COG4849 is a novel family of nucleotidyltransferases

Journal of Molecular Recognition

Volumn 18, Issue 5, 2005, Pages 422-425

  Kim, Bong Hyun ^a   Sadreyev, Ruslan ^b   Grishin, Nick V ^a,b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

Homology based modeling; Structure prediction; tRNA nucleotidyltransferase

Indexed keywords

BACTERIAL PROTEIN; RNA POLYMERASE; TRANSFER RIBONUCLEIC ACID NUCLEOTIDYLTRANSFERASE;

ARTICLE; BIOLOGY; CHEMISTRY; ENZYME ACTIVE SITE; GENETICS; PROTEIN TERTIARY STRUCTURE;

BACTERIAL PROTEINS; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; PROTEIN STRUCTURE, TERTIARY; RNA NUCLEOTIDYLTRANSFERASES;

EID: 25144468498     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/jmr.746     Document Type: Article

References (24)

1. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25: 3389-3402.
2. Aravind L, Koonin EV. 1999. DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucl. Acids Res. 27: 1609-1618.
3. Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. 2001. Structure prediction meta server. Bioinformatics 17: 750-751.
4. Chivian D, Kim DE, Malmstrom L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D. 2003. Automated prediction of CASP-5 structures using the Roberta server. Proteins 53(Suppl. 6): 524-533.
5. Fischer D. 2000. Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pacific Symposium on Biocomputing 5: 119-130.
6. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 2003. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19: 1015-1018.
7. Gough J, Karplus K, Hughey R, Chothia C. 2001. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol. 313: 903-919.
8. Jones DT. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.
9. Karplus K, Barrett C, Hughey R. 1998. Hidden Markov models for detecting remote protein homologies. Bioinformatics 14: 846-856.
10. Kelley LA, MacCallum RM, Sternberg MJ. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299: 499-520.
11. Lambert C, Leonard N, De Bolle X, Depiereux E. 2002. ESyPredSD: Prediction of proteins 3D structures. Bioinformatics 18: 1250-1256.
12. Li F, Xiong Y, Wang J, Cho HD, Tomita K, Weiner AM, Steitz TA. 2002. Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP. Cell 111: 815-824.
13. Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A. 2001. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci. 10: 2354-2362.
14. McGuffin LJ, Jones DT. 2003. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19: 874-881.
15. Pei J, Sadreyev R, Grishin NV. 2003. PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics 19: 427-428.
16. Rychlewski L, Jaroszewski L, Li W, Godzik A. 2000. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci. 9: 232-241.
17. Sadreyev R, Grishin N. 2003. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol. 326: 317-336.
18. Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J. 1994. Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Science 264: 1930-1935.
19. Shi J, Blundell TL, Mizuguchi K. 2001. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310: 243-257.
20. Tatusov RL, Koonin EV, Lipman DJ. 1997. A genomic perspective on protein families. Science 278: 631-637.
21. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformat. 4: 41.
22. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. 2003. STRING: a database of predicted functional associations between proteins. Nucl. Acids Res. 31: 258-261.
23. Walker DR, Koonin EV. 1997. SEALS: a system for easy analysis of lots of sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5: 333-339.
24. Yue D, Maizels N, Weiner AM. 1996. CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. Rna 2: 895-908.