Supersites within superfolds. Binding site similarity in the absence of homology

Journal of Molecular Biology

Volumn 282, Issue 4, 1998, Pages 903-918

  Russell, Robert B ^a   Sasieni, Peter D ^a   Sternberg, Michael J E ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

Binding sites; Convergent evolution; Homology; Protein function; Protein structure

Indexed keywords

FERREDOXIN;

ACCURACY; ARTICLE; BINDING SITE; DATA BASE; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY;

EID: 0032475963     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2043     Document Type: Article

References (67)

1. Alexandrov N.N., Fischer D. Analysis of topological and non-topological structural similarities in the PDB-new examples with old structures. Proteins: Struct. Funct. Genet. 25:1996;354-365
2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410
3. Antson A.A., Otridge J., Brzozowski A.M., Dodson E.J., Dodson G.G., Wilson K.S., Smith T.M., Yang M., Kurecki T., Gollnick P. The structure of trp RNA binding attenuation protein. Nature. 374:1995;693-700
4. Artymiuk P.J., Poirrette A.R., Rice D.W., Willet P. A palm domain in adenylyl cyclase? Nature. 388:1997;33-34
5. Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F., Brice M.D., Rodgers J.R., Kennard O., Shimanovichi T., Tasumi M. The Protein Data Bank a computer-based archival file for macro-molecular structures. J. Mol. Biol. 112:1977;535-542
6. Brannigan J.A., Dodson G., Duggleby H.J., Moody P.C.E., Smith J.L., Tomchick D.R., Murzin A.G. A protein catalytic framework with an N-terminal nucleophile is capable of self-activation. Nature. 378:1995;416-419
7. Brick J.L., O'Hare M.C., Skarzynski T., Lloyd L.F., Curry V.A., Clark I.M., Bgg H.F., Hazleman B.L., Cawston T.E., Blow D.M. Structure of a full-length porcine synovial collagenase reveals a C-terminal domain containing a calcium-linked four-bladed β-propeller. Structure. 3:1995;541-549
8. Choi J., Chen J., Schreiber S.L., Clardy J. Structure of the FKBP12-rapamycin complex interacting with the binding domain of human frap. Science. 273:1996;239-242
9. Chothia C. One thousand families for the molecular biologist. Nature. 357:1992;543-544
10. Chothia C., Levitt M., Richardson D. Helix to helix packing in proteins. J. Mol. Biol. 145:1981;215-250
11. Cohen F.E., Sternberg M.J.E., Taylor W.R. Analysis of the teritary structure of protein β sheet sandwiches. J. Mol. Biol. 148:1981;253-272
12. Copley R.R., Barton G.J. A structural analysis of phosphate and sulphate binding sites estimation of propensities for binding and conservation of phosphate binding sites. J. Mol. Biol. 242:1994;321-329
13. Doolittle R.F. Searching through sequence databases. Methods Enzymol. 183:1990;99-110
14. Faber H.R., Groom C.R., Baker H.M., Morgan W.T.A.S., Baker E.N. 1.8 Å crystal structure of the C-terminal domain of rabbit serum haemopexin. Structure. 3:1995;551-559
15. Farber G.K., Petsko G.A. The evolution of α/β barrel enzymes. Trends Biochem. Sci. 15:1990;228-234
16. Fischer D., Eisenberg D. Assigning folds to the proteins encoded by the genome of mycoplasma genitalium. Proc. Natl Acad. Sci. USA. 94:1997;11929-11934
17. Flower D.R. Structural relationship of streptavidin to the calycin protein superfamily. FEBS Letters. 333:1993;99-102
18. Guasch A., Coll M., Aviles F.X., Huber R. Three-dimensional structure of porcine pancreatic procarboxypeptidase A. A comparison of the A and B zymogens and their determinants for inhibition and activation. J. Mol. Biol. 224:1992;141-157
19. Hall T.M.T., Porter J.A., Beachy P.A., Leahy D.J. A potential catalytic site within the amino-terminal signalling domain of sonc hedgehog. Nature. 378:1995;212-216
