High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and SufE suggest that all members of the YgdK/SufE protein family are enhancers of cysteine desulfurases

Protein Science

Volumn 14, Issue 6, 2005, Pages 1597-1608

  Liu, Gaohua ^a,b   Li, Zhaohui ^a,c   Chiang, Yiwen ^a,d,e   Acton, Thomas ^a,d,e   Montelione, Gaetano T ^a,d,e   Murray, Diana ^a,c   Szyperski, Thomas ^a,b  

^a Northeast Structural Genomics Consortium ^*  (United States)

^b UNIVERSITY AT BUFFALO   (United States)

^c WEILL CORNELL MEDICAL COLLEGE   (United States)

^d RUTGERS UNIVERSITY   (United States)

^e RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

Fe S cluster; Homology modeling; IscU; NMR; SufE; YgdK

Indexed keywords

BACTERIAL PROTEIN; CYSTATHIONINE GAMMA LYASE; PROTEIN; PROTEIN CSDA; PROTEIN SUFE; PROTEIN SUFS; PROTEIN YGDK; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ESCHERICHIA COLI; EUKARYOTE; GENOMICS; IRON METABOLISM; MOLECULAR MODEL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; OPERON; PRIORITY JOURNAL; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

ANIMALS; CARBON-SULFUR LYASES; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HUMANS; MULTIPROTEIN COMPLEXES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; STRUCTURAL HOMOLOGY, PROTEIN;

ESCHERICHIA COLI; EUKARYOTA; PROKARYOTA;

EID: 22444449790     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.041322705     Document Type: Article

References (49)

