Six rossmannoid folds, including the class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a class II aminoacyl-tRNA synthetase

Bioinformatics

Volumn 26, Issue 6, 2010, Pages 709-714

  Cammer, Stephen ^a   Carter Jr , Charles W ^b  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; CODON; METABOLISM; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN FOLDING; PROTEOMICS; X RAY CRYSTALLOGRAPHY;

AMINO ACYL-TRNA SYNTHETASES; BINDING SITES; CODON; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEOMICS;

EID: 77951965210     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq039     Document Type: Article

References (27)

1. Aravind, L. et al. (2002)Trends inp rotein evolution inferred from sequence and structure analysis. Curr. Opin. Struct. Biol., 12, 392-399.
2. Barker, J.A. and Thornton, J.W. (2003) An algorithm for constraint-based structural template matching: application to 3D templastes with statistical analysis. Bioinformatics, 19, 1644-1649.
3. Birck, C. et al. (1999) Conformational changes induced by phosphorylation of the FixJ receiver domain. Struct. Fold. Design, 7, 1505-1515.
4. Cammer, S.A. et al. (2002) Identification of sequence-specific tertiary packing motifs in protein structures using Delaunay tessellation. In Schlick, T. and Gan, H.H. (eds) Lecture Notes in Computational Science and Engineering, Vol. 24. Springer, New York, pp. 477-494.
5. Chothia, C. and Janin, J. (1982) Orthogonal packing of b-pleated sheets in proteins. Biochemistry, 21, 3955-3965.
6. Chothia, C. et al. (1977) Structure of proteins: packing of a-helices and pleated sheets. Proc. Natl Acad. Sci. USA, 74, 4130-4134.
7. Chothia, C. et al. (1981) Helix to helix packing in proteins. J. Mol. Biol., 145, 215-250.
8. Crick, F.H.C. (1953) The packing of a-helices: simple coiled-coils. Acta Cryst., 6, 689-697.
9. Dror, O. et al. (2003) Multiple structural alignment by secondary structures: algorithm and applications. Prot. Sci., 12, 2492-2507.
10. Fetrow, J.S. et al. (1999) Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-I subfamily. FASEB J., 13, 1866-1874.
11. Fetrow, J.S. and Skolnik, J. (1998) Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and t1 ribonucleases. J. Mol. Biol., 281, 949-968.
12. Fischer, D. et al. (1994) Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding. Prot. Sci., 3, 769-778.
13. Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
14. Janin, J. and Chothia, C. (1980) Packing of alpha-helices onto beta-pleated sheets and the anatomy of alpha/beta proteins. J. Mol. Biol., 143, 95-128.
15. Jambon, M. et al. (2003) A new bioinformatic approach to detect common 3D sites in protein structures. Proteins, Structure, Function and Bioinformatics, 52, 137-145
16. Kaguni, L.S. (2004) DNA polymerase g, the mitochondrial replicase. Ann. Rev. Biochem., 73, 293-320.
17. Kapustina, M. et al. (2007) A conformational transition state accompanies amino acid activation by B. stearothermphilus tryptophanyl-trna synthetase. Structure, 15, 1272-1284.
18. Madej, T. et al. (1995) Threading a database of protein cores. Proteins, Structure, Function and Genetics, 23, 536-540.
19. Murzin, A.G. et al. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
20. Orengo, C.A. and Taylor, W.R. (1990) A rapid method for protein structure alignment. J. Theor. Biol., 147, 517-551.
21. Schuster, M. et al. (2001) Conformational coupling in the chemotaxis response regulator chey. Proc. Natl Acad. Sci. USA, 98, 6003-6008.
22. Shakhnovich, B.E. et al. (2003) Functional fingerprints of folds: evidence for correlated structure-function evolution. J. Mol. Biol., 326, 1-9.
23. Shindyalov, I.N. and Bourne, P.E. (1998) Protein structure alignment by incremental combinatorial extension of the optimal path. Prot. Eng., 11, 739-747.
24. Stark, A. et al. (2003) A model for the statistical significance of local similarities in structure. J. Mol. Biol., 326, 1307-1316.
25. Tropsha, A. et al. (2003) Simplicial Neighborhood Analysis of Protein Packing (SNAPP): a computational geometry approach to studying proteins. Meth. Enz., 374, 509-544.
26. 2+-assisted catalysis by B. stearothermophilus trprs is promoted by allosteric effects. Structure, 17, 952-964.
27. Yaremchuk, A. et al. (2000) Crystal structure of a eukaryote/archaeon-like protyl-tRNA synthetase and its complex with tRNApro(cgg). EMBO J., 19, 4745-4758