Modular architecture of nucleotide-binding pockets

Nucleic Acids Research

Volumn 38, Issue 11, 2010, Pages 3809-3816

  Gherardini, Pier Federico ^a   Ausiello, Gabriele ^a   Russell, Robert B ^b   Helmer Citterich, Manuela ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; NUCLEIC ACID BASE; NUCLEOTIDE; PHOSPHATE; RIBOSE;

ARTICLE; BINDING SITE; CONVERGENT EVOLUTION; GENETIC VARIABILITY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STRUCTURE;

AMINO ACID MOTIFS; BINDING SITES; EVOLUTION, MOLECULAR; LIGANDS; MODELS, MOLECULAR; NUCLEOTIDES; PROTEINS;

EID: 77954364272     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq090     Document Type: Article

References (40)

1. Carroll, S.B. (2001) Chance and necessity: the evolution of morphological complexity and diversity. Nature, 409, 1102-1109.
2. Patthy, L. (1999) Genome evolution and the evolution of exon-shuffling-a review. Gene, 238, 103-114.
3. Schlessinger, J. (2000) Cell signaling by receptor tyrosine kinases. Cell, 103, 211-225.
4. Pawson, T. (1995) Protein modules and signalling networks. Nature, 373, 573-580.
5. Wagner, G.P. and Altenberg, L. (1996) Perspective: complex adaptations and the evolution of evolvability. Evolution, 50, 967-976.
6. Minakhin, L., Bhagat, S., Brunning, A., Campbell, E.A., Darst, S.A., Ebright, R.H. and Severinov, K. (2001) Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly. Proc. Natl Acad. Sci. USA, 98, 892-897.
7. Gavin, A.C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L.J., Bastuck, S., Dümpelfeld, B. et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature, 440, 631-636.
8. Sturniolo, T., Bono, E., Ding, J., Raddrizzani, L., Tuereci, O., Sahin, U., Braxenthaler, M., Gallazzi, F., Protti, M.P., Sinigaglia, F. et al. (1999) Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat. Biotechnol., 17, 555-561.
9. Brannetti, B., Via, A., Cestra, G., Cesareni, G. and Helmer-Citterich, M. (2000) SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family. J. Mol. Biol., 298, 313-328.
10. Petsalaki, E., Stark, A., García-Urdiales, E. and Russell, R.B. (2009) Accurate prediction of peptide binding sites on protein surfaces. PLoS Comput. Biol., 5, e1000335.
11. Reichmann, D., Rahat, O., Albeck, S., Meged, R., Dym, O. and Schreiber, G. (2005) The modular architecture of protein-protein binding interfaces. Proc. Natl Acad. Sci. USA, 102, 57-62.
12. Hajduk, P.J. and Greer, J. (2007) A decade of fragment-based drug design: strategic advances and lessons learned. Nat. Rev. Drug Discov., 6, 211-219.
13. Ausiello, G., Gherardini, P.F., Gatti, E., Incani, O. and Helmer-Citterich, M. (2009) Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics, 10, 182.
14. Ji, H.F., Kong, D.X., Shen, L., Chen, L.L., Ma, B.G. and Zhang, H.Y. (2007) Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery. Genome Biol., 8, R176.
15. Denessiouk, K.A. and Johnson, M.S. (2003) "Acceptor-donor-acceptor" motifs recognize the Watson-Crick, Hoogsteen and Sugar "donor-acceptor-donor" edges of adenine and adenosine-containing ligands. J. Mol. Biol., 333, 1025-1043.
16. Traut, T.W. (1994) The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites. Eur. J. Biochem., 222, 9-19.
17. Vetter, I.R. and Wittinghofer, A. (1999) Nucleoside triphosphate-binding proteins: different scaffolds to achieve phosphoryl transfer. Q. Rev. Biophys., 32, 1-56.
18. Cappello, V., Tramontano, A. and Koch, U. (2002) Classification of proteins based on the properties of the ligand-binding site: the case of adenine-binding proteins. Proteins, 47, 106-115.
