Toward mechanistic classification of enzyme functions

Current Opinion in Chemical Biology

Volumn 15, Issue 3, 2011, Pages 435-442

  Almonacid, Daniel E ^a,b   Babbitt, Patricia C ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND;

DATA BASE; ENZYME ACTIVITY; ENZYME MECHANISM; REVIEW; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; CATALYSIS; DATABASES, PROTEIN; ENZYMES; EVOLUTION, MOLECULAR; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 79958017886     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2011.03.008     Document Type: Review

References (60)

1. IUBMB Enzyme Nomenclature 1992: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes 1992, Academic Press.
2. Babbitt P.C. Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol 2003, 7:230-237.
3. Gerlt J.A., Babbitt P.C. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem 2001, 70:209-246.
4. Glasner M.E., Gerlt J.A., Babbitt P.C. Evolution of enzyme superfamilies. Curr Opin Chem Biol 2006, 10:492-497.
5. Omelchenko M.V., Galperin M.Y., Wolf Y.I., Koonin E.V. Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol Direct 2010, 5:31.
6. Martin A.C.R. PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt. Bioinformatics 2004, 20:986-988.
7. Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
8. Jensen R.A. Enzyme recruitment in evolution of new function. Annu Rev Microbiol 1976, 30:409-425.
9. Petsko G.A., Kenyon G.L., Gerlt J.A., Ringe D., Kozarich J.W. On the origin of enzymatic species. Trends Biochem Sci 1993, 18:372-376.
10. Babbitt P.C., Gerlt J.A. Understanding enzyme superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities. J Biol Chem 1997, 272:30591-30594.
11. Teichmann S.A., Rison S.C.G., Thornton J.M., Riley M., Gough J., Chothia C. The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J Mol Biol 2001, 311:693-708.
12. Bartlett G.J., Borkakoti N., Thornton J.M. Catalysing new reactions during evolution: economy of residues and mechanism. J Mol Biol 2003, 331:829-860.
13. Nowotny M. Retroviral integrase superfamily: the structural perspective. EMBO Rep 2009, 10:144-151.
14. Mindnich R.D., Penning T.M. Aldo-keto reductase (AKR) superfamily: genomics and annotation. Hum Genomics 2009, 3:362-370.
15. Allen K.N., Dunaway-Mariano D. Markers of fitness in a successful enzyme superfamily. Curr Opin Struct Biol 2009, 19:658-665.
16. Linsky T., Fast W. Mechanistic similarity and diversity among the guanidine-modifying members of the pentein superfamily. Biochim Biophys Acta 2010, 1804:1943-1953.
17. Nobeli I., Spriggs R.V., George R.A., Thornton J.M. A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E. coli. J Mol Biol 2005, 347:415-436.
18. Chiang R.A., Sali A., Babbitt P.C. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol 2008, 4:e1000142.
19. Gerlt J.A. A protein structure (or function?) initiative. Structure 2007, 15:1353-1356.
20. Gherardini P.F., Wass M.N., Helmer-Citterich M., Sternberg M.J.E. Convergent evolution of enzyme active sites is not a rare phenomenon. J Mol Biol 2007, 372:817-845.
21. Otto T.D., Guimarães A.C.R., Degrave W.M., de Miranda A.B. AnEnPi: identification and annotation of analogous enzymes. BMC Bioinformatics 2008, 9:544.
22. Nagano N., Noguchi T., Akiyama Y. Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database. Proteins 2007, 66:147-159.
23. Almonacid D.E., Yera E.R., Mitchell J.B.O., Babbitt P.C. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PLoS Comput Biol 2010, 6:e1000700.
24. Pegg S.C.-H., Brown S.D., Ojha S., Seffernick J., Meng E.C., Morris J.H., Chang P.J., Huang C.C., Ferrin T.E., Babbitt P.C. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry 2006, 45:2545-2555.
25. Holliday G.L., Almonacid D.E., Bartlett G.J., O'Boyle N.M., Torrance J.W., Murray-Rust P., Mitchell J.B.O., Thornton J.M. MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Res 2007, 35:D515-D520.
26. Nagano N. EzCatDB: the Enzyme Catalytic-mechanism Database. Nucleic Acids Res 2005, 33:D407-D412.
27. Gariev I.A., Varfolomeev S.D. Hierarchical classification of hydrolases catalytic sites. Bioinformatics 2006, 22:2574-2576.
28. Atkinson H.J., Morris J.H., Ferrin T.E., Babbitt P.C. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One 2009, 4:e4345.
29. Seffernick J.L., Dodge A.G., Sadowsky M.J., Bumpus J.A., Wackett L.P. Bacterial ammeline metabolism via guanine deaminase. J Bacteriol 2010, 192:1106-1112.
30. Cummings J.A., Fedorov A.A., Xu C., Brown S., Fedorov E., Babbitt P.C., Almo S.C., Raushel F.M. Annotating enzymes of uncertain function: the deacylation of d-amino acids by members of the amidohydrolase superfamily. Biochemistry 2009, 48:6469-6481.
