Analysis of topological and nontopological structural similarities in the PDB: New examples with old structures

Proteins: Structure, Function and Genetics

Volumn 25, Issue 3, 1996, Pages 354-365

  Alexandrov, Nickolai N ^a,b   Fischer, Daniel ^a,c  

^a NATIONAL CANCER INSTITUTE   (United States)

^b AMGEN INC   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

bacteriochlorophyll a protein; classification of protein structures; method for structural comparison; porin; sequence structure relationship; WWW

Indexed keywords

BACTERIOCHLOROPHYLL; CITRATE SYNTHASE; CYTOCHROME P450; DNA DIRECTED DNA POLYMERASE GAMMA; LIPID; POLYPEPTIDE; PORIN; PROTEIN;

ARTICLE; CLUSTER ANALYSIS; DATA BASE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE;

EID: 0030017889     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199607)25:3<354::AID-PROT7>3.3.CO;2-W     Document Type: Article

References (32)

1. Farber, G.K., Petsko, G.A. The evolution of α/β barrel enzymes. Trends Biochem Sci 15:228-234, 1990.
2. Branden, C.-I. Relation between structure and function of α/β proteins. Q. Rev. Biophys. 13:317-338, 1980.
3. Holm, L., Sander, C. Globin fold in a bacterial toxin. Nature 361:309, 1993.
4. Holm, L., Sander, C. Searching protein structure database has come of age. Proteins 19:165-173, 1994.
5. Orengo, C. Classification of protein folds. Curr. Opin. Struct. Biol. 4:429-440, 1994.
6. Alexandrov, N.N., Takahashi, K., Go, N. Common spatial arrangements of backbone fragments in homologous and non-homologous proteins. J. Mol. Biol. 225:5-9, 1992.
7. Holm, L., Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:123-138, 1993.
8. Orengo, C.A., Taylor, W.R. A local alignment method for protein structure motif. J. Mol. Biol. 233:488-497, 1993.
9. Maiorov, V.N., Crippen, G.M. Significance of RMSD in comparing three-dimensional structures of globular proteins. J. Mol. Biol. 235:625-634, 1994.
10. Alexandrov, N.N., Go, N. Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins. Protein Sci. 3:866-875, 1994.
11. Fischer, D., Tsai, C.J., Nussinov, R. A 3-D sequence-independent representation of the protein data bank. Protein Eng., 8:981-997, 1995.
12. Abagyan, R.A., Maiorov, V.N. A simple qualitative representation of polypeptide chain folds: Comparison of protein tertiary structures. J. Biomol. Struct. Dynam. 5:1267-1279, 1988.
13. Mitchell, E.M., Artymiuk, P.J., Rice, D.W., Willet, P. Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J. Mol. Biol. 212:151-166, 1989.
14. Mizuguchi, K., Go, N. Comparison of spatial arrangements of secondary structural elements in proteins. Protein Eng. 8:353-362, 1995.
15. 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. 247:536-540, 1995.
16. Orengo, C.A., Flores, T.P., Taylor, W.R., Thornton, J.M. Identification and classification of protein fold families. Protein Eng. 6:485-500, 1993.
17. Holm, L., Sander, C. The FSSP database of structurally aligned protein families. Nucleic Acids Res. 22:3600-3609, 1994.
18. Unger, R., Harel, D., Wherland, S., Sussman, J.L. A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins 5:355-373, 1989.
19. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24:946-950, 1991.
20. Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F., Weng, J. Protein data bank. In: "Crystallographic Databases: Information Content, Software Systems, Scientific Applications." Allen, F.H., Bergerhoff, G., Sievers, R. (eds.): Bonn/Cambridge/Chester: Data Commission of the International Union of Crystallography, 1987:107-132.
21. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M. The Protein Data Bank: A computer-based archival file for macromolecule structures. J. Mol. Biol. 112:535-542, 1977.
22. Saitou, N., Nei, M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425, 1987.
23. Tronrud, D.E., Schmid, M.F., Matthews, B.W. Structure and X-ray amino acid sequence of a bacteriochlorophyll a protein from Prosthecochloris aestuarii refined at 1.9 Å resolution. J. Mol. Biol. 188:443-454, 1986.
24. Cowan, S.W., Schirmer, T., Rummel, G., Steiert, M., Ghosh, R., Pauptit, R.A., Jansonius, J.N., Rosenbusch, J.P. Crystal structures explain functional properties of two E. coli porins. Nature 358:727-733, 1992.
25. Bauer, A.J., Rayment, I., Frey, P.A., Holden, H.M. The molecular structure of UDP-galactose 4-epimerase from Escherichia coli determined at 2.5 angstroms resolution. Proteins 12:372-381, 1992.
26. Cheng, X., Kumar, S., Posfai, J., Pflugrath, J.W., Roberts, R.J. Crystal structure of the Hhal DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell 74:299-307, 1993.
27. Finkelstein, A.V., Ptitsyn, O.B. Why do globular proteins fit the limited set of folding patterns? Prog. Biophys. Mol. Biol. 50:171-190, 1987.
28. Wilson, K.P., Shewchuk, L.M., Brennan, R.G., Otsuka, A.J. Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. Proc. Natl. Acad. Sci. U.S.A. 89:9257-9261, 1992.
29. Kong, X.-P., Onrust, R., O'Donnell, M., Kuriyan, J. Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: A sliding DNA clamp. Cell 69:425-437, 1992.
30. Orengo, C.A., Jones, D.T., Thornton, J.M. Protein super-families and domain superfolds. Nature 372:631-634, 1994.
31. Taylor, W.R., Orengo, C.A. Protein structure alignment. J. Mol. Biol. 208:1-22, 1989.
32. Artymiuk, P.J., Rice, D.W., Poirrette, A.R., Willet, P. A tale of two synthetases. Struct. Biol. 1:758-760, 1994.