1. Acton, T.B., Gunsalus, K.C., Xiao, R., Ma, L.-C., Aramini, J.M., Baran, M.C., Chiang, Y.-W., Climent, T., Cooper, B., Denissova, N., et al. 2005. Robotic cloning and protein productions platform of the Northeast Structural Genomics Consortium. Methods Enzymol. 394: 210-243.
2. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. Aurora, R. and Rose, G.D. 1998. Helix capping. Protein Sci. 7: 21-38.
4. 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 6: 1-10.
5. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
6. Billeter, M. 1992. Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals. Q. Rev. Biophys. 25: 325-377.
7. Bowie, J.U., Luthy, R., and Eisenberg, D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253: 164-169.
8. Cavanagh, J., Fairbrother, W.J., Palmer, A.G., and Skelton, N.J. 1996. Heteronuclear NMR experiments. In Protein NMR spectroscopy, pp. 410-453. Wiley, New York.
9. Clore, G.M. and Gronenborn, A.M. 1998. New methods of structure refinement for macromolecular structure determination by NMR. Proc. Natl Acad. Sci. 95: 5891-5898.
10. 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.
11. Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., and Bax, A. 1995. NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6: 277-293.
12. Fiser, A., Sanchez, R., Melo, F., and Sali, A. 2000. Comparative protein structure modeling. In Computational biochemistry and biophysics (eds. M. Watanabe et al. ), pp. 275-312. Marcel Dekker, New York.
13. 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.
14. Goldsmith-Fischman, S., Kuzin, A., Edstrom, W.C., Benach, J., Shastry, R., Xiao, R., Acton, T.B., Honig, B., Montelione, G.T., and Hunt, J.F. 2004. The SufE sulfur-acceptor protein contains a conserved core structure that mediates interdomain interactions in a variety of redox protein complexes. J. Mol. Biol. 344: 549-565.
15. 13C chemical-shifts. J. Biomol. NMR 4: 455-458.
16. Güntert, P., Mumenthaler, C., and Wüthrich, K. 1997. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273: 283-298.
17. Harper, E.T. and Rose, G.D. 1993. Helix stop signals in proteins and peptides: The capping box. Biochemistry 32: 7605-7609.
18. Henikoff, S. and Henikoff, J.G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. 89: 10915-10919.
19. Holm, L. and Sander, C. 1995. Dali: A network tool for protein structure comparison. Trends Biochem. Sci. 20: 478-480.
20. 13C-enriched fusion proteins in Escherichia coli. J. Biomol. NMR 7: 131-141.
21. Koradi, R., Billeter, M., and Wüthrich, K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graphics 14: 51-55.
22. Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26: 283-291.
23. 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 proteins structures solved by NMR. J. Biomol. NMR 8: 477-486.
24. Liu, J. and Rost, B. 2002. Target space for structural genomics revisited. Bioinformatics 18: 922-933.
25. Liu, J., Hegyi, H., Acton, T.B., and Montelione, G.T. 2004. Automatic target selection for structural genomics on eukaryotes. Proteins 56: 188-200.
26. Loiseau, L., Ollangnier-de-Choudens, S., Nachin, L., Fontecave, M., and Barras, F. 2003. Biogenesis of Fe-S cluster by the bacterial Suf system. J. Biol. Chem. 278: 38352-38359.
27. Luthy, R., Bowie, J.U., and Eisenberg, D. 1992. Assessment of protein models with three-dimensional profiles. Nature 356: 83-85.
28. Marti-Renom, M.A., Stuart, A.C., Fiser, A., Sanchez, R., Melo, F., and Sali, A. 2000. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29: 291-325.
29. Mihara, H. and Esaki, N. 2002. Bacterial cysteine desulfurases: Their function and mechanisms. Appl. Microbiol. Biotechnol. 60: 12-23.
30. Mihara, H., Fujii, T., Kato, S., Kurihara, T., Hata, Y., and Esaki, N. 2002. Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: Implications for its specificity toward selenocysteine. J. Biochem. 131: 679-685.
31. Nicholls, A., Sharp, K., and Honig, B. 1991. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11: 281-296.
32. Ollagnier-de-Choudens, S., Lascoux, D., Loiseau, L., Barras, F., Forest, E., and Fontecave, M. 2003. Mechanistic studies of the SufS-SufE cysteine desulfurase: Evidence for sulfur transfer from SufS to SufE. FEBS Lett. 555: 263-267.
33. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thornton, J.M. 1997. CATH - A hierarchic classification of protein domain structures. Structure 5: 1093-1108.
34. Outten, F.W., Wood, M.J., Munoz, F.M., and Storz, G. 2003. The SufE protein and the SufBCD complex enhance SufS cysteine desulfurase activity as part of a sulfur transfer pathway for Fe-S cluster assembly in Escherichia coli. J. Biol. Chem. 278: 45713-45719.
35. Palmer, A.G. 2001. NMR probes of molecular dynamics: Overview and comparison with other techniques. Annu. Rev. Biophys. Biomol. Struct. 30: 129-155.
36. Pearl, F.M.G., Lee, D., Bray, J.E., Sillitoe, I., Todd, A.E., Harrison, A.P., Thornton, J.M., and Orengo, C.A. 2000. Assigning genomic sequences to CATH. Nucleic Acids Res. 28: 277-282.
37. Petrey, D., Xiang, X., Tang, C., Xie, L., and Gimpelev, M. 2003. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins 53: 430-435.
38. Ramelot, T.A., Cort, J.R., Goldsmith-Fischman, S., Kornhaber, G.J., Xiao, R., Shastry, R., Acton, T.B., Montelione, G.T., and Kennedy, M.A. 2004. Solution NMR structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site. J. Mol. Biol. 344: 567-583.
39. Schwede, T., Diemand, A., Guex, N., and Peitsch, M.C. 2000. Protein structure computing in the genomic era. Res. Microbiol. 151: 107-112.
40. Shindyalov, I.N. and Bourne, P.E. 1998. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11: 739-747.
41. Sippl, M.J. 1993. Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355-362.
42. Smith, A.D., Agar, J.N., Johnson, K.A., Frazzon, J., Amster, I.J., Dean, D.R., and Johnson, M.K. 2001. Sulfur transfer from IscS to IscU: The first step in iron-sulfur cluster biosynthesis. J. Am. Chem. Soc. 123: 11103-11104.
43. Szyperski, T., Yeh, D.C., Sukumaran, D.K., Moseley, H.N.B., and Montelione, G.T. 2002. Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment. Proc. Natl Acad. Sci. 99: 8009-8014.
44. Tramontano, A. and Morea, V. 2003. Assessment of homology-based predictions in CASP5. Proteins 53: 352-386.
45. Urbina, H.D., Silberg, J.J., Hoff, K.G., and Vickery, L.E. 2001. Transfer of sulfur from IscS to IscU during Fe/S cluster assembly. J. Biol. Chem. 276: 44521-44526.
46. 15N-enriched proteins. J. Am. Chem. Soc. 115: 7772-7777.
47. Wunderlich, Z., Acton, T.B., Liu, J., Kornhaber, G., Everett, J., Carter, P., Lan, N., Echols, N., Gerstein, M., Rost, B., et al. 2004. The protein target list of the Northeast Structural Genomics Consortium. Proteins 56: 181-187.
48. 1H distances in proteins. In NMR of proteins and nucleic acids, pp. 117-129. Wiley, New York.
49. Yang, A.S. and Honig, B. 1999. Sequence to structure alignment in comparative modeling using PrISM. Proteins 3(Suppl.): 66-72.