19. Mao, L., Wang, Y., Liu, Y. and Hu, X. (2004) Molecular determinants for ATP-binding in proteins: a data mining and quantum chemical analysis. J. Mol. Biol., 336, 787-807.
20. Kobayashi, N. and Go, N. (1997) A method to search for similar protein local structures at ligand binding sites and its application to adenine recognition. Eur. Biophys. J., 26, 135-144.
21. Nobeli, I., Laskowski, R.A., Valdar, W.S. and Thornton, J.M. (2001) On the molecular discrimination between adenine and guanine by proteins. Nucleic Acids Res., 29, 4294-4309.
22. Kinoshita, K., Sadanami, K., Kidera, A. and Go, N. (1999) Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes. Protein Eng., 12, 11-14.
23. Brakoulias, A. and Jackson, R.M. (2004) Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching. Proteins, 56, 250-260.
24. Watson, J.D. and Milner-White, E.J. (2002) A novel main-chain anion-binding site in proteins: the nest. A particular combination of phi, psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions. J. Mol. Biol., 315, 171-182.
25. Via, A., Ferre, F., Brannetti, B., Valencia, A. and Helmer-Citterich, M. (2000) Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution. J. Mol. Biol., 303, 455-465.
26. Ausiello, G., Via, A. and Helmer-Citterich, M. (2005) Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics, 6(Suppl. 4), S5.
27. Ausiello, G., Gherardini, P.F., Marcatili, P., Tramontano, A., Via, A. and Helmer-Citterich, M. (2008) FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics, 9(Suppl. 2), S2.
28. Saraste, M., Sibbald, P.R. and Wittinghofer, A. (1990) The P-loop-a common motif in ATP-and GTP-binding proteins. Trends Biochem. Sci., 15, 430-434.
29. Wierenga, R.K., Terpstra, P. and Hol, W.G. (1986) Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint. J. Mol. Biol., 187, 101-107.
30. Ma, B., Chen, L., Ji, H., Chen, Z., Yang, F. et al. (2008) Characters of very ancient proteins. Biochem. Biophys. Res. Commun., 366, 607-611.
31. Wang, M., Boca, S.M., Kalelkar, R., Mittenthal, J. and Caetano-Anolles, G. (2006) A phylogenomic reconstruction of the protein world based on a genomic census of protein fold architecture. Complexity, 12, 27-40.
32. Day, R., Beck, D.A.C., Armen, R.S. and Daggett, V. (2003) A consensus view of fold space: combining SCOP, CATH, and the Dali domain dictionary. Protein Sci., 12, 2150-2160.
33. Holm, L. and Park, J. (2000) DaliLite workbench for protein structure comparison. Bioinformatics, 16, 566-567.
34. Aravind, L., Mazumder, R., Vasudevan, S. and Koonin, E.V. (2002) Trends in protein evolution inferred from sequence and structure analysis. Curr. Opin. Struct. Biol., 12, 392-399.
35. Dym, O. and Eisenberg, D. (2001) Sequence-structure analysis of FAD-containing proteins. Protein Sci., 10, 1712-1728.
36. Cheek, S., Zhang, H. and Grishin, N.V. (2002) Sequence and structure classification of kinases. J. Mol. Biol., 320, 855-881.
37. Kull, F.J., Vale, R.D. and Fletterick, R.J. (1998) The case for a common ancestor: kinesin and myosin motor proteins and G proteins. J. Muscle Res. Cell Motil., 19, 877-886.
38. Koonin, E.V. (2006) The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Biol. Direct., 1, 22.
39. Neduva, V. and Russell, R.B. (2005) Linear motifs: evolutionary interaction switches. FEBS Lett., 579, 3342-3345.
40. Gherardini, P.F., Wass, M.N., Helmer-Citterich, M. and Sternberg, M.J.E. (2007) Convergent evolution of enzyme active sites is not a rare phenomenon. J. Mol. Biol., 372, 817-845.