use flavin mononucleotide (FMN) as a cofactor. Consistent with this, purified XacGSP protein binds to both FMN and flavin adenine dinucleotide (FAD), suggesting that XacGSP may help the bacteria to react against the oxidative stress induced by the defense mechanisms of the plant.
Collapse
Affiliation(s)
- Eduardo Hilario
- Department of Biochemistry, University of California-Riverside, Riverside, California, USA
| | | | | | | |
Collapse
|
11
|
Mashalidis EH, Mukherjee T, Śledź P, Matak-Vinković D, Boshoff H, Abell C, Barry CE. Rv2607 from Mycobacterium tuberculosis is a pyridoxine 5'-phosphate oxidase with unusual substrate specificity. PLoS One 2011; 6:e27643. [PMID: 22110704 PMCID: PMC3215729 DOI: 10.1371/journal.pone.0027643] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 10/21/2011] [Indexed: 11/26/2022] Open
Abstract
Despite intensive effort, the majority of the annotated Mycobacterium tuberculosis genome consists of genes encoding proteins of unknown or poorly understood function. For example, there are seven conserved hypothetical proteins annotated as homologs of pyridoxine 5′-phosphate oxidase (PNPOx), an enzyme that oxidizes pyridoxine 5′-phosphate (PNP) or pyridoxamine 5′-phosphate (PMP) to form pyridoxal 5′-phosphate (PLP). We have characterized the function of Rv2607 from Mycobacterium tuberculosis H37Rv and shown that it encodes a PNPOx that oxidizes PNP to PLP. The kcat and KM for this reaction were 0.01 s−1 and 360 µM, respectively. Unlike many PNPOx enzymes, Rv2607 does not recognize PMP as a substrate.
Collapse
Affiliation(s)
- Ellene H. Mashalidis
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tathagata Mukherjee
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Paweł Śledź
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Helena Boshoff
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (CA); (CEB)
| | - Clifton E. Barry
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (CA); (CEB)
| |
Collapse
|
12
|
di Salvo ML, Contestabile R, Safo MK. Vitamin B6 salvage enzymes: Mechanism, structure and regulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1597-608. [DOI: 10.1016/j.bbapap.2010.12.006] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
|
13
|
Mooney S, Hellmann H. Vitamin B6: Killing two birds with one stone? PHYTOCHEMISTRY 2010; 71:495-501. [PMID: 20089286 DOI: 10.1016/j.phytochem.2009.12.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 12/23/2009] [Accepted: 12/30/2009] [Indexed: 05/24/2023]
Abstract
Vitamin B6 comprises a group of compounds that are involved in a surprisingly high diversity of biochemical reactions. Actually, most of these reactions are co-catalyzed by a single B6 vitamer, pyridoxal 5'-phosphate, making it a crucial and versatile co-factor in many metabolic processes in the cell. In addition, it has been demonstrated in recent years that vitamin B6 has a second important function by being an effective antioxidant. Because of these two characteristics the vitamin is an interesting compound to study in plants. This review provides a brief overview and update on such important aspects like vitamin B6-dependent enzymes and known biosynthetic pathways in plants, phenotypes of plant mutants affected in vitamin B6 biosynthesis, and the potential benefits of modifying vitamin B6 content in plants.
Collapse
Affiliation(s)
- Sutton Mooney
- Washington State University, Pullman, Abelson Hall, WA 99164, USA
| | | |
Collapse
|
14
|
Musayev FN, Di Salvo ML, Saavedra MA, Contestabile R, Ghatge MS, Haynes A, Schirch V, Safo MK. Molecular basis of reduced pyridoxine 5'-phosphate oxidase catalytic activity in neonatal epileptic encephalopathy disorder. J Biol Chem 2009; 284:30949-56. [PMID: 19759001 DOI: 10.1074/jbc.m109.038372] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutations in pyridoxine 5'-phosphate oxidase are known to cause neonatal epileptic encephalopathy. This disorder has no cure or effective treatment and is often fatal. Pyridoxine 5'-phosphate oxidase catalyzes the oxidation of pyridoxine 5'-phosphate to pyridoxal 5'-phosphate, the active cofactor form of vitamin B(6) required by more than 140 different catalytic activities, including enzymes involved in amino acid metabolism and biosynthesis of neurotransmitters. Our aim is to elucidate the mechanism by which a homozygous missense mutation (R229W) in the oxidase, linked to neonatal epileptic encephalopathy, leads to reduced oxidase activity. The R229W variant is approximately 850-fold less efficient than the wild-type enzyme due to an approximately 192-fold decrease in pyridoxine 5'-phosphate affinity and an approximately 4.5-fold decrease in catalytic activity. There is also an approximately 50-fold reduction in the affinity of the R229W variant for the FMN cofactor. A 2.5 A crystal structure of the R229W variant shows that the substitution of Arg-229 at the FMN binding site has led to a loss of hydrogen-bond and/or salt-bridge interactions between FMN and Arg-229 and Ser-175. Additionally, the mutation has led to an alteration of the configuration of a beta-strand-loop-beta-strand structure at the active site, resulting in loss of two critical hydrogen-bond interactions involving residues His-227 and Arg-225, which are important for substrate binding and orientation for catalysis. These results provide a molecular basis for the phenotype associated with the R229W mutation, as well as providing a foundation for understanding the pathophysiological consequences of pyridoxine 5'-phosphate oxidase mutations.
