Using Reaction Mechanism to Measure Enzyme Similarity

Journal of Molecular Biology

Volumn 368, Issue 5, 2007, Pages 1484-1499

  O'Boyle, Noel M ^a   Holliday, Gemma L ^a,b   Almonacid, Daniel E ^a   Mitchell, John B O ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

enzyme classification; enzyme mechanism; enzyme reaction; MACiE; reaction similarity

Indexed keywords

CARBOXYPEPTIDASE; DEOXYRIBONUCLEASE; ESTER; MUTASE; PHOSPHOLIPASE A2; PHOSPHOLIPASE C;

ALDOL REACTION; ARTICLE; CATALYSIS; DATA BASE; ENZYME DEGRADATION; ENZYME MECHANISM; ENZYME STRUCTURE; HYDROLYSIS; PRIORITY JOURNAL; REACTION ANALYSIS; SEQUENCE ALIGNMENT;

EID: 34247324354     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.02.065     Document Type: Article

References (77)

1. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., et al. The Pfam protein families database. Nucl. Acids Res. 32 (2004) D138-D141
2. Orengo C.A., Michie A.D., Jones S., Jones D.T., Swindells M.B., and Thornton J.M. CATH-a hierarchic classification of protein domain structures. Structure 5 (1997) 1093-1108
3. Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP-a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
4. Holm L., and Sander C. Mapping the protein universe. Science 273 (1996) 595-602
5. Nomenclature Committee of the International Union of Biochemistry and Molecular Biology, and Webb E.C. Enzyme Nomenclature: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes. 6th edit. (1992), Academic Press, San Diego
6. Kotera M., Okuno Y., Hattori M., Goto S., and Kanehisa M. Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J. Am. Chem. Soc. 126 (2004) 16487-16498
7. Nagano N. EzCatDB: the Enzyme Catalytic-mechanism Database. Nucl. Acids Res. 33 (2005) D407-D412
8. Babbitt P.C., and Gerlt J.A. Understanding enzyme superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities. J. Biol. Chem. 272 (1997) 30591-30594
9. Todd A.E., Orengo C.A., and Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307 (2001) 1113-1143
10. Bartlett G.J., Borkakoti N., and Thornton J.M. Catalysing new reactions during evolution: economy of residues and mechanism. J. Mol. Biol. 331 (2003) 829-860
11. Gourley D.G., Shrive A.K., Polikarpov I., Krell T., Coggins J.R., Hawkins A.R., et al. The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction. Nature Struct. Biol. 6 (1999) 521-525
12. Coutinho P.M., Deleury E., Davies G.J., and Henrissat B. An evolving hierarchical family classification for glycosyltransferases. J. Mol. Biol. 328 (2003) 307-317
13. Pegg S.C.-H., Brown S.D., Ojha S., Seffernick J., Meng E.C., Morris J.H., et al. Leveraging enzyme-structure function relationships for functional inference and experimental design: the Structure-Function Linkage Database. Biochemistry 45 (2006) 2545-2555
14. Gariev I.A., and Varfolomeev S.D. Hierachical classification of hydrolases catalytic sites. Bioinformatics 22 (2006) 2574-2576
15. Chen L., and Gasteiger J. Knowledge discovery in reaction databases: landscaping organic reactions by a self-organizing neural network. J. Am. Chem. Soc. 119 (1997) 4033-4042
16. Satoh H., Sacher O., Nakata T., Chen L., Gasteiger J., and Funatsu K. Classification of organic reactions: similarity of reactions based on changes in the electronic features of oxygen atoms at the reaction sites. J. Chem. Inf. Comput. Sci. 38 (1998) 210-219
17. Latino D.A.R.S., and Aires-de-Sousa J. Genome-scale classification of metabolic reactions: a cheminformatics approach. Angew. Chem. Int. Ed. 45 (2006) 2066-2069
18. Holliday G.L., Bartlett G.J., Almonacid D.E., O'Boyle N.M., Murray-Rust P., Thornton J.M., and Mitchell J.B.O. MACiE: a database of enzyme reaction mechanisms. Bioinformatics 21 (2005) 4315-4316
