1
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Truong DP, Rousseau S, Machala BW, Huddleston JP, Zhu M, Hull KG, Romo D, Raushel FM, Sacchettini JC, Glasner ME. Second-Shell Amino Acid R266 Helps Determine N-Succinylamino Acid Racemase Reaction Specificity in Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Enzymes. Biochemistry 2021; 60:3829-3840. [PMID: 34845903 DOI: 10.1021/acs.biochem.1c00627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Catalytic promiscuity is the coincidental ability to catalyze nonbiological reactions in the same active site as the native biological reaction. Several lines of evidence show that catalytic promiscuity plays a role in the evolution of new enzyme functions. Thus, studying catalytic promiscuity can help identify structural features that predispose an enzyme to evolve new functions. This study identifies a potentially preadaptive residue in a promiscuous N-succinylamino acid racemase/o-succinylbenzoate synthase (NSAR/OSBS) enzyme from Amycolatopsis sp. T-1-60. This enzyme belongs to a branch of the OSBS family which includes many catalytically promiscuous NSAR/OSBS enzymes. R266 is conserved in all members of the NSAR/OSBS subfamily. However, the homologous position is usually hydrophobic in other OSBS subfamilies, whose enzymes lack NSAR activity. The second-shell amino acid R266 is close to the catalytic acid/base K263, but it does not contact the substrate, suggesting that R266 could affect the catalytic mechanism. Mutating R266 to glutamine in Amycolatopsis NSAR/OSBS profoundly reduces NSAR activity but moderately reduces OSBS activity. This is due to a 1000-fold decrease in the rate of proton exchange between the substrate and the general acid/base catalyst K263. This mutation is less deleterious for the OSBS reaction because K263 forms a cation-π interaction with the OSBS substrate and/or the intermediate, rather than acting as a general acid/base catalyst. Together, the data explain how R266 contributes to NSAR reaction specificity and was likely an essential preadaptation for the evolution of NSAR activity.
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Affiliation(s)
- Dat P Truong
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - Simon Rousseau
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - Benjamin W Machala
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - Jamison P Huddleston
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843-3255, United States
| | - Mingzhao Zhu
- Baylor Synthesis and Drug-Lead Discovery Laboratory, Department of Chemistry and Biochemistry, Baylor University, One Bear Place, Waco, Texas 76798-7348, United States
| | - Kenneth G Hull
- Baylor Synthesis and Drug-Lead Discovery Laboratory, Department of Chemistry and Biochemistry, Baylor University, One Bear Place, Waco, Texas 76798-7348, United States
| | - Daniel Romo
- Baylor Synthesis and Drug-Lead Discovery Laboratory, Department of Chemistry and Biochemistry, Baylor University, One Bear Place, Waco, Texas 76798-7348, United States
| | - Frank M Raushel
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States.,Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843-3255, United States
| | - James C Sacchettini
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843-3255, United States
| | - Margaret E Glasner
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
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2
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Martínez-Rodríguez S, Soriano-Maldonado P, Gavira JA. N-succinylamino acid racemases: Enzymatic properties and biotechnological applications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140377. [PMID: 31982578 DOI: 10.1016/j.bbapap.2020.140377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 01/28/2023]
Abstract
The N-succinylamino acid racemase/o-succinylbenzoate synthase (NSAR/OSBS) subfamily from the enolase superfamily contains different enzymes showing promiscuous N-substituted-amino acid racemase (NxAR) activity. These enzymes were originally named as N-acylamino acid racemases because of their industrial application. Nonetheless, they are pivotal in several enzymatic cascades due to their versatility to catalyze a wide substrate spectrum, allowing the production of optically pure d- or l-amino acids from cheap precursors. These compounds are of paramount economic interest, since they are used as food additives, in the pharmaceutical and cosmetics industries and/or as chiral synthons in organic synthesis. Despite its economic importance, the discovery of new N-succinylamino acid racemases has become elusive, since classical sequence-based annotation methods proved ineffective in their identification, due to a high sequence similarity among the members of the enolase superfamily. During the last decade, deeper investigations into different members of the NSAR/OSBS subfamily have shed light on the classification and identification of NSAR enzymes with NxAR activity of biotechnological potential. This review aims to gather the dispersed information on NSAR/OSBS members showing NxAR activity over recent decades, focusing on their biotechnological applications and providing practical advice to identify new enzymes.
