A novel member of the YchN-like fold: Solution structure of the hypothetical protein Tm0979 from Thermotoga maritima

Protein Science

Volumn 14, Issue 1, 2005, Pages 216-223

  Gaspar, Joe A ^a   Liu, Chengsong ^a,b   Vassall, Kenrick A ^a   Meglei, Gabriela ^a   Stephen, Ricardo ^a   Stathopulos, Peter B ^a   Pineda Lucena, Antonio ^b   Wu, Bin ^b   Yee, Adelinda ^b   Arrowsmith, Cheryl H ^b   Meiering, Elizabeth M ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

DsrH; Flavodoxin like fold; Half barrel; Northeast Structural Genomics Consortium; Protein fold evolution; Protein protein interaction; Thermotoga maritima; YchN

Indexed keywords

BACTERIAL PROTEIN; DIMER; FLAVODOXIN; PROTEIN TM0979; SULFUR; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; DIMERIZATION; HYDROPHOBICITY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE SEQUENCE; OXIDATION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN SECONDARY STRUCTURE; PROTEOMICS; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; THERMOTOGA MARITIMA;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; PROTEOMICS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOLUTIONS; THERMOTOGA MARITIMA;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; THERMOTOGA MARITIMA;

EID: 19944428553     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.041068605     Document Type: Article

References (32)

1. Bartels, C., Xia, T.-H., Billeter, M., Güntert, P., and Wüthrich, K. 1995. The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR 5: 1-10.
2. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32: D138-D141.
3. Bax, A., Vuister, G.W., Grzesiek, S., Delaglio, F., Wang, A.C., Tschudin, R., and Zhu, G. 1994. Measurement of homo- and heteronuclear J couplings from quantitative J correlation. Methods Enzymol. 239: 79-105.
4. Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. 1998. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54: 905-921.
5. Christendat, D., Saridakis, V., Kim, Y., Kumar, P.A., Xu, X., Semesi, A., Joachimiak, A., Arrowsmith, C.H., and Edwards, A.M. 2002. The crystal structure of hypothetical protein Mth1491 from Methanobacterium thermoautotrophicum. Protein Sci. 11: 1409-1414.
6. Cornilescu, G., Delaglio, F., and Bax, A. 1999. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13: 289-302.
7. Davison, T.S., Nie, X., Ma, W., Lin, Y., Kay, C., Benchimol, S., and Arrowsmith, C.H. 2001. Structure and functionality of a designed p53 dimer. J. Mol. Biol. 307: 605-617.
8. Elcock, A.H. and McCammon, J.A. 2001. Identification of protein oligomerization states by analysis of interface conservation. Proc. Natl. Acad. Sci. 98: 2990-2994.
9. Fraczkiewicz, R. and Braun, W. 1998. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J. Comp. Chem. 19: 319-333.
10. Glaser, F., Pupko, T., Paz, I., Bell, R.E., Bechor-Shental, D., Martz, E., and Ben-Tal, N. 2003. ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164.
11. Herrmann, T., Guntert, P., and Wuthrich, K. 2002. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319: 209-227.
12. Hocker, B., Beismann-Driemeyer, S., Hettwer, S., Lustig, A., and Sterner, R. 2001. Dissection of a (βα)8-barrel enzyme into two folded halves. Nat. Struct. Biol. 8: 32-36.
13. Hocker, B., Schmidt, S., and Sterner, R. 2002. A common evolutionary origin of two elementary enzyme folds. FEBS Lett. 510: 133-135.
14. Holm, L. and Sander, C. 1998. Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26: 316-319.
15. Huber, R., Langworthy, T.A., Koenig, H., Thomm, M., Woese, C.R., Sleytr, W.B., and Stetter, K.O. 1986. Thermotoga maritima sp.nov represents a new genus of unique extremely thermophilic eubacteria growing up to 90°C. Arch. Microbiol. 144: 324-333.
16. Kay, L.E. 1997. NMR methods for the study of protein structure and dynamics. Biochem. Cell Biol. 75: 1-15.
17. Koradi, R., Billeter, M., and Wuthrich, K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14: 51-55.
18. Lang, D., Thoma, R., Henn-Sax, M., Sterner, R., and Wilmanns, M. 2000. Structural evidence for evolution of the β/α barrel scaffold by gene duplication and fusion. Science 289: 1546-1550.
19. Laskowski, R.A., Rullmann, J.A., MacArthur, M.W., Kaptein, R., and Thornton, J.M. 1996. AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8: 477-486.
20. Lee, W., Revington, M.J., Arrowsmith, C., and Kay, L.E. 1994. A pulsed field gradient isotope-filtered 3D 13C HMQC-NOESY experiment for extracting intermolecular NOE contacts in molecular complexes. FEBS Lett. 350: 87-90.
21. LeFevre, K.R. and Cordes, M.H. 2003. Retroevolution of λ Cro toward a stable monomer. Proc. Natl. Acad. Sci. 100: 2345-2350.
22. Murzin, A.G. 1998. How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol. 8: 380-387.
23. Murzin, A.C., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
24. Nooren, I.M. and Thornton, J.M. 2003. Diversity of protein-protein interactions. EMBO J. 22: 3486-3492.
25. O'Neill, J.W., Kim, D.E., Johnsen, K., Baker, D., and Zhang, K.Y. 2001. Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus. Structure (Camb.) 9: 1017-1027.
26. Pott, A.S. and Dahl, C. 1998. Sirohaem sulfite reductase and other proteins encoded by genes at the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur. Microbiology 144: 1881-1894.
27. Shin, D.H., Yokota, H., Kim, R., and Kim, S.H. 2002. Crystal structure of a conserved hypothetical protein from Escherichia coli. J. Struct. Funct. Genomics 2: 53-66.
28. Todd, A.E., Orengo, C.A., and Thornton, J.M. 2001. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307: 1113-1143.
29. Valdar, W.S. and Thornton, J.M. 2001. Protein-protein interfaces: Analysis of amino acid conservation in homodimers. Proteins 42: 108-124.
30. Wu, B., Yee, A., Pineda-Lucena, A., Semesi, A., Ramelot, T.A., Cort, J.R., Jung, J.W., Edwards, A., Lee, W., Kennedy, M., et al. 2003. Solution structure of ribosomal protein S28E from Methanobacterium thermoautotrophicum. Protein Sci. 12: 2831-2837.
31. Xia, Y., Yee, A., Arrowsmith, C.H., and Gao, X. 2003. 1H(C) and 1H(N) total NOE correlations in a single 3D NMR experiment. 15N and 13C time-sharing in t1 and t2 dimensions for simultaneous data acquisition. J. Biomol. NMR 27: 193-203.
32. Yee, A., Chang, X., Pineda-Lucena, A., Wu, B., Semesi, A., Le, B., Ramelot, T., Lee, G.M., Bhattacharyya, S., Gutierrez, P., et al. 2002. An NMR approach to structural proteomics. Proc. Natl. Acad. Sci. 99: 1825-1830.