19. Marsh E.N.G., and Drennan C.L. Adenosylcobalamin-dependent isomerases: new insights into structure and mechanism. Curr. Opin. Chem. Biol. 5 (2001) 499-505
20. Mancia F., Keep N.H., Nakagawa A., Leadlay P.F., McSweeney S., Rasmussen B., et al. How coenzyme B12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2 Å resolution. Structure 4 (1996) 339-350
21. Heinz D.W., Essen L.O., and Williams R.L. Structural and mechanistic comparison of prokaryotic and eukaryotic phosphoinositide-specific phospholipases C. J. Mol. Biol. 275 (1998) 635-650
22. Hondal R.J., Zhao Z., Kravchuk A.V., Liao H., Riddle S.R., Yue X., et al. Mechanism of phosphatidylinositol-specific phospholipase C: a unified view of the mechanism of catalysis. Biochemistry 37 (1998) 4568-4580
23. Ryan M., Liu T., Dahlquist F.W., and Griffith O.H. A catalytic diad involved in substrate-assisted catalysis: NMR study of hydrogen bonding and dynamics at the active site of phosphatidylinositol-specific phospholipase C. Biochemistry 40 (2001) 9743-9750
24. Jones S.J., Worrall A.F., and Connolly B.A. Site-directed mutagenesis of the catalytic residues of bovine pancreatic deoxyribonuclease I. J. Mol. Biol. 264 (1996) 1154-1163
25. Martin S.F., and Hergenrother P.F. Catalytic cycle of the phosphatidylcholine-preferring phospholipase C from Bacillus cereus. Solvent viscosity, deuterium isotope effects, and proton inventory studies. Biochemistry 38 (1999) 4403-4408
26. Skamnaki V.T., Owen D.J., Noble M.E., Lowe E.D., Lowe G., Oikonomakos N.G., and Johnson L.N. Catalytic mechanism of phosphorylase kinase probed by mutational studies. Biochemistry 38 (1999) 14718-14730
27. Bullock T.L., Branchaud B., and Remington S.J. Structure of the complex of L-benzylsuccinate with wheat serine carboxypeptidase II at 2.0-Å resolution. Biochemistry 33 (1994) 11127-11134
28. Ho Y.S., Sheffield P.J., Masuyama J., Arai H., Li J., Aoki J., et al. Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase. Protein Eng. 12 (1999) 693-700
29. Ho Y.S., Swenson L., Derewenda U., Serre L., Wei Y., Dauter Z., et al. Brain acetylhydrolase that inactivates platelet-activating factor is a G-protein-like trimer. Nature 385 (1997) 89-93
30. Wyckoff T.J., and Raetz R.C. The active site of Escherichia coli UDP-N-acetylglucosamine acyltransferase. Chemical modification and site-directed mutagenesis. J. Biol. Chem. 274 (1999) 27047-27055
31. Scott D.L., and Sigler P.B. Structure and catalytic mechanism of secretory phospholipases A2. Advan. Protein Chem. 45 (1994) 53-88
32. 2+ reveal trimeric packing. J. Mol. Biol. 279 (1998) 223-232
33. Tipton K., and Boyce S. History of the enzyme nomenclature system. Bioinformatics 16 (2000) 34-40
34. Cameron A.D., Ridderström M., Olin B., Kavarana M.J., Creighton D.J., and Mannervik B. Reaction mechanism of glyoxalase I explored by an X-ray crystallographic analysis of the human enzyme in complex with a transition state analogue. Biochemistry 38 (1999) 13480-13490
35. Himo F., and Siegbahn P.E.M. Catalytic mechanism of glyoxalase I: a theoretical study. J. Am. Chem. Soc. 123 (2001) 10280-10289
36. Armstrong R.N. Mechanistic diversity in a metalloenzyme superfamily. Biochemistry 39 (2000) 13625-13632
37. McCarthy A.A., Baker H.M., Shewry S.C., Patchett M.L., and Baker E.N. Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: a novel enzymatic function on an ancient metal binding scaffold. Structure 9 (2001) 637-646
38. Howard B.R., Endrizzi J.A., and Remington S.J. Crystal structure of Escherichia coli malate synthase G complexed with magnesium and glyoxylate at 2.0 Å resolution: mechanistic implications. Biochemistry 39 (2000) 3156-3168