20. Hol W.G.J., van Duijnen P.T., Berendsen H.J.C. The α helix dipole and the properties of proteins. Nature. 273:1978;443-446
21. Holm L., Sander C. Searching protein structure databases has come of age. Proteins: Struct. Funct. Genet. 19:1994;165-173
22. Holm L., Sander C. The fssp database-fold classification based on structure alignment of proteins. Nucl. Acids Res. 24:1996;206-209
23. Holm L., Sander C. Decision support system for the evolutionary classification of protein structures. Intel. Sys. Mol. Biol. 5:1997;140-146
24. Holm L., Sander C. An evolutionary treasure unification of a broad set of amidohydrolases related to urease. Proteins: Struct. Funct. Genet. 28:1997;72-82
25. Holm L., Sander C. Enzyme hit. Trends Biochem. Sci. 22:1997;116-117
26. Ito N., Phillips S.E., Stevens C., Ogel Z.B., McPherson M.J., Keen J.N., Yadav K.D., Knowles P.F. Novel thioether bond revealed by a 1.7 Å crystal structure of galactose oxidase. Nature. 350:1991;87-90
27. Janin J. Shared structural motif in proteins. Nature. 365:1993;21
28. Jones D.T. Progress in protein structure prediction. Curr. Opin. Struct. Biol. 7:1997;377-387
29. Kim Y., Geiger J.H., Hahn S., Sigler P.B. Crystal structure of the YTBP/TATA-box complex. Nature. 365:1993;512-520
30. Lemer C.M.R., Rooman M.J., Wodak S.J. Protein-structure prediction by threading methods-evaluation of current techniques. Proteins: Struct. Funct. Genet. 23:1995;337-355
31. Marchler-Bauer A., Bryant S.H. A measure of success in fold recognition. Trends Biochem. Sci. 22:1997;236-240
32. Martin J.L., Bardwell J.C.A., Kuriyan J. Crystal structure of the DsbA protein required for disuphide bond formation in vivo. Nature. 365:1993;464-468
33. Morera S., Chiadmi M., Lebras G., Lascu I., Janin J. Mechanism of phosphate transfer by nucleoside diphosphate kinase X-ray structures of a phospho-histidine intermediate of the enzymes from Drosophila and Dictyostelium. Biochemistry. 34:1995;11062-11070
34. Murzin A. A ribosomal protein module in EF-G and DNA gyrase. Nature Struct. Biol. 2:1995;25-26
35. Murzin A., Brenner S.E., Hubbard T., Chothia C. SCOP a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540
36. Murzin A.G. Sweet tasting protein monellin is related to the cystatin family of thiol proteinase inhibitors. J. Mol. Biol. 230:1993;689-694
37. Murzin A.G. Can homologous proteins evolve different enzymatic activities? J. Mol. Biol. 18:1993;403-405
38. Murzin A.G. Structural classification of proteins new superfamilies. Curr. Opin. Struct. Biol. 6:1996;386-394
39. Murzin A.G. Probable circular permutation in the flavin-binding domain. Nature Struct. Biol. 5:1998;101
40. Orengo C. Classification of protein folds. Curr. Opin. Struct. Biol. 4:1994;429-440
41. Orengo C.A., Flores T.P., Taylor W.R., Thornton J.M. Identification and classification of protein fold families. Protein Eng. 6:1993;485-500
42. Orengo C.A., Jones D.T., Thornton J.M. Protein superfamilies and domain superfolds. Nature. 372:1994;631-634
43. Orengo C.A., Swindells M.B., Michie A.D., Zvelebil M.J., Driscoll P.C., Waterfield M.D., Thornton J.M. Structural similarity between the pleckstrin homology domain and verotoxin-the problem of measuring and evaluating structural similarity. Protein Sci. 4:1995;1977-1983
44. Orengo C.A., Michie A.D., Jones S., Jones D.T., Swindells M.B., Thornton J.M. CATH-a hierarchic classification of protein domain structures. Structure. 5:1997;1093-1108
45. Pennisi P. Taking a structured approach to understanding proteins. Science. 279:1998;978-979
46. Prasad L., Sharma S., Vandonselaar M., Quail J.W., Lee J.S., Waygood E.B., Wilson K.S., Dauter Z., Delbaere L.T.J. Evalutation of mutagenesis for epitope mapping structure of an antibody/protein antigen complex. J. Biol. Chem. 268:1993;10705-10708