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Affiliation(s)
- Sergio Martínez-Rodríguez
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, Facultad de Medicina, Granada 18071, Spain; Laboratorio de Estudios Cristalográficos, CSIC, 18100 Granada, Spain.
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3
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Holliday GL, Brown SD, Mischel D, Polacco BJ, Babbitt PC. A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. Database (Oxford) 2020; 2020:baaa034. [PMID: 32449511 PMCID: PMC7246345 DOI: 10.1093/database/baaa034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/18/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022]
Abstract
Determining the molecular function of enzymes discovered by genome sequencing represents a primary foundation for understanding many aspects of biology. Historically, classification of enzyme reactions has used the enzyme nomenclature system developed to describe the overall reactions performed by biochemically characterized enzymes, irrespective of their associated sequences. In contrast, functional classification and assignment for the millions of protein sequences of unknown function now available is largely done in two computational steps, first by similarity-based assignment of newly obtained sequences to homologous groups, followed by transferring to them the known functions of similar biochemically characterized homologs. Due to the fundamental differences in their etiologies and practice, `how' these chemistry- and evolution-centric functional classification systems relate to each other has been difficult to explore on a large scale. To investigate this issue in a new way, we integrated two published ontologies that had previously described each of these classification systems independently. The resulting infrastructure was then used to compare the functional assignments obtained from each classification system for the well-studied and functionally diverse enolase superfamily. Mapping these function assignments to protein structure and reaction similarity networks shows a profound and complex disconnect between the homology- and chemistry-based classification systems. This conclusion mirrors previous observations suggesting that except for closely related sequences, facile annotation transfer from small numbers of characterized enzymes to the huge number uncharacterized homologs to which they are related is problematic. Our extension of these comparisons to large enzyme superfamilies in a computationally intelligent manner provides a foundation for new directions in protein function prediction for the huge proportion of sequences of unknown function represented in major databases. Interactive sequence, reaction, substrate and product similarity networks computed for this work for the enolase and two other superfamilies are freely available for download from the Structure Function Linkage Database Archive (http://sfld.rbvi.ucsf.edu).
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
- Present Address: Medicines Discovery Catapult, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
| | - David Mischel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
| | - Benjamin J Polacco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
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4
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Odokonyero D, McMillan AW, Ramagopal UA, Toro R, Truong DP, Zhu M, Lopez MS, Somiari B, Herman M, Aziz A, Bonanno JB, Hull KG, Burley SK, Romo D, Almo SC, Glasner ME. Comparison of Alicyclobacillus acidocaldarius o-Succinylbenzoate Synthase to Its Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Relatives. Biochemistry 2018; 57:3676-3689. [PMID: 29767960 DOI: 10.1021/acs.biochem.8b00088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studying the evolution of catalytically promiscuous enzymes like those from the N-succinylamino acid racemase/ o-succinylbenzoate synthase (NSAR/OSBS) subfamily can reveal mechanisms by which new functions evolve. Some enzymes in this subfamily have only OSBS activity, while others catalyze OSBS and NSAR reactions. We characterized several NSAR/OSBS subfamily enzymes as a step toward determining the structural basis for evolving NSAR activity. Three enzymes were promiscuous, like most other characterized NSAR/OSBS subfamily enzymes. However, Alicyclobacillus acidocaldarius OSBS (AaOSBS) efficiently catalyzes OSBS activity but lacks detectable NSAR activity. Competitive inhibition and molecular modeling show that AaOSBS binds N-succinylphenylglycine with moderate affinity in a site that overlaps its normal substrate. On the basis of possible steric conflicts identified by molecular modeling and sequence conservation within the NSAR/OSBS subfamily, we identified one mutation, Y299I, that increased NSAR activity from undetectable to 1.2 × 102 M-1 s-1 without affecting OSBS activity. This mutation does not appear to affect binding affinity but instead affects kcat, by reorienting the substrate or modifying conformational changes to allow both catalytic lysines to access the proton that is moved during the reaction. This is the first site known to affect reaction specificity in the NSAR/OSBS subfamily. However, this gain of activity was obliterated by a second mutation, M18F. Epistatic interference by M18F was unexpected because a phenylalanine at this position is important in another NSAR/OSBS enzyme. Together, modest NSAR activity of Y299I AaOSBS and epistasis between sites 18 and 299 indicate that additional sites influenced the evolution of NSAR reaction specificity in the NSAR/OSBS subfamily.
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Affiliation(s)
- Denis Odokonyero
- Department of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States
| | - Andrew W McMillan
- Department of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States
| | | | | | - Dat P Truong
- Department of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States
| | - Mingzhao Zhu
- CPRIT Synthesis and Drug-Lead Discovery Lab, Department of Chemistry and Biochemistry , Baylor University , One Bear Place , Waco , Texas 76798-7348 , United States
| | - Mariana S Lopez
- Department of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States
| | - Belema Somiari
- Department of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States
| | - Meghann Herman
- Department of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States
| | - Asma Aziz
- Department of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States
| | | | - Kenneth G Hull
- CPRIT Synthesis and Drug-Lead Discovery Lab, Department of Chemistry and Biochemistry , Baylor University , One Bear Place , Waco , Texas 76798-7348 , United States
| | - Stephen K Burley
- RCSB Protein Data Bank, Institute for Quantitative Biomedicine , Rutgers, The State University of New Jersey , Piscataway , New Jersey 08854-8076 , United States.,Rutgers Cancer Institute of New Jersey , New Brunswick , New Jersey 08903-2681 , United States
| | - Daniel Romo
- CPRIT Synthesis and Drug-Lead Discovery Lab, Department of Chemistry and Biochemistry , Baylor University , One Bear Place , Waco , Texas 76798-7348 , United States
| | | | - Margaret E Glasner
- Department of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States
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5
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Dungan SZ, Chang BSW. Epistatic interactions influence terrestrial-marine functional shifts in cetacean rhodopsin. Proc Biol Sci 2018; 284:rspb.2016.2743. [PMID: 28250185 DOI: 10.1098/rspb.2016.2743] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/03/2017] [Indexed: 12/12/2022] Open
Abstract
Like many aquatic vertebrates, whales have blue-shifting spectral tuning substitutions in the dim-light visual pigment, rhodopsin, that are thought to increase photosensitivity in underwater environments. We have discovered that known spectral tuning substitutions also have surprising epistatic effects on another function of rhodopsin, the kinetic rates associated with light-activated intermediates. By using absorbance spectroscopy and fluorescence-based retinal release assays on heterologously expressed rhodopsin, we assessed both spectral and kinetic differences between cetaceans (killer whale) and terrestrial outgroups (hippo, bovine). Mutation experiments revealed that killer whale rhodopsin is unusually resilient to pleiotropic effects on retinal release from key blue-shifting substitutions (D83N and A292S), largely due to a surprisingly specific epistatic interaction between D83N and the background residue, S299. Ancestral sequence reconstruction indicated that S299 is an ancestral residue that predates the evolution of blue-shifting substitutions at the origins of Cetacea. Based on these results, we hypothesize that intramolecular epistasis helped to conserve rhodopsin's kinetic properties while enabling blue-shifting spectral tuning substitutions as cetaceans adapted to aquatic environments. Trade-offs between different aspects of molecular function are rarely considered in protein evolution, but in cetacean and other vertebrate rhodopsins, may underlie multiple evolutionary scenarios for the selection of specific amino acid substitutions.
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Affiliation(s)
- Sarah Z Dungan
- Department Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Belinda S W Chang
- Department Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2 .,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada M5S 3B2.,Department Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5
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6
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Kumar G, Johnson JL, Frantom PA. Improving Functional Annotation in the DRE-TIM Metallolyase Superfamily through Identification of Active Site Fingerprints. Biochemistry 2016; 55:1863-72. [PMID: 26935545 DOI: 10.1021/acs.biochem.5b01193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Within the DRE-TIM metallolyase superfamily, members of the Claisen-like condensation (CC-like) subgroup catalyze C-C bond-forming reactions between various α-ketoacids and acetyl-coenzyme A. These reactions are important in the metabolic pathways of many bacterial pathogens and serve as engineering scaffolds for the production of long-chain alcohol biofuels. To improve functional annotation and identify sequences that might use novel substrates in the CC-like subgroup, a combination of structural modeling and multiple-sequence alignments identified active site residues on the third, fourth, and fifth β-strands of the TIM-barrel catalytic domain that are differentially conserved within the substrate-diverse enzyme families. Using α-isopropylmalate synthase and citramalate synthase from Methanococcus jannaschii (MjIPMS and MjCMS), site-directed mutagenesis was used to test the role of each identified position in substrate selectivity. Kinetic data suggest that residues at the β3-5 and β4-7 positions play a significant role in the selection of α-ketoisovalerate over pyruvate in MjIPMS. However, complementary substitutions in MjCMS fail to alter substrate specificity, suggesting residues in these positions do not contribute to substrate selectivity in this enzyme. Analysis of the kinetic data with respect to a protein similarity network for the CC-like subgroup suggests that evolutionarily distinct forms of IPMS utilize residues at the β3-5 and β4-7 positions to affect substrate selectivity while the different versions of CMS use unique architectures. Importantly, mapping the identities of residues at the β3-5 and β4-7 positions onto the protein similarity network allows for rapid annotation of probable IPMS enzymes as well as several outlier sequences that may represent novel functions in the subgroup.
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Affiliation(s)
- Garima Kumar
- Department of Chemistry, The University of Alabama , 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
| | - Jordyn L Johnson
- Department of Chemistry, The University of Alabama , 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
| | - Patrick A Frantom
- Department of Chemistry, The University of Alabama , 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
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7
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Xiang DF, Patskovsky Y, Nemmara VV, Toro R, Almo SC, Raushel FM. Function discovery and structural characterization of a methylphosphonate esterase. Biochemistry 2015; 54:2919-30. [PMID: 25873441 PMCID: PMC4477287 DOI: 10.1021/acs.biochem.5b00199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pmi1525, an enzyme of unknown function from Proteus mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG ). The structure was also determined with manganese and butyrate in the active site (PDB id: 4QSF ). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. The substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization, and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat/Km values of 580 s(-1) and 1.2 × 10(5) M(-1) s(-1), respectively) and 4-nitrophenyl butyrate (kcat and kcat/Km values of 140 s(-1) and 1.4 × 10(5) M(-1) s(-1), respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents.
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Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Yury Patskovsky
- Department of Biochemistry, Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Venkatesh V. Nemmara
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Rafael Toro
- Department of Biochemistry, Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Steven C. Almo
- Department of Biochemistry, Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461,To whom correspondence may be sent: (FMR) Telephone: 979-845-3373; , (SCA) Telephone: 718-430-2746;
| | - Frank M. Raushel
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012,To whom correspondence may be sent: (FMR) Telephone: 979-845-3373; , (SCA) Telephone: 718-430-2746;
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8
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Sánchez-Tarín M, Swiderek K, Roca M, Tuñón I. Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods. J Phys Chem B 2015; 119:1899-911. [DOI: 10.1021/jp511147b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- María Sánchez-Tarín
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Katarzyna Swiderek
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, 90-924, Lodz, Poland
| | - Maite Roca
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
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9
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Soriano-Maldonado P, Andújar-Sánchez M, Clemente-Jiménez JM, Rodríguez-Vico F, Las Heras-Vázquez FJ, Martínez-Rodríguez S. Biochemical and Mutational Characterization of N-Succinyl-Amino Acid Racemase from Geobacillus stearothermophilus CECT49. Mol Biotechnol 2015; 57:454-65. [DOI: 10.1007/s12033-015-9839-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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10
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Huddleston JP, Burks EA, Whitman CP. Identification and characterization of new family members in the tautomerase superfamily: analysis and implications. Arch Biochem Biophys 2014; 564:189-96. [PMID: 25219626 DOI: 10.1016/j.abb.2014.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/26/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
Abstract
Tautomerase superfamily members are characterized by a β-α-β building block and a catalytic amino terminal proline. 4-Oxalocrotonate tautomerase (4-OT) and malonate semialdehyde decarboxylase (MSAD) are the title enzymes of two of the five known families in the superfamily. Two recent developments in these families indicate that there might be more metabolic diversity in the tautomerase superfamily than previously thought. 4-OT homologues have been identified in three biosynthetic pathways, whereas all previously characterized 4-OTs are found in catabolic pathways. In the MSAD family, homologues have been characterized that lack decarboxylase activity, but have a modest hydratase activity using 2-oxo-3-pentynoate. This observation stands in contrast to the first characterized MSAD, which is a proficient decarboxylase and a less efficient hydratase. The hydratase activity was thought to be a vestigial and promiscuous activity. However, this recent discovery suggests that the hydratase activity might reflect a new activity in the MSAD family for an unknown substrate. These discoveries open up new avenues of research in the tautomerase superfamily.
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Affiliation(s)
- Jamison P Huddleston
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, United States
| | - Elizabeth A Burks
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, United States
| | - Christian P Whitman
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, United States.
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11
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Brown SD, Babbitt PC. New insights about enzyme evolution from large scale studies of sequence and structure relationships. J Biol Chem 2014; 289:30221-30228. [PMID: 25210038 PMCID: PMC4215206 DOI: 10.1074/jbc.r114.569350] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes.
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Affiliation(s)
- Shoshana D Brown
- Departments of Bioengineering and Therapeutic Sciences and University of California, San Francisco, California 94158-2330
| | - Patricia C Babbitt
- Departments of Bioengineering and Therapeutic Sciences and University of California, San Francisco, California 94158-2330; Departments of Pharmaceutical Chemistry, School of Pharmacy, and University of California, San Francisco, California 94158-2330; California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158-2330.
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12
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Kumar G, Frantom PA. Evolutionarily Distinct Versions of the Multidomain Enzyme α-Isopropylmalate Synthase Share Discrete Mechanisms of V-Type Allosteric Regulation. Biochemistry 2014; 53:4847-56. [DOI: 10.1021/bi500702u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Garima Kumar
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Patrick A. Frantom
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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13
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McMillan AW, Lopez MS, Zhu M, Morse BC, Yeo IC, Amos J, Hull K, Romo D, Glasner ME. Role of an Active Site Loop in the Promiscuous Activities of Amycolatopsis sp. T-1-60 NSAR/OSBS. Biochemistry 2014; 53:4434-44. [DOI: 10.1021/bi500573v] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Andrew W. McMillan
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - Mariana S. Lopez
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | | | - Benjamin C. Morse
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - In-Cheol Yeo
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - Jaleesia Amos
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | | | | | - Margaret E. Glasner
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
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Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family. Proc Natl Acad Sci U S A 2014; 111:8535-40. [PMID: 24872444 DOI: 10.1073/pnas.1318703111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The rate of protein evolution is determined by a combination of selective pressure on protein function and biophysical constraints on protein folding and structure. Determining the relative contributions of these properties is an unsolved problem in molecular evolution with broad implications for protein engineering and function prediction. As a case study, we examined the structural divergence of the rapidly evolving o-succinylbenzoate synthase (OSBS) family, which catalyzes a step in menaquinone synthesis in diverse microorganisms and plants. On average, the OSBS family is much more divergent than other protein families from the same set of species, with the most divergent family members sharing <15% sequence identity. Comparing 11 representative structures revealed that loss of quaternary structure and large deletions or insertions are associated with the family's rapid evolution. Neither of these properties has been investigated in previous studies to identify factors that affect the rate of protein evolution. Intriguingly, one subfamily retained a multimeric quaternary structure and has small insertions and deletions compared with related enzymes that catalyze diverse reactions. Many proteins in this subfamily catalyze both OSBS and N-succinylamino acid racemization (NSAR). Retention of ancestral structural characteristics in the NSAR/OSBS subfamily suggests that the rate of protein evolution is not proportional to the capacity to evolve new protein functions. Instead, structural features that are conserved among proteins with diverse functions might contribute to the evolution of new functions.
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