Superfamily active site templates

Proteins: Structure, Function and Genetics

Volumn 55, Issue 4, 2004, Pages 962-976

  Meng, Elaine C ^a   Polacco, Benjamin J ^a   Babbitt, Patricia C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Conserved residues; Enolase superfamily; Enzyme; Functional inference; Haloacid dehalogenase superfamily; Structure

Indexed keywords

ENOLASE; ENZYME; HALOACID; HALOACID DEHALOGENASE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; DATA BASE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FUNCTION; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY;

BINDING SITES; ENZYMES; HYDROLASES; MODELS, MOLECULAR; PHOSPHOPYRUVATE HYDRATASE; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 2542555845     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20099     Document Type: Article

References (86)

1. Brenner SE. Errors in genome annotation. Trends Genet 1999; 15(4):132-133.
2. Wilson CA, Kreychman J, Gerstein M. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J Mol Biol 2000;297(1):233-249.
3. Devos D, Valencia A. Intrinsic errors in genome annotation. Trends Genet 2001;17(8):429-431.
4. Gerlt JA, Babbitt PC. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem 2001;70:209-246.
5. Babbitt PC, Gerlt JA. New functions from old scaffolds: how nature reengineers enzymes for new functions. Adv Protein Chem 2000;55:1-28.
6. Gerlt JA, Babbitt PC. Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis. Curr Opin Chem Biol 1998;2(5):607-612.
7. Teichmann SA, Rison SC, Thornton JM, 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(4):693-708.
8. Todd AE, Orengo CA, Thornton JM. Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 2001;307(4):1113-1143.
9. Jensen RA. Enzyme recruitment in evolution of new function. Annu Rev Microbiol 1976;30:409-425.
10. Petsko GA, Kenyon GL, Gerlt JA, Ringe D, Kozarich JW. On the origin of enzymatic species. Trends Biochem Sci 1993;18(10):372-376.
11. Babbitt PC, Gerlt JA. Understanding enzyme superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities. J Biol Chem 1997;272(49):30591-30594.
12. Nagano N, Orengo CA, Thornton JM. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol 2002;321(5):741-765.
13. Riley M. Systems for categorizing functions of gene products. Curr Opin Struct Biol 1998;8(3):388-392.
14. Todd AE, Orengo CA, Thornton JM. Plasticity of enzyme active sites. Trends Biochem Sci 2002;27(8):419-426.
15. Bartlett GJ, Borkakoti N, Thornton JM. Catalyzing new reactions during evolution: economy of residues and mechanism. J Mol Biol 2003;331(4):829-860.
16. Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA. The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. Biochemistry 1996;35(51): 16489-16501.
17. Koonin EV, Tatusov RL. Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search. J Mol Biol 1994;244(1):125-132.
18. Baker AS, Ciocci MJ, Metcalf WW, Kim J, Babbitt PC, Wanner BL, Martin BM, Dunaway-Mariano D. Insights into the mechanism of catalysis by the P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis. Biochemistry 1998;37(26):9305-9315.
19. Aravind L, Galperin MY, Koonin EV. The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold. Trends Biochem Sci 1998;23(4):127-129.
20. Fetrow JS, Skolnick J. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J Mol Biol 1998;281(5):949-968.
21. Di Gennaro JA, Siew N, Hoffman BT, Zhang L, Skolnick J, Neilson LI, Fetrow JS. Enhanced functional annotation of protein sequences via the use of structural descriptors. J Struct Biol 2001;134(2-3):232-245.
22. Artymiuk PJ, Poirrette AR, Grindley HM, Rice DW, Willett P. A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J Mol Biol 1994;243(2):327-344.
23. Russell RB. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J Mol Biol 1998;279(5):1211-1227.
24. Wallace AC, Borkakoti N, Thornton JM. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci 1997;6(11):2308-2323.
25. Wallace AC, Laskowski RA, Thornton JM. Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci 1996;5(6):1001-1013.
26. Kleywegt GJ. Recognition of spatial motifs in protein structures. J Mol Biol 1999;285(4):1887-1897.
27. Madsen D, Kleywegt GJ. Interactive motif and fold recognition in protein structures. J Appl Cryst 2002;35:137-139.
28. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28(1):235-242.
29. Neidhart DJ, Howell PL, Petsko GA, Powers VM, Li RS, Kenyon GL, Gerlt JA. Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5 Å resolution: identification of the active site and possible catalytic residues. Biochemistry 1991;30(38):9264-9273.