Collapse
Affiliation(s)
- Faik N Musayev
- Department of Medicinal Chemistry, School of Pharmacy, and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23219, USA
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Huang SH, Shi RJ, Zhang JY, Wang Z, Huang LQ. Cloning and characterization of a pyridoxine 5'-phosphate oxidase from silkworm, Bombyx mori. INSECT MOLECULAR BIOLOGY 2009; 18:365-371. [PMID: 19523068 DOI: 10.1111/j.1365-2583.2009.00880.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A cDNA encoding Pyridoxine 5'-phosphate oxidase (PNPO) from Bombyx mori was cloned and characterized (GenBank accession number: DQ452398). The cDNA encodes a polypeptide of 257 amino acid residues. The recombinant enzyme purified from Escherichia coli exhibited maximal activity at pH 9.0, and the K(m) values for the substrates of pyridoxine 5'-phosphate and pyridoxamine 5'-phosphate were determined as 0.65 and 1.15 micromol/l. It was found that B. mori PNPO shares 51.44% homology with humans, but several function-related, key amino acid residues in B. mori PNPO are different from the human and E. Coli gene. B. mori has a single copy of the PNPO gene, which spans a 3.5 kb region and contains five exons and four introns. B. mori PNPO is a homodimer, with each monomer containing nine antiparallel beta-strands and five alpha-helical segments. The secondary structure was deduced from computational study.
Collapse
Affiliation(s)
- S-H Huang
- Anhui Agricultural University, Hefei, People's Republic of China
| | | | | | | | | |
Collapse
|
16
|
Proteomic and transcriptomic analyses reveal genes upregulated by cis-dichloroethene in Polaromonas sp. strain JS666. Appl Environ Microbiol 2009; 75:3733-44. [PMID: 19363075 DOI: 10.1128/aem.00031-09] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polaromonas sp. strain JS666 is the only bacterial isolate capable of using cis-dichloroethene (cDCE) as a sole carbon and energy source. Studies of cDCE degradation in this novel organism are of interest because of potential bioremediation and biocatalysis applications. The primary cellular responses of JS666 to growth on cDCE were explored using proteomics and transcriptomics to identify the genes upregulated by cDCE. Two-dimensional gel electrophoresis revealed upregulation of genes annotated as encoding glutathione S-transferase, cyclohexanone monooxygenase, and haloacid dehalogenase. DNA microarray experiments confirmed the proteomics findings that the genes indicated above were among the most highly upregulated by cDCE. The upregulation of genes with antioxidant functions and the inhibition of cDCE degradation by elevated oxygen levels suggest that cDCE induces an oxidative stress response. Furthermore, the upregulation of a predicted ABC transporter and two sodium/solute symporters suggests that transport is important in cDCE degradation. The omics data were integrated with data from compound-specific isotope analysis (CSIA) and biochemical experiments to develop a hypothesis for cDCE degradation pathways in JS666. The CSIA results indicate that the measured isotope enrichment factors for aerobic cDCE degradation ranged from -17.4 to -22.4 per thousand. Evidence suggests that cDCE degradation via monooxygenase-catalyzed epoxidation (C C cleavage) may be only a minor degradation pathway under the conditions of these experiments and that the major degradation pathway involves carbon-chloride cleavage as the initial step, a novel mechanism. The results provide a significant step toward elucidation of cDCE degradation pathways and enhanced understanding of cDCE degradation in JS666.
Collapse
|
17
|
Mooney S, Leuendorf JE, Hendrickson C, Hellmann H. Vitamin B6: a long known compound of surprising complexity. Molecules 2009; 14:329-51. [PMID: 19145213 PMCID: PMC6253932 DOI: 10.3390/molecules14010329] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 01/07/2009] [Accepted: 01/09/2009] [Indexed: 12/31/2022] Open
Abstract
In recent years vitamin B6 has become a focus of research describing the compound’s critical function in cellular metabolism and stress response. For many years the sole function of vitamin B6 was considered to be that of an enzymatic cofactor. However, recently it became clear that it is also a potent antioxidant that effectively quenches reactive oxygen species and is thus of high importance for cellular well-being. In view of the recent findings, the current review takes a look back and summarizes the discovery of vitamin B6 and the elucidation of its structure and biosynthetic pathways. It provides a detailed overview on vitamin B6 both as a cofactor and a protective compound. Besides these general characteristics of the vitamin, the review also outlines the current literature on vitamin B6 derivatives and elaborates on recent findings that provide new insights into transport and catabolism of the compound and on its impact on human health.
Collapse
Affiliation(s)
- Sutton Mooney
- School of Biological Sciences, Washington State University, Pullman, WA, USA; E-mail: (S. M.), (C. H.)
| | - Jan-Erik Leuendorf
- Angewandte Genetik, Freie Universität Berlin, 14195 Berlin, Germany E-mail: (J-E. L.)
| | - Christopher Hendrickson
- School of Biological Sciences, Washington State University, Pullman, WA, USA; E-mail: (S. M.), (C. H.)
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA, USA; E-mail: (S. M.), (C. H.)
- Author to whom correspondence should be addressed; E-Mail:
| |
Collapse
|