39. Mathieu M., Modis Y., Zeelen J.Ph., Engel C.K., Abagyan R.A., Ahlberg A., et al. The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism. J. Mol. Biol. 273 (1997) 714-728
40. Modis Y., and Wierenga R.K. Crystallographic analysis of the reaction pathway of Zoogloea ramigera biosynthetic thiolase. J. Mol. Biol. 297 (2000) 1171-1182
41. Hall D.R., Leonard G.A., Reed C.D., Watt C.I., Berry A., and Hunter W.N. The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity. J. Mol. Biol. 287 (1999) 383-394
42. Carpenter E.P., Hawkins A.R., Frost J.W., and Browns K.A. Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis. Nature 394 (1998) 299-302
43. Karpusas M., Branchaud B., and Remington S.J. Proposed mechanism for the condensation reaction of citrate synthase: 1.9-A structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme A. Biochemistry 29 (1990) 2213-2219
44. Lesburg C.A., Zhai G., Cane D.E., and Christianson D.W. Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology. Science 277 (1997) 1820-1824
45. Seemann M., Zhai G., Umezawa K., and Cane D. Pentalenene synthase. Histidine-309 is not required for catalytic activity. J. Am. Chem. Soc. 121 (1999) 591-592
46. Strater N., Schnappauf G., Braus G., and Lipscomb W.N. Mechanisms of catalysis and allosteric regulation of yeast chorismate mutase from crystal structures. Structure 5 (1997) 1437-1452
47. Ma J., Zheng X., Schnappauf G., Braus G., Karplus M., and Lipscomb W.N. Yeast chorismate mutase in the R state: simulations of the active site. Proc. Natl Acad. Sci. USA 95 (1998) 14640-14645
48. Martí S., Andrés J., Moliner V., Silla E., Tuñón I., and Bertrán J. Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case. Chem. Eur. J. 9 (2003) 984-991
49. Xue Y., and Lipscomb W.N. Location of the active site of allosteric chorismate mutase from Saccharomyces cerevisiae, and comments on the catalytic and regulatory mechanisms. Proc. Natl Acad. Sci. USA 92 (1995) 10595-10598
50. Finer-Moore J.S., Santi D.V., and Stroud R.M. Lessons and conclusions from dissecting the mechanism of a bisubstrate enzyme: thymidylate synthase mutagenesis, function, and structure. Biochemistry 42 (2003) 248-256
51. Hyatt D.C., Maley F., and Montfort W.R. Use of strain in a stereospecific catalytic mechanism: crystal structures of Escherichia coli thymidylate synthase bound to FdUMP and methylenetetrahydrofolate. Biochemistry 36 (1997) 4585-4594
52. Chiericatti G., and Santi D.V. Aspartate 221 of thymidylate synthase is involved in folate cofactor binding and in catalysis. Biochemistry 37 (1998) 9038-9042
53. Benning M.M., Haller T., Gerlt J.A., and Holden H.M. New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli. Biochemistry 39 (2000) 4630-4639
54. Matte A., Tari L.W., Goldie H., and Delbaere L.T. Structure and mechanism of phosphoenolpyruvate carboxykinase. J. Biol. Chem. 272 (1997) 8105-8108
55. Roszak A.W., Robinson D.A., Krell T., Hunter I.S., Fredrickson M., Abell C., et al. The structure and mechanism of the type II dehydroquinase from Streptomyces coelicolor. Structure 10 (2002) 493-503
56. Oliva G., Fontes M.R.M., Garratt R.C., Altamirano M.M., Calcagno M.L., and Horjales E. Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution. Structure 3 (1995) 1323-1332
57. Montero-Moran G.M., Lara-Gonzalez S., Alvarez-Anorve L.I., Plumbridge J.A., and Calcagno M.L. On the multiple functional roles of the active site histidine in catalysis and allosteric regulation of Escherichia coli glucosamine 6-phosphate deaminase. Biochemistry 40 (2001) 10187-10196
