Crystal structure of the nickel-responsive transcription factor NikR

Nature Structural Biology

Volumn 10, Issue 10, 2003, Pages 794-799

  Schreiter, Eric R ^a   Sintchak, Michael D ^a   Guo, Yayi ^a   Chivers, Peter T ^a,b   Sauer, Robert T ^a   Drennan, Catherine L ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; CYSTEINE; DNA BINDING PROTEIN; HISTIDINE; NICKEL; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NIKR; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; CRYSTALLIZATION; DNA BINDING; ESCHERICHIA COLI; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MOLECULAR SEQUENCE DATA; NICKEL; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS;

ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0141841775     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb985     Document Type: Article

References (31)

1. Maroney, M.J. Structure/function relationships in nickel metallobiochemistry. Curr. Opin. Chem. Biol. 3, 188-199 (1999).
2. 2+-dependent interaction of NikR with wild-type and mutant operator sites. J. Biol. Chem. 275, 19735-19741 (2000).
3. Navarro, C., Wu, L.F. & Mandrand-Berthelot, M.A. The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system for nickel. Mol. Microbiol. 9, 1181-1191 (1993).
4. Chivers, P.T. & Sauer, R.T. NikR repressor: high-affinity nickel binding to the C-terminal domain regulates binding to operator DNA. Chem. Biol. 9, 1141-1148 (2002).
5. Carrington, P.E., Chivers, P.T., Al-Mjeni, F., Sauer, R.T. & Maroney, M.J. Nickel coordination is regulated by the DNA-bound state of NikR. Nat. Struct. Biol. 10, 126-130 (2003).
6. Chivers, P.T. & Sauer, R.T. NikR is a ribbon-helix-helix DNA-binding protein. Protein Sci. 8, 2494-2500 (1999).
7. Breg, J.N., van Opheusden, J.H., Burgering, M.J., Boelens, R. & Kaptein, R. Structure of Arc repressor in solution: evidence for a family of β-sheet DNA-binding proteins. Nature 346, 586-589 (1990).
8. Burgering, M.J. et al. Solution structure of dimeric Mnt repressor (1-76). Biochemistry 33, 15036-15045 (1994).
9. Gomis-Ruth, F.X. et al. The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator. EMBO J. 17, 7404-7415 (1998).
10. Rafferty, J.B., Somers, W.S., Saint-Girons, I. & Phillips, S.E. Three-dimensional crystal structures of Escherichia coli met repressor with and without corepