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PreprintCited by 15Enzyme Structure and FunctionProtein Structure and DynamicsPhysical Organic Chemistry and Reaction Kinetics

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The 3D modules of enzyme catalysis: deconstructing active sites into distinct functional entities

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Riziotis, Ioannis G., Ribeiro, António J. M., Borkakoti, Neera, Thornton, Janet M.·2023·Journal of Molecular Biology
DOI 10.1101/2023.06.01.543252

Preprint — published as 10.1016/j.jmb.2023.168254

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Abstract

Enzyme catalysis is governed by a limited toolkit of residues and organic or inorganic co-factors. Therefore, it is expected that recurring residue arrangements will be found across the enzyme space, which perform a defined catalytic function, are structurally similar and occur in unrelated enzymes. Leveraging the integrated information in the Mechanism and Catalytic Site Atlas (M-CSA) (enzyme structure, sequence, catalytic residue annotations, catalysed reaction, detailed mechanism description), 3D templates were derived to represent compact groups of catalytic residues. A fuzzy template-template search, allowed us to identify those recurring motifs, which are conserved or convergent, that we define as the “modules of enzyme catalysis”. We show that a large fraction of these modules facilitate binding of metal ions, co-factors and substrates, and are frequently the result of convergent evolution. A smaller number of convergent modules perform a well-defined catalytic role, such as the variants of the catalytic triad (i.e. Ser-His-Asp/Cys-His-Asp) and the saccharide-cleaving Asp/Glu triad. It is also shown that enzymes whose functions have diverged during evolution preserve regions of their active site unaltered, as shown by modules performing similar or identical steps of the catalytic mechanism. We have compiled a comprehensive library of catalytic modules, that characterise a broad spectrum of enzymes. These modules can be used as templates in enzyme design and for better understanding catalysis in 3D.

