Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-against-all structural comparison using geometric matching

Proteins: Structure, Function and Genetics

Volumn 56, Issue 2, 2004, Pages 250-260

  Brakoulias, Andreas ^a   Jackson, Richard M ^b  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

Di nucleotide binding motif; P loop; Structural bioinformatics; Structure comparison

Indexed keywords

NUCLEOTIDE; PHOSPHATE; PROTEIN;

ARTICLE; BINDING SITE; GEOMETRY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STRUCTURE;

ALGORITHMS; AMINO ACID MOTIFS; BINDING SITES; CLUSTER ANALYSIS; DATABASES, PROTEIN; FLAVIN-ADENINE DINUCLEOTIDE; LIGANDS; MACROMOLECULAR SUBSTANCES; NADP; NUCLEOTIDES; PEPTIDE FRAGMENTS; PHOSPHATES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; RIBONUCLEASE H, CALF THYMUS; SERINE PROTEINASE INHIBITORS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 3042809615     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20123     Document Type: Article

References (40)

1. Falquet L, Pagni M, Bucher P, Hulo N, Sigrist CJ, Hofmann K, Bairoch A. The PROSITE database, its status in 2002. Nucleic Acids Res 2002;30:235-238.
2. Attwood TK, Blythe MJ, Flower DR, Gaulton A, Mabey JE, Maudling N, McGregor L, Mitchell AL, Moulton G, Paine K, Scordis P. PRINTS and PRINTS-S shed light on protein ancestry. Nucleic Acids Res 2002;30:239-241.
3. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. The Pfam protein families database. Nucleic Acids Res 2002;30:276-280.
4. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH - a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
5. 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;247:536-540.
6. Holm L, Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 1997;25:231-234.
7. Swindells MB. Classification of doubly wound nucleotide binding topologies using automated loop searches. Protein Sci 1993;2:2146-2153.
8. Via A, Ferre F, Brannetti B, Valencia A, Helmer-Citterich M. Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution. J Mol Biol 2000;303:455-465.
9. Doherty AJ, Serpell LC, Ponting CP. The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Nucleic Acids Res 1996;24:2488-2497.
10. Jones S, Barker JA, Nobeli I, Thornton JM. Using structural motif templates to identify proteins with DNA binding function. Nucleic Acids Res 2003;31:2811-2823.
11. Kasuya A, Thornton JM. Three-dimensional structure analysis of PROSITE patterns. J Mol Biol 1999;286:1673-1691.
12. 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;243:327-344.
13. 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;6:2308-2323.
14. Russell RB. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J Mol Biol 1998;279:1211-1227.
15. Wallace A, Thornton J. PROCAT, a database of 3D enzyme active site templates. http://www.biochem.ucl.ac.uk/bsm/PROCAT/PROCAT.html.
16. Aloy P, Querol E, Aviles FX, Sternberg MJ. Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 2001;311:395-408.
17. de Rinaldis M, Ausiello G, Cesareni G, Helmer-Citterich M. Three-dimensional profiles: A new tool to identify protein surface similarities. J Mol Biol 1998;284:1211-1221.
18. Jackson RM, Russell RB. The serine protease inhibitor canonical loop conformation: examples found in extracellular hydrolases, toxins, cytokines and viral proteins. J Mol Biol 2000;296:325-334.
19. Bachar O, Fischer D, Nussinov R, Wolfson H. A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Protein Eng 1993;6:279-288.
20. Pennec X, Ayache N. A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics 1998; 14:516-522.
21. McLachlan AD. Gene duplications in the structural evolution of chymotrypsin. J Mol Biol 1979;128:49-79.
22. Bron C, Kerbosch J. Algorithm 457: finding all cliques of an undirected graph. Commun ACM 1973;16:575-577.
23. Martin AC, Thornton JM. Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies. J Mol Biol 1996;263:800-815.
24. Mojena R. Hierarchical grouping methods and stopping rules: an evaluation. The Computer Journal 1977;20:359-363.
25. Fuchs R. Predicting protein function: a versatile tool for the Apple Macintosh. Comput Appl Biosci 1994;10:171-178.
26. Copley RR, Barton GJ. A structural analysis of phosphate and sulphate binding sites in proteins. Estimation of propensities for binding and conservation of phosphate binding sites. J Mol Biol 1994;242:321-329.
27. Kinoshita K, Sadanami K, Kidera A, Go N. Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes. Protein Eng 1999;12:11-14.
28. Eppink MH, Schreuder HA, Van Berkel WJ. Identification of a novel conserved sequence motif in flavoprotein hydroxylases with a putative dual function in FAD/NAD(P)H binding. Protein Sci 1997;6:2454-2458.
29. Murzin AG. Structural classification of proteins: new superfamilies. Curr Opin Struct Biol 1996;6:386-394.
30. Schulz G. Binding of nulceotides by proteins. Curr Opin Struct Biol 1992;2:61-67.
31. Traut TW. The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites. Eur J Biochem 1994;222:9-19.
32. Denessiouk KA, Rantanen VV, Johnson MS. Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins. Proteins 2001;44:282-291.
33. Lupas AN, Ponting CP, Russell RB. On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J Struct Biol 2001;134:191-203.
34. Stark A, Sunyaev S, Russell RB. A model for statistical significance of local similarities in structure. J Mol Biol 2003;326:1307-1316.
35. Bottoms CA, Smith PE, Tanner JJ. A structurally conserved water molecule in Rossmann dinucleotide-binding domains. Protein Sci 2002;11:2125-2137.
36. Lehtonen JV, Denessiouk K, May AC, Johnson MS. Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm. Proteins 1999;34: 341-355.
37. Oldfield TJ. Data mining the protein data bank: residue interactions. Proteins 2002;49:510-528.
38. Stark A, Russell RB. Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res 2003;31:3341-3344.
39. Jambon M, Imberty A, Deleage G, Geourjon C. A new bioinformatic approach to detect common 3D sites in protein structures. Proteins 2003;52:137-145.
40. Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci 1995;20:374.