30. Gulick AM, Hubbard BK, Gerlt JA, Rayment I. Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli. Biochemistry 2000;39(16): 4590-4602.
31. Helin S, Kahn PC, Guha BL, Mallows DG, Goldman A. The refined X-ray structure of muconate lactonizing enzyme from Pseudomonas putida PRS2000 at 1. 85 Å resolution. J Mol Biol 1995;254(5): 918-941.
32. Levy CW, Buckley PA, Sedelnikova S, Kato Y, Asano Y, Rice DW, Baker PJ. Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase. Structure (Camb) 2002; 10(1):105-113.
33. Gulick AM, Schmidt DM, Gerlt JA, Rayment I. Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis. Biochemistry 2001;40(51):15716-15724.
34. 2+ and o-succinylbenzoate. Biochemistry 2000;39(35):10662-10676.
35. Wedekind JE, Reed GH, Rayment I. Octahedral coordination at the high-affinity metal site in enolase: crystallographic analysis of the Mg(II)-enzyme complex from yeast at 1.9 Å resolution. Biochemistry 1995;34(13):4325-4330.
36. Larsen TM, Wedekind JE, Rayment I, Reed GH. A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 Å resolution. Biochemistry 1996;35(14):4349-4358.
37. Landro JA, Gerlt JA, Kozarich JW, Koo CW, Shah VJ, Kenyon GL, Neidhart DJ, Fujita S, Petsko GA. The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate. Biochemistry 1994;33(3):635-643.
38. Schafer SL, Barrett WC, Kallarakal AT, Mitra B, Kozarich JW, Gerlt JA, Clifton JG, Petsko GA, Kenyon GL. Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the D270N mutant. Biochemistry 1996;35(18): 5662-5669.
39. Kallarakal AT, Mitra B, Kozarich JW, Gerlt JA, Clifton JG, Petsko GA, Kenyon GL. Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the K166R mutant. Biochemistry 1995;34(9):2788-2797.
40. Mitra B, Kallarakal AT, Kozarich JW, Gerlt JA, Clifton JG, Petsko GA, Kenyon GL. Mechanism of the reaction catalyzed by mandelate racemase: importance of electrophilic catalysis by glutamic acid 317. Biochemistry 1995;34(9):2777-2787.
41. Gulick AM, Hubbard BK, Gerlt JA, Rayment I. Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli. Biochemistry 2001;40(34):10054-10062.
42. Gulick AM, Palmer DR, Babbitt PC, Gerlt JA, Rayment I. Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida. Biochemistry 1998;37(41):14358-14368.
43. Wieczorek SJ, Kalivoda KA, Clifton JG, Ringe D, Petsko GA, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: identification of a "new" general acid catalyst in the active site of D-galactonate dehydratase from Escherichia coli. J Am Chem Soc 1999;121:4540-4541.
44. Schell U, Helin S, Kajander T, Schlomann M, Goldman A. Structural basis for the activity of two muconate cycloisomerase variants toward substituted muconates. Proteins 1999;34(1):125-136.
45. Hasson MS, Schlichting I, Moulai J, Taylor K, Barrett W, Kenyon GL, Babbitt PC, Gerlt JA, Petsko GA, Ringe D. Evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase. Proc Natl Acad Sci USA 1998; 95(18):10396-10401.
46. Kajander T, Kahn PC, Passila SH, Cohen DC, Lehtio L, Adolfsen W, Warwicker J, Schell U, Goldman A. Buried charged surface in proteins. Structure Fold Des 2000;8(11):1203-1214.
47. Kleywegt GJ, Hoier H, Jones TA. A re-evaluation of the crystal structure of chloromuconate cycloisomerase. Acta Cryst D 1996;52: 858-863.
48. Asuncion M, Blankenfeldt W, Barlow JN, Gani D, Naismith JH. The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step. J Biol Chem 2002;277(10):8306-8311.
49. 2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1 Å resolution. Biochemistry 1994;33(31):9333-9342.
50. Stec B, Lebioda L. Refined structure of yeast apo-enolase at 2.25 Å resolution. J Mol Biol 1990;211(1):235-248.
51. Lebioda L, Stec B. Crystal structure of holoenolase refined at 1.9 Å resolution: trigonal-bipyramidal geometry of the cation binding site. J Am Chem Soc 1989;111(22):8511-8513.
52. 2+-phosphoglycolate complexes at 2.2 Å resolution. Biochemistry 1991;30(11):2823-2827.
53. 2+-2-phosphoglycerate/phosphoenolpyruvate complex at 2.2 Å resolution. Biochemistry 1991;30(11):2817-2822.
54. 2+-F(-)-Pi complex at 2. 6 Å resolution. Proteins 1993;16(3):219-225.
55. 2+-phosphonoacetohydroxamate complex at 2.4-A resolution. Biochemistry 1994;33(20):6295-6300.
56. Zhang E, Brewer JM, Minor W, Carreira LA, Lebioda L. Mechanism of enolase: the crystal structure of asymmetric dimer enolase-2-phospho-D-glycerate/enolase-phosphoenolpyruvate at 2.0 Å resolution. Biochemistry 1997;36(41):12526-12534.
57. Kuhnel K, Luisi BF. Crystal structure of the Escherichia coli RNA degradosome component enolase. J Mol Biol 2001;313(3):583-592.