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  1. 10.1093/nar/gkx1012 · DOI
  2. 10.1093/nar/gkt1243 · DOI
  3. A.R. Dewanti , J.A. Duine , Ca2+-assisted, direct hydride transfer, and rate-determining tautomerization of C5-reduced PQQ to PQQH2, in the oxidation of β-D-glucose by soluble, quinoprotein glucose dehydrogenase, Biochemistry. 39 (2000). https://doi.org/10.1021/bi992810x. · DOI
  4. M. Leopoldini , N. Russo , M. Toscano , The preferred reaction path for the oxidation of methanol by PQQ-containing methanol dehydrogenase: Addition-elimination versus hydride-transfer mechanism, Chemistry - A European Journal. 13 (2007). https://doi.org/10.1002/chem.200601123. · DOI
  5. L. Simón , J.M. Goodman , Enzyme catalysis by hydrogen bonds: The balance between transition State binding and substrate binding in oxyanion holes, Journal of Organic Chemistry. 75 (2010). https://doi.org/10.1021/jo901503d. · DOI
  6. R. Ménard , A.C. Storer , Oxyanion Hole Interactions in Serine and Cysteine Proteases, Biol Chem Hoppe Seyler. 373 (1992). https://doi.org/10.1515/bchm3.1992.373.2.393. · DOI
  7. C. Martinez , A. Nicolas , H. van Tilbeurgh , M.P. Egloff , C. Cambillau , C. Cudrey , R. Verger , Cutinase, a Lipolytic Enzyme with a Preformed Oxyanion Hole, Biochemistry. 33 (1994). https://doi.org/10.1021/bi00167a011. · DOI
  8. R.J. Kubiak , X. Yue , R.J. Hondal , C. Mihai , M.D. Tsai , K.S. Bruzik , Involvement of the Arg - Asp - His catalytic triad in enzymatic cleavage of the phosphodiester bond, Biochemistry. 40 (2001). https://doi.org/10.1021/bi002371y. · DOI
  9. L. Polgár , The catalytic triad of serine peptidases, Cellular and Molecular Life Sciences. 62 (2005). https://doi.org/10.1007/s00018-005-5160-x. · DOI
  10. 10.1110/ps.035436.108 · DOI
  11. 10.1073/pnas.1221050110 · DOI
  12. 2022, Capturing the geometry, function, and evolution of enzymes with 3D templates, Protein Science, 31, e4363, 10.1002/pro.4363 · DOI
  13. G.L. Holliday , C. Andreini , J.D. Fischer , S.A. Rahman , D.E. Almonacid , S.T. Williams , W.R. Pearson , MACiE: Exploring the diversity of biochemical reactions, Nucleic Acids Res. 40 (2012). https://doi.org/10.1093/nar/gkr799. · DOI
  14. 10.1016/j.jmb.2015.11.010 · DOI
  15. 2019, CATH: Expanding the horizons of structure-based functional annotations for genome sequences, Nucleic Acids Res, 47, D280, 10.1093/nar/gky1097 · DOI
  16. S. Romero-Romero , S. Kordes , F. Michel , B. Höcker , Evolution, folding, and design of TIM barrels and related proteins, Curr Opin Struct Biol. 68 (2021). https://doi.org/10.1016/j.sbi.2020.12.007. · DOI
  17. I.G. Riziotis , A.J.M. Ribeiro , N. Borkakoti , J.M. Thornton , Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues, J Mol Biol. 434 (2022). https://doi.org/10.1016/j.jmb.2022.167517. · DOI
  18. R.A. Laskowski , J.D. Watson , J.M. Thornton , ProFunc: A server for predicting protein function from 3D structure, Nucleic Acids Res. 33 (2005). https://doi.org/10.1093/nar/gki414. · DOI
  19. A. Stark , R.B. Russell , Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures, Nucleic Acids Res. 31 (2003). https://doi.org/10.1093/nar/gkg506. · DOI
  20. 10.1006/jmbi.1998.2393 · DOI
  21. G. Wang , R.L. Dunbrack , PISCES: A protein sequence culling server, Bioinformatics. 19 (2003). https://doi.org/10.1093/bioinformatics/btg224. · DOI
  22. 10.1093/bioinformatics/btg226 · DOI
  23. P. Shannon , A. Markiel , O. Ozier , N.S. Baliga , J.T. Wang , D. Ramage , N. Amin , B. Schwikowski , T. Ideker , Cytoscape: A software Environment for integrated models of biomolecular interaction networks, Genome Res. 13 (2003). https://doi.org/10.1101/gr.1239303. · DOI · Paper page
  24. R.H.H. Van Den Heuvel , D.I. Svergun , M. V. Petoukhov , A. Coda , B. Curti , S. Ravasio , M.A. Vanoni , A. Mattevi , The active conformation of glutamate synthase and its binding to ferredoxin, J Mol Biol. 330 (2003). https://doi.org/10.1016/S0022-2836(03)00522-9. · DOI
  25. J.L. Smith , Glutamine PRPP amidotransferase: Snapshots of an enzyme in action, Curr Opin Struct Biol. 8 (1998). https://doi.org/10.1016/S0959-440X(98)80087-0. · DOI
  26. Y. Cheng , D.J. Patel , Crystallographic structure of the nuclease domain of 3′hExo, a DEDDh family member, bound to rAMP, J Mol Biol. 343 (2004). https://doi.org/10.1016/j.jmb.2004.08.055. · DOI
  27. G. Andrés Cisneros , L. Perera , R.M. Sehaaper , L.C. Pedersen , R.E. London , L.G. Pedersen , T.A. Darden , Reaction mechanism of the ε subunit of E. coli DNA polymerase III: Insights into active site metal coordination and catalytically significant residues, J Am Chem Soc. 131 (2009). https://doi.org/10.1021/ja8082818. · DOI
