Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

Protein Science

Volumn 6, Issue 11, 1997, Pages 2308-2323

  Wallace, Andrew C ^a   Borkakoti, Neera ^b   Thornton, Janet M ^a,c  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b ROCHE PRODUCTS LTD   (United Kingdom)

^c UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

3D structure; Catalytic triad; Database; Protein function; Template

Indexed keywords

CYSTEINE PROTEINASE; ENZYME; HISTIDINE; HYDROLASE; LYSOZYME; RIBONUCLEASE A; SERINE PROTEINASE; TRIACYLGLYCEROL LIPASE;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; DATA BASE; ENZYME ACTIVE SITE; ENZYME STRUCTURE; EUKARYOTE; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE;

EUKARYOTA; PROKARYOTA;

EID: 0030724039     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560061104     Document Type: Article

References (69)

1. Alber T, Dao-Pin S, Nye JA, Muchmore DC, Matthews BW. 1987. T4 temperature sensitive mutations of bacteriophage T4 lysozyme occur at sites with low mobility and low solvent accessibility in the folded protein. Biochemistry 26:3754-3758.
2. Alexandrov NN, Takahashi K, Go N. 1992. Common spatial arrangements of backbone fragments in homologous and non-homologous proteins. J Mol Biol 225:5-9.
3. Altschul SF, Gish W, Miller W, Eugene WM, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403-410.
4. 1 at 184 Å resolution: Structural variations at the base recognition and catalytic sites. Biochemistry 31:3126-3135.
5. Artymiuk PJ, Poirette AR, Grindley HM, Rice DW, Willett P. 1994. Graph theoretic approach to the identification of three-dimensional patterns of amino-acid side-chains in protein structures. J Mol Biol 243:327-344.
6. Attwood TK, Beck ME., Bleasby AJ, Parry-Smith DJ. 1994. PRINTS - A database of protein motif fingerprints. Nucleic Acids Res 22:3590-3696.
7. Bacon DJ, Anderson WF, 1988. A fast algorithm for rendering space-filling molecular pictures. J Mol Graph 6:219-220.
8. Bairoch A, Boeckmann B. 1994. The SWISS-PROT protein sequence databank: Current status. Nucleic Acid Res 22:3578-3589.
9. Bairoch A, Bucher P. 1994. PROSITE: Recent developments. Nucleic Acids Res 22:3583-3582.
10. Beintema JJ, Confalone E, Sasso MP, Furia A. 1990. Structure mechanism and function of ribonucleases. In: Cuchillo MC, Llorens R, Nogues MV, Pares X, eds. Structure mechanism and function of ribonucleases. Gerona, Italy. pp 275-281.
11. Beintema JJ, Schuller C, Masachika I, Carsana A. 1988. Molecular evolution of the ribonuclease superfamily. Prog Biophys Mol Biol 51:165-192.
12. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shoimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
13. Bewley MC, Boustead CM, Walker JH, Waller DA, Huber R. 1993. Structure of chicken annexin V at 225 Å resolution. Biochemistry 32:3923-3929.
14. Blackburn P, Moore S. 1982. Pancreatic ribonuclease. In: Boyer PD, ed. The enzymes. New York: Academic Press, pp 317-433.
15. Blake CCF, Koenig DF, Mair GA, North ACT, Phillips DC, Sarma VR. 1965. Structure of hen egg-white lysozyme, a three-dimensional Fourier synthesis at 2 Å resolution. Nature 206:757-780.
16. Bleasby AJ, Akrigg D, Attwood TK. 1994. OWL - A non-redundant, composite protein sequence database. Nucleic Acid Res 22:3574-3577.
17. Blow DM, Birktoft JJ, Hartley BS. 1969. Role of a buried acid group in the mechanism of action of chymotrypsin. Nature 221:337-340.
18. Boel E, Brady L, Brzozowski AM, Derewenda Z, Dodson GG, Jensen VJ, Peterson SB, Swift H, Thim L, Woldike HF. 1990. Calcium binding in α-amylases: An X-ray diffraction study at 21 Å resolution of two enzymes from Aspergillus. Biochemistry 29:6244-6249.
19. Bone R, Fujishige A, Kettner CA, Agard DA. 1991. Structural basis for broad specificity in α-lytic protease mutants. Biochemistry 30:10388-10398.
20. Borkakoti N, Moss DS, Stanford MJ, Palmer RA. 1982. The refined structure of ribonuclease A at 145 Å resolution. J Crystallogr Spectros Res 14:467-471.