31. Xiang D.F., Xu C., Kumaran D., Brown A.C., Sauder J.M., Burley S.K., Swaminathan S., Raushel F.M. Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes. Biochemistry 2009, 48:4567-4576.
32. Xiang D.F., Kolb P., Fedorov A.A., Meier M.M., Fedorov L.V., Nguyen T.T., Sterner R., Almo S.C., Shoichet B.K., Raushel F.M. Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily. Biochemistry 2009, 48:2237-2247.
33. Andreini C., Bertini I., Cavallaro G., Holliday G.L., Thornton J.M. Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics 2009, 25:2088-2089.
34. Fischer J.D., Holliday G.L., Thornton J.M. The CoFactor database: organic cofactors in enzyme catalysis. Bioinformatics 2010, 26:2496-2497.
35. Holliday G.L., Almonacid D.E., Mitchell J.B.O., Thornton J.M. The chemistry of protein catalysis. J Mol Biol 2007, 372:1261-1277.
36. Andreini C., Bertini I., Cavallaro G., Holliday G.L., Thornton J.M. Metal ions in biological catalysis: from enzyme databases to general principles. J Biol Inorg Chem 2008, 13:1205-1218.
37. Holliday G.L., Mitchell J.B.O., Thornton J.M. Understanding the functional roles of amino acid residues in enzyme catalysis. J Mol Biol 2009, 390:560-577.
38. Fischer J.D., Holliday G.L., Rahman S.A., Thornton J.M. The structures and physicochemical properties of organic cofactors in biocatalysis. J Mol Biol 2010, 403:803-824.
39. Nagao C., Nagano N., Mizuguchi K. Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies. Proteins 2010, 78:2369-2384.
40. Porter C.T., Bartlett G.J., Thornton J.M. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 2004, 32:D129-D133.
41. Bashton M., Nobeli I., Thornton J.M. PROCOGNATE: a cognate ligand domain mapping for enzymes. Nucleic Acids Res 2008, 36:D618-D622.
42. Willett P. Similarity methods in chemoinformatics. Annu Rev Inform Sci 2009, 43:1-117.
43. Nobeli I., Ponstingl H., Krissinel E.B., Thornton J.M. A structure-based anatomy of the E. coli metabolome. J Mol Biol 2003, 334:697-719.
44. Koch M.A., Schuffenhauer A., Scheck M., Wetzel S., Casaulta M., Odermatt A., Ertl P., Waldmann H. Charting biologically relevant chemical space: a structural classification of natural products (SCONP). Proc Natl Acad Sci U S A 2005, 102:17272-17277.
45. Macchiarulo A., Thornton J.M., Nobeli I. Mapping human metabolic pathways in the small molecule chemical space. J Chem Inf Model 2009, 49:2272-2289.
46. Adams J.C., Keiser M.J., Basuino L., Chambers H.F., Lee D.-S., Wiest O.G., Babbitt P.C. A mapping of drug space from the viewpoint of small molecule metabolism. PLoS Comput Biol 2009, 5:e1000474.
47. Jaccard P. La distribution de la flore dans la zone alpine. Rev Gen Sci Pures Appl 1907, 18:961-967.
48. Raymond J.W., Willett P. Maximum common subgraph isomorphism algorithms for the matching of chemical structures. J Comput Aided Mol Des 2002, 16:521-533.
49. Rahman S.A., Bashton M., Holliday G.L., Schrader R., Thornton J.M. Small Molecule Subgraph Detector (SMSD) toolkit. J Cheminform 2009, 1:12.
50. Yamanishi Y., Hattori M., Kotera M., Goto S., Kanehisa M. E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics 2009, 25:i179-i186.
51. Saigo H., Hattori M., Kashima H., Tsuda K. Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism. BMC Bioinformatics 2010, 11:S31.
52. Egelhofer V., Schomburg I., Schomburg D Automatic assignment of EC numbers. PLoS Comput Biol 2010, 6:e1000661.
53. Leber M., Egelhofer V., Schomburg I., Schomburg D. Automatic assignment of reaction operators to enzymatic reactions. Bioinformatics 2009, 25:3135-3142.
54. Latino D.A.R.S., Zhang Q.-Y., Aires-de-Sousa J. Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps. Bioinformatics 2008, 24:2236-2244.
55. Latino D.A.R.S., Aires-de-Sousa J. Assignment of EC numbers to enzymatic reactions with MOLMAP reaction descriptors and random forests. J Chem Inf Model 2009, 49:1839-1846.
56. Sacher O., Reitz M., Gasteiger J. Investigations of enzyme-catalyzed reactions based on physicochemical descriptors applied to hydrolases. J Chem Inf Model 2009, 49:1525-1534.
57. Hu X., Yan A., Tan T., Sacher O., Gasteiger J. Similarity perception of reactions catalyzed by oxidoreductases and hydrolases using different classification methods. J Chem Inf Model 2010, 50:1089-1100.
58. O'Boyle N.M., Holliday G.L., Almonacid D.E., Mitchell J.B.O. Using reaction mechanism to measure enzyme similarity. J Mol Biol 2007, 368:1484-1499.
59. George R.A., Spriggs R.V., Thornton J.M., Al-Lazikani B., Swindells M.B. SCOPEC: a database of protein catalytic domains. Bioinformatics 2004, 20:i130-i136.
60. Zhang Z., Tang Y.-R. Genome-wide analysis of enzyme structure-function combination across three domains of life. Protein Pept Lett 2007, 14:291-297.