  28. J.F. Rakus , A.A. Fedorov , E. V. Fedorov , M.E. Glasner , B.K. Hubbard , J.D. Delli , P.C. Babbitt , S.C. Almo , J.A. Gerlt , Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase, Biochemistry. 47 (2008). https://doi.org/10.1021/bi800914r. · DOI
  29. M. Nagar , B.N. Wyatt , M. St. Maurice , S.L. Bearne , Inactivation of mandelate racemase by 3-hydroxypyruvate reveals a potential mechanistic link between enzyme superfamilies, Biochemistry. 54 (2015). https://doi.org/10.1021/acs.biochem.5b00221. · DOI
  30. S.Y. Wen , A.A. Fedorov , E. V. Fedorov , S.C. Almo , J.A. Gerlt , Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2, Biochemistry. 46 (2007). https://doi.org/10.1021/bi7008882. · DOI
  31. K. Yamada , N. Kunishima , K. Mayanagi , T. Ohnishi , T. Nishino , H. Iwasaki , H. Shinagawa , K. Morikawa , Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8, Proc Natl Acad Sci U S A. 98 (2001). https://doi.org/10.1073/pnas.98.4.1442. · DOI
  32. G. Yang , T. Sandalova , K. Lohman , Y. Lindqvist , A.R. Rendina , Active site mutants of Escherichia coli dethiobiotin synthetase: Effects of mutations on enzyme catalytic and structural properties, Biochemistry. 36 (1997). https://doi.org/10.1021/bi9631677. · DOI
  33. A.C. Eliot , J. Sandmark , G. Schneider , J.F. Kirsch , The dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation, Biochemistry. 41 (2002). https://doi.org/10.1021/bi026339a. · DOI
  34. C.E. Pugh , J.L. Harwood , R.A. John , Mechanism of glutamate semialdehyde aminotransferase: Roles of diamino- and dioxo-intermediates in the synthesis of aminolevulinate, Journal of Biological Chemistry. 267 (1992). https://doi.org/10.1016/s0021-9258(18)45985-6. · DOI
  35. D.M.E. Szebenyi , F.N. Musayev , M.L. Di Salvo , M.K. Safo , V. Schirch , Serine hydroxymethyltransferase: Role of Glu75 and evidence that serine is cleaved by a retroaldol mechanism, Biochemistry. 43 (2004). https://doi.org/10.1021/bi049791y. · DOI
  36. J.A. Gerlt , P.C. Babbitt , Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies, Annu Rev Biochem. 70 (2001). https://doi.org/10.1146/annurev.biochem.70.1.209. · DOI
  37. F. Baier , J.N. Copp , N. Tokuriki , Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence-Function Relationships, Biochemistry. 55 (2016). https://doi.org/10.1021/acs.biochem.6b00723. · DOI
  38. A.C. Wallace , R.A. Laskowski , J.M. Thornton , Derivation of 3D coordinate templates for searching structural databases: Application to Ser-His-Asp catalytic triads in the serine proteinases and lipases, Protein Science. 5 (1996). https://doi.org/10.1002/pro.5560050603. · DOI
  39. R.D. Gupta , Recent advances in enzyme promiscuity, Sustainable Chemical Processes. 4 (2016). https://doi.org/10.1186/s40508-016-0046-9. · DOI
  40. T. Devamani , A.M. Rauwerdink , M. Lunzer , B.J. Jones , J.L. Mooney , M.A.O. Tan , Z.J. Zhang , J.H. Xu , A.M. Dean , R.J. Kazlauskas , Catalytic Promiscuity of Ancestral Esterases and Hydroxynitrile Lyases, J Am Chem Soc. 138 (2016). https://doi.org/10.1021/jacs.5b12209. · DOI
  41. 10.1093/nar/gkv1274 · DOI
  42. 10.1042/BST20160400 · DOI
  43. A.J.M. Ribeiro , J.D. Tyzack , N. Borkakoti , J.M. Thornton , Identifying pseudoenzymes using functional annotation: pitfalls of common practice, FEBS Journal. 287 (2020). https://doi.org/10.1111/febs.15142. · DOI
  44. 10.1016/j.str.2018.02.009 · DOI
  45. 10.1093/bioinformatics/btq442 · DOI
  46. C. Andreini , I. Bertini , G. Cavallaro , G.L. Holliday , J.M. Thornton , Metal ions in biological catalysis: From enzyme databases to general principles, Journal of Biological Inorganic Chemistry. 13 (2008). https://doi.org/10.1007/s00775-008-0404-5. · DOI · Paper page
  47. C. Andreini , I. Bertini , G. Cavallaro , G.L. Holliday , J.M. Thornton , Metal-MACiE: A database of metals involved in biological catalysis, Bioinformatics. 25 (2009). https://doi.org/10.1093/bioinformatics/btp256. · DOI
  48. Y.W. Lin , Rational design of artificial metalloproteins and metalloenzymes with metal clusters, Molecules. 24 (2019). https://doi.org/10.3390/molecules24152743. · DOI
  49. A.J.M. Ribeiro , I.G. Riziotis , J.D. Tyzack , N. Borkakoti , J.M. Thornton , EzMechanism: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions, BioRxiv. (2022). · DOI
  50. G.A. Jaña , F. Mendoza , M.I. Osorio , J.B. Alderete , P.A. Fernandes , M.J. Ramos , V.A. Jiménez , A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI from: Streptococcus mutans, Org Biomol Chem. 16 (2018). https://doi.org/10.1039/c8ob00284c. · DOI
  51. J.D. Dimitrov , T.L. Vassilev , Cofactor-mediated protein promiscuity, Nat Biotechnol. 27 (2009). https://doi.org/10.1038/nbt1009-892a. · DOI