21. Brady L, Brzozowski AM, Derewenda ZS, Dodson E, Dodson G, Tolley S, Turkenburg JP, Christianson L, Huge Jensen B, Norskov L, Thim L, Menge U. 1990. A serine protease triad forms the catalytic centre of triacylglycerol lipase. Nature 343:767-770.
22. Crestfield AM, Stein WH, Moore S. 1963. Alkylation and identification of the histidine residues at the active site of ribonuclease. J Biol Chem 238:2413-2420.
23. deMel VS, Martin PD, Doscher MS, Edwards BF. 1992. Structural changes that accompany the reduced catalytic efficiency of two semisynthetic ribonuclease analogs. J Biol Chem 267:247-256.
24. Diamond R. 1975. Real-space refinement of the structure of hen egg-white lysozyme. J Mol Biol 82:371-396.
25. Drenth J, Jansonius JN, Koekoek R, Swen HM, Wolthers BG. 1968. Structure of papain. Nature 218:929-934.
26. Fischer D, Wolfson H, Shuo LL, Nussinov R. 1994. Three-dimensional, sequence order-independent comparison of a serine protease against the crystallographic database reveals active site similarities: Potential implications to evolution and to protein folding. Protein Sci 3:769-778.
27. Fischmann TO, Bentley GA, Bhat TN, Boulot TN, Mariuzza RA Phillips SEV, Tello D, Poljak RJ. 1991. Crystallographic refinement of the 3D structure of the Fabdi13-lysozyme complex at 25 Å resolution. J Biol Chem 266:12915-12920.
28. Fujinaga M, James MNG. 1987. Rat submaxillary serine proteinase, tonin structure solution and refinement at 18 Å resolution. J Mol Biol 195:373-391.
29. Glusker JP. 1991. Structural aspects of metal liganding to functional groups in proteins. Adv Protein Chem 42:1-76.
30. Grochulski P, Li Y, Schrag JD, Bouthillier F, Smith P, Harrison D, Rubin B, Cygler M. 1993. Insights into interfacial activation from an "open" structure of Candida rugosa lipase. J Biol Chem 268:12843-12847.
31. Harata K, Muraki M, Jigami Y. 1993. Role of Arg 115 in the catalytic action of human lysozyme - X-ray structure of His 115 and Glu 115 mutants. J Mol Biol 233:524-535.
32. Holm L, Sander C. 1993. Protein structure comparison by alignment of distance matrices. J Mol Biol 233:123-138
33. Hutchinson EG, Thornton JM. 1996. PROMTOIF - A program to identify and analyse structural motifs in proteins. Protein Sci 5:212-220.
34. Jernigan R, Raghunathan G, Bahar I. 1994. Characterization of interactions and metal-ion binding-sites in proteins. Curr Opin Struct Biol 4:256-263.
35. Johnson LN, Phillips DC. 1965. Structure of some crystalline-inhibitor complexes determined by X-ray analysis at 6 Å resolution. Nature 206:761-764.
36. Jongsun K, Rees DC. 1992. Crystallographic structure and functional implications of the nitrogenase molybdenum-iron protein from Azotobacter vinelandii. Nature 360:553-560.
37. Kraulis PJ. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-950.
38. Lamdan Y, Schwartz JT, Wolfson HJ. 1988. On recognising 3D objects from 2D images. Proceedings of IEEE Int Conf on Robotics and Automation, Philadelphia, Pennsylvania, pp 1407-1413.
39. Lawson CL, Van Montfort R, Strokkopytov B, Rozeboom HJ, Kalk KH, De Vries GE, Penninga D, Dijkhuizen L, Dijkstra BW. 1994. Nucleotide sequence and X-ray structure of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 in a maltose-dependent crystal form. J Mol Biol 236:590-600.
40. Lemer CMR, Rooman MJ, Wodak SJ. 1995. Protein structure prediction by threading methods: Evaluation and current techniques. Proteins Struct Funct Genet 23:337-355.
41. 1 and guanosine-3′,5′-bisphosphate. Acta Crystallogr B 47:521-527.
42. Lundqvist T, Schneider G. 1989. Crystal structure of the complex of ribulose-1,5-bisphosphate carboxylase and a transition state analogue, 2-carboxy-D-arabinitol 1,5-bisphosphate. J Biol Chem 264:7078-7083.
43. Matthews BW, Remington SJ. 1974. The three-dimensional structure of the lysozyme from bacteriophage T4. Proc Natl Acad Sci USA 71:4178-4182.
44. Matthews BW, Rossmann MG 1985. Comparison of protein structures. Methods Enzymol 115:397-420.
45. Mitchell EM, Artymiuk PJ, Rice DW, Willet P. 1990. Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J Mol Biol 212:151-166.
46. Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540.
47. Ollis DL, Cheah E, Miroslaw C, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J, Sussman JL, Verschueren KHG, Goldman A. 1992. The α/β hydrolase fold. Protein Eng 5:197-211.
48. Orengo CA, Flores TP, Taylor WR, Thornton JM. 1993. Identification and classification of protein fold families. Protein Eng 6:485-500.
49. Ohkawa H, Hogue C, Bryant S, Kans J, Epstein J, Schuler G, Ostler J. 1997. MMDB: Entrez's Structure Database - FAQ. http://www.ncbi.nlm.nih.gov/ structure/struchelp.html.
50. Parry N, Fox G, Rowlands D, Brown F, Fry E, Acharaya R, Logan D, Stuart D. 1990. Structural and serological evidence for a novel mechanism of anti-genic variation in foot-and-mouth disease virus. Nature 347:569-572.
51. Phillips DC. 1966. The three-dimensional structure of an enzyme molecule. Sci Am 215:78-90.
52. Rao ST, Hogle J, Sundaralingam M. 1983. Studies of monoclinic hen-egg white lysozyme. The refinement at 25 Å resolution - Conformational variability between the two independent molecules. Acta Crystallogr C 39:237-242.
53. Rao Z, Esnouf R, Isaacs N, Stuart D. 1995. A strategy for rapid and effective refinement applied to black swan lysozyme. Acta Crystallogr D 51:331-335.
54. Remington SJ, Matthews BW. 1978. Method to assess the similarity of protein structures, with applications to T4 bacteriophage lysozyme. Proc Natl Acad Sci USA 75:2180-2184.
55. Sheriff S, Silverton EW, Padlan EA, Cohen GH, Smith-Gill SJ, Finzel BC, Davies DR. 1987. Three-dimensional structure of an antibody-antigen complex. Proc Natl Acad Sci USA 84:8075-8079.
56. Schneider G, Lindqvist Y, Lundqvist T. 1990. Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 17 Å resolution. J Mol Biol 211:989-1008.
57. Sussman JL, Harel M, Frolow F, Oefner C, Goldman A, Toker L, Silman I. 1991. Atomic structure of acetylcholinesterase from Torpedo californica: A prototypic acetylcholine-binding protein. Science 253:872-879.
58. Timkovich R, Dickerson RE. 1976. The structure of Paracoccus denitrificans cytochrome C500. J Biol Chern 251:4033-4055.
59. Thayer MM, Flaherty KM, McKay DB. 1991. Three-dimensional structure of the elastase of Pseudomonas aeroginosa at 15 Å resolution. J Biol Chem 266:2864-2871.
60. Tsuge H, Ago H, Noma M, Nitta K, Sugai S, Miyano M. 1992. Lysozyme from equine milk at 25 Å resolution. J Biochem 111:141-143.
61. Varadarajan R, Richards FM. 1992. Crystallographic structures of ribonuclease S variants with nonpolar substitutions at position 12: Packing and cavities. Biochemistry 31:12315-12327.
62. Verschueren HG, Seljee F, Rozeboom HJ, Kalk KH, Dijkstra BW. 1993. Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase. Nature 363:693-698.
63. Wallace AC, Laskowski RA, Thornton JM. 1996. Derivation of 3D coordinate templates for searching structural databases: Application to the Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci 5:1001-1013.
64. Weaver LH, Grutter MG, Matthews BW. 1995. The refined structures of goose lysozyme and its complex with a hound trisaccharide show that the "goose-type" lysozymes lack a catalytic aspartate residue. J Mol Biol 245:54-68.
65. Weaver LH, Matthews BW. 1987. Structure of bacteriophage T4 lysozyme refined at 17 Å resolution. J Mol Biol 193:189-199.
66. Wei Y, Schottel JL, Derewenda U, Swenson L, Patkar S, Derewenda ZS. 1995. A novel variant of the catalytic triad in the Streptomyces scabies esterase. Nature Struct Biol 2:218-223.
67. Wright CS, Alden RA, Kraut J. 1969. Structure of subtilisin bpn at 25 Å resolution. Nature 221:235-242.
68. Young ACM, Dewan JC, Nave C, Tilton RF. 1993. Comparison of radiation-induced and structure refinement from X-ray data collected from lysozyme crystals at low and ambient temperatures. J Appl Crystallogr 26:309-319.
69. Zegers I, Verhelst P, Choe HW, Steyaert J, Heinemann U, Saenger W, Wyns L. 1992. The role of histidine-40 in ribonuclease t1 catalysis: 3-Dimensional structures of the partially active His40Lys mutant. Biochemistry 31:11317-11325.