58. Duquerroy S, Camus C, Janin J. X-ray structure and catalytic mechanism of lobster enolase. Biochemistry 1995;34(39):12513-12523.
59. Hoier H, Schlomann M, Hammer A, Glusker JP, Carrell HL, Goldman A, Stezowski JJ, Heinemann U. Crystal structure of chloromuconate cycloisomerase from Alcaligenes eutrophus JMP134 (pJP4) at 3 Å resolution. Acta Cryst D 1994;50:75-84.
60. Ridder IS, Rozeboom HJ, Kalk KH, Dijkstra BW. Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase. J Biol Chem 1999;274(43):30672-30678.
61. Morais MC, Zhang W, Baker AS, Zhang G, Dunaway-Mariano D, Allen KN. The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily. Biochemistry 2000;39(34):10385-10396.
62. Ridder IS, Rozeboom HJ, Kalk KH, Janssen DB, Dijkstra BW. Three-dimensional structure of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 complexed with the substrateanalogue formate. J Biol Chem 1997;272(52):33015-33022.
63. Hisano T, Hata Y, Fujii T, Liu JQ, Kurihara T, Esaki N, Soda K. Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold. J Biol Chem 1996;271(34): 20322-20330.
64. Li YF, Hata Y, Fujii T, Hisano T, Nishihara M, Kurihara T, Esaki N. Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism. J Biol Chem 1998;273(24):15035-15044.
65. Wang W, Cho HS, Kim R, Jancarik J, Yokota H, Nguyen HH, Grigoriev IV, Wemmer DE, Kim SH. Structural characterization of the reaction pathway in phosphoserine phosphatase: crystallographic "snapshots" of intermediate states. J Mol Biol 2002;319(2): 421-431.
66. Cho H, Wang W, Kim R, Yokota H, Damo S, Kim SH, Wemmer D, Kustu S, Yan D. BeF(3)(-) acts as a phosphate analog in proteins phosphorylated on aspartate: structure of a BeF(3)(-) complex with phosphoserine phosphatase. Proc Natl Acad Sci U S A 2001;98(15):8525-8530.
67. Galburt EA, Pelletier J, Wilson G, Stoddard BL. Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase. Structure (Camb) 2002;10(9):1249-1260.
68. Lahiri SD, Zhang G, Dunaway-Mariano D, Allen KN. Caught in the act: the structure of phosphorylated beta-phosphoglucomutase from Lactococcus lactis. Biochemistry 2002;41(26):8351-8359.
69. Parsons JF, Lim K, Tempczyk A, Krajewski W, Eisenstein E, Herzberg O. From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase. Proteins 2002;46(4):393-404.
70. Argiriadi MA, Morisseau C, Hammock BD, Christianson DW. Detoxification of environmental mutagens and carcinogens: structure, mechanism, and evolution of liver epoxide hydrolase. Proc Natl Acad Sci USA 1999;96(19):10637-10642.
71. Toyoshima C, Nakasako M, Nomura H, Ogawa H. Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution. Nature 2000;405(6787):647-655.
72. Wu TD, Schmidler SC, Hastie T, Brutlag DL. Modeling and superposition of multiple protein structures using affine transformations: analysis of the globins. Pac Symp Biocomput 1998:509-520.
73. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233(1):123-138.
74. Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998;11(9):739-747.
75. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247(4):536-540.
76. Webb EC, editor. Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes. San Diego: Academic Press; 1992.
77. Orengo CA, Taylor WR. SSAP: sequential structure alignment program for protein structure comparison. Methods Enzymol 1996;266:617-635.
78. Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol 1996;6(3):377-385.
79. Madej T, Gibrat JF, Bryant SH. Threading a database of protein cores. Proteins 1995;23(3):356-369.
80. Szustakowski JD, Weng Z. Protein structure alignment using a genetic algorithm. Proteins 2000;38(4):428-440.
81. Fischer D, Wolfson H, Lin SL, Nussinov R. Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding. Protein Sci 1994;3(5):769-778.
82. 2+-binding site in the P-type ATPase and phosphatase members of the HAD (haloacid dehalogenase) superfamily by structural similarity to the response regulator protein CheY. Biochem J 1999;339 (Pt 2):223-226.
83. Argiriadi MA, Morisseau C, Goodrow MH, Dowdy DL, Hammock BD, Christianson DW. Binding of alkylurea inhibitors to epoxide hydrolase implicates active site tyrosines in substrate activation. J Biol Chem 2000;275(20):15265-15270.
84. Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK. Structural genomics: a pipeline for providing structures for the biologist. Protein Sci 2002;11(4):723-738.
85. Gerlt JA, Raushel FM. Evolution of function in (beta/alpha)(8)-barrel enzymes. Curr Opin Chem Biol 2003;7(2):252-264.
86. Babbitt PC. Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol 2003;7(2):230-237.