  52. 2023, UniProt: the Universal Protein Knowledgebase in 2023, Nucleic Acids Res, 51, D523, 10.1093/nar/gkac1052 · DOI · Paper page
  53. J.M. Thornton , R.A. Laskowski , N. Borkakoti , AlphaFold heralds a data-driven revolution in biology and medicine, Nat Med. 27 (2021). https://doi.org/10.1038/s41591-021-01533-0. · DOI · Paper page
  54. M. Varadi , S. Anyango , M. Deshpande , S. Nair , C. Natassia , G. Yordanova , D. Yuan , O. Stroe , G. Wood , A. Laydon , A. Žídek , T. Green , K. Tunyasuvunakool , S. Petersen , J. Jumper , E. Clancy , R. Green , A. Vora , M. Lutfi , M. Figurnov , A. Cowie , N. Hobbs , P. Kohli , G. Kleywegt , E. Birney , D. Hassabis , S. Velankar , AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models, Nucleic Acids Res. 50 (2022). https://doi.org/10.1093/nar/gkab1061. · DOI · Paper page
  55. R.A. Laskowski , J.D. Watson , J.M. Thornton , Protein function prediction using local 3D templates, J Mol Biol. 351 (2005). https://doi.org/10.1016/j.jmb.2005.05.067. · DOI · Paper page
  56. 2004, Superfamily active site templates, Proteins: Structure, Function and Genetics, 55, 962
  57. S. Jones , J.A. Barker , I. Nobeli , J.M. Thornton , Using structural motif templates to identify proteins with DNA binding function, Nucleic Acids Res. 31 (2003). https://doi.org/10.1093/nar/gkg386. · DOI
  58. 2001, Directed enzyme evolution, Curr Opin Biotechnol, 12, 545, 10.1016/S0958-1669(01)00261-0 · DOI
  59. M. Goldsmith , D.S. Tawfik , Directed enzyme evolution: Beyond the low-hanging fruit, Curr Opin Struct Biol. 22 (2012). https://doi.org/10.1016/j.sbi.2012.03.010. · DOI
  60. F. Richter , A. Leaver-Fay , S.D. Khare , S. Bjelic , D. Baker , De novo enzyme design using Rosetta3, PLoS One. 6 (2011). https://doi.org/10.1371/journal.pone.0019230. · DOI
  61. S. Velankar , C. Best , B. Beuth , C.H. Boutselakis , N. Cobley , A.W. Sousa da Silva , D. Dimitropoulos , A. Golovin , M. Hirshberg , M. John , E.B. Krissinel , R. Newman , T. Oldfield , A. Pajon , C.J. Penkett , J. Pineda-Castillo , G. Sahni , S. Sen , R. Slowley , A. Suarez-Uruena , J. Swaminathan , G. van Ginkel , W.F. Vranken , K. Henrick , G.J. Kleywegt , PDBe: Protein Data Bank in Europe, Nucleic Acids Res. 38 (2009). https://doi.org/10.1093/nar/gkp916. · DOI
  62. 1997, Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites, Protein Science, 6, 2308, 10.1002/pro.5560061104 · DOI
  63. A. Stark , S. Sunyaev , R.B. Russell , A model for statistical significance of local similarities in structure, J Mol Biol. 326 (2003). https://doi.org/10.1016/S0022-2836(03)00045-7. · DOI
  64. 1995, The application of hydrogen bonding analysis in x-ray crystallography to help orientate asparagine, glutamine and histidine side chains, Protein Engineering, Design and Selection, 8, 217, 10.1093/protein/8.3.217 · DOI
  65. 10.1107/S0567739476001873 · DOI
  66. 10.1529/biophysj.105.066654 · DOI
  67. K.F. Tipton , Enzyme nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes, Academic Press. 6 (1992).
  68. 10.1016/j.jmb.2009.05.015 · DOI
  69. 10.1074/jbc.REV119.006289 · DOI
  70. 10.1093/nar/gkw1092 · DOI · Paper page
  71. 10.1093/nar/gkr1126 · DOI
  72. 10.1016/S0022-2836(03)00734-4 · DOI
  73. 2022, Using mechanism similarity to understand enzyme evolution, Biophys Rev, 14, 1273, 10.1007/s12551-022-01022-9 · DOI
  74. S.A. Rahman , S.M. Cuesta , N. Furnham , G.L. Holliday , J.M. Thornton , EC-BLAST: A tool to automatically search and compare enzyme reactions, Nat Methods. 11 (2014). https://doi.org/10.1038/nmeth.2803. · DOI

Metadata

Authors
Riziotis, I. G., Ribeiro, A. J. M., Borkakoti, N., & Thornton, J. M.
Affiliations
European Bioinformatics Institute (GB)
Corresponding author
Riziotis, Ioannis G.
ORCID
Venue
Journal of Molecular Biology
Publisher
openRxiv
Published
2023-06-05
Volume
435
Issue
20
Pages
168254-168254
ISSN
0022-2836 (ISSN-L)
DOI
10.1101/2023.06.01.543252
OpenAlex
W4386247125
Cited by
15
References
1
Citations by year
2026: 6 · 2025: 5 · 2024: 3 · 2023: 1
FWCI
1.11
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Journal of Molecular Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed (publishedVersion)
Funders
European Molecular Biology Laboratory
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Organic Chemistry › Physical Organic Chemistry and Reaction Kinetics
Keywords
enzyme catalysis, catalytic module, active site, catalytic residues, 3D templates, convergent evolution, catalytic triad, metal ion binding, substrate binding, enzyme design
MeSH terms
Catalysis, Enzymes, Models, Molecular, Protein Conformation, Evolution, Molecular, Catalytic Domain, Biocatalysis

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