47. Russell R.B. Identification of protein three-dimensional side-chain patterns new examples of convergent evolution. J. Mol. Biol. 279:1998;1211-1227
48. Russell R.B., Barton G.J. Multiple protein sequence alignment from tertiary structure comparison assignment of global and residue confidence levels. Proteins: Struct. Funct. Genet. 14:1992;309-323
49. Russell R.B., Barton G.J. An SH2-SH3 domain hybrid. Nature. 364:1993;765
50. Russell R.B., Sternberg M.J.E. A novel binding site in catalase is suggested by similarity to the calycin superfamily. Protein Eng. 9:1996;107-111
51. Russell R.B., Sternberg M.J.E. Two new examples of protein structural similarities within the structure-function twighlight zone. Protein Eng. 10:1997;333-338
52. Russell R.B., Saqi M.A., Sayle R.A., Bates P.A., Sternberg M.J.E. Recognition of analogous and homologous protein folds analysis of sequence and structure conservation. J. Mol. Biol. 269:1997;423-439
53. Russell R.B., Saqi M.A., Bates P.A., Sayle R.A., Sternberg M.J. Recognition of analogous and homologous protein folds assessment of fold recogntion success and assocated alignment accuracy. Protein Eng. 11:1998;1-9
54. Schultz S.C., Shields G.C., Steitz T.A. Crystal structure of CAP-DNA complex the DNA is bent by 90 degrees. Science. 253:1991;1001-1007
55. Schreuder H.A., Prick P.A., Wierenga R.K., Vriend G., Wilson K.S., Hol W., Drenth J. Crystal structure of the p-hydroxybenzoate hydroxylase-substrate complex refined at 1.9 Å resolution. Analysis of the enzyme-substrate and enzyme-product complexes. J. Mol. Biol. 208:1989;679-696
56. Soisson S.M., MacDougall-Shackleton B., Schleif R., Wolberger C. Structural basis for ligand-regulated oligomerization of AraC. Science. 276:1997;421-425
57. Springer T.A. Adhesion receptors of the immune system. Nature. 346:1990;425-434
58. Stevens R.C., Gouaux J.E., Lipscomb W.N. Structural consequences of effector binding to the T state of aspartate carbamoyltransferase. Crystal structures of the unligated ATP-, and CTP-complexed enzymes at 2.6 Å resolution. Biochemistry. 29:1990;7691-7701
59. Swindells M.B., Orengo C.A., Jones D.T., Pearl L.H., Thornton J.M. Recurrence of a binding motif? Nature. 362:1993;299
60. Swindells M.B., Orengo C.A., Jones D.T., Pearl L.H., Thornton J.M. Shared strucural motif in proteins. Nature. 365:1993;21
61. Swindells M.B., Martin A., Jones D.T., Orengo C.A. Contemporary approaches to protein structure classification. Bioessays. 1998;. in the press
62. Thibodeau L.A. Sensitivity and specifcity. Kotz S., Johnson N.L., Read C.B. Encyclopedia of Statistical Sciences. 8:1988;370-372 John Wiley and Sons, Inc, New York
63. Thompson J.D., Higgins D.G., Gibson T.J. Clustal w improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties an weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680
64. Varghese J.N., Laver W.G., Colman P.M. Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 Å resolution. Nature. 303:1983;35-40
65. Weber P.C., Salemme F.R. Structural and functional diversity in 4-α-helical proteins. Nature. 287:1980;82-84
66. Williams R.L., Oren D.A., Munoz-Dorado J., Inouye S., Inouye M., Arnold E. Crystal structure of Myxococcus xanthus nucleosde diphosphate kinase and its interaction with a nucleotide substrate at 2.0 Å resolution. J. Mol. Biol. 234:1993;1230-1247
67. Xia Z.X., Dai W.W., Xiong J.P., Hao Z.P., Davidson V.L., White S., Mathews F.S. The three-dimensional structures of methanol dehydrogenase from two methylotrophic bacteria at 2.6 Å resolution. J. Biol. Chem. 267:1992;22289-22297