58. Tiffany K.A., Roberts D.L., Wang M., Paschke R., Mohsen A.W., Vockley J., and Kim J.J. Structure of human isovaleryl-CoA dehydrogenase at 2.6 Å resolution: structural basis for substrate specificity. Biochemistry 36 (1997) 8455-8464
59. Thorpe C., and Kim J.J. Structure and mechanism of action of the acyl-CoA dehydrogenases. FASEB J. 9 (1995) 718-725
60. Seemann J.E., and Schulz G.E. Structure and mechanism of L-fucose isomerase from Escherichia coli. J. Mol. Biol. 273 (1997) 256-268
61. Collyer C.A., and Blow D.M. Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by D-xylose isomerase. Proc. Natl Acad. Sci. USA 87 (1990) 1362-1366
62. Yang G., Liu R.Q., Taylor K.L., Xiang H., Price J., and Dunaway-Mariano D. Identification of active site residues essential to 4-chlorobenzoyl-coenzyme A dehalogenase catalysis by chemical modification and site directed mutagenesis. Biochemistry 35 (1996) 10879-10885
63. Zheng Y.-J., and Bruice T.C. On the dehalogenation mechanism of 4-chlorobenzoyl CoA by 4-chlorobenzoyl CoA dehalogenase: insights from study based on the nonenzymatic reaction. J. Am. Chem. Soc. 119 (1997) 3868-3877
64. Maveyraud L., Pratt R.F., and Samama J.P. Crystal structure of an acylation transition-state analog of the TEM-1 beta-lactamase. Mechanistic implications for class A beta-lactamases. Biochemistry 37 (1998) 2622-2628
65. Pitarch J., Pascual-Ahuir J.-L., Silla E., and Tunon I. A quantum mechanics/molecular mechanics study of the acylation reaction of TEM1 beta-lactamase and penicillanate. J. Chem. Soc. Perkin Trans. 2 (2000) 761-767
66. Castillo R., Silla E., and Tunon I. Role of protein flexibility in enzymatic catalysis: quantum mechanical-molecular mechanical study of the deacylation reaction in class A beta-lactamases. J. Am. Chem. Soc. 124 (2002) 1809-1816
67. Hermann J.C., Ridder L., Mulholland A.J., and Holtje H.-D. Identification of Glu166 as the general base in the acylation reaction of class A beta-lactamases through QM/MM modeling. J. Am. Chem. Soc. 125 (2003) 9590-9591
68. Ortlund E., Lacount M.W., Lewinski K., and Lebioda L. Reactions of Pseudomonas 7A glutaminase-asparaginase with diazo analogues of glutamine and asparagine result in unexpected covalent inhibitions and suggests an unusual catalytic triad Thr-Tyr-Glu. Biochemistry 39 (2000) 1199-1204
69. Wang Z., Fast W., Valentine A.M., and Benkovic S.J. Metallo-beta-lactamase: structure and mechanism. Curr. Opin. Chem. Biol. 3 (1999) 614-622
70. Leech A.P., Boetzel R., McDonald C., Shrive A.K., Moore G.R., Coggins J.R., et al. Re-evaluating the role of His-143 in the mechanism of type I dehydroquinase from Escherichia coli using two-dimensional 1H,13C NMR. J. Biol. Chem. 273 (1998) 9602-9607
71. Kwak J.E., Lee J.Y., Han B.W., Moon J., Sohn S.H., and Suh S.W. Crystallization and preliminary X-ray crystallographic analysis of type II dehydroquinase from Helicobacter pylori. Acta Crystallog. sect. D 57 (2001) 279-280
72. Ingold C.K. Structure and Mechanism in Organic Chemistry. 2nd edit. (1969), Cornell University Press, Ithaca, NY
73. Jaccard P. La distribution de la flore dans la zone alpine. Rev. Gen. Sci. Pures Appl. 18 (1907) 961-967
74. Durbin R., Eddy S.R., Krogh A., and Mitchison G. Biological Sequence Analysis (1998), Cambridge University Press, Cambridge, UK
75. Waterman M.S. Introduction to Computational Biology: Maps, Sequences, and Genomes: Interdisciplinary Statistics (1995), Chapman and Hall/CRC, Boca Raton, FL
76. Needleman S.B., and Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48 (1970) 443-453
77. Smith T.F., and Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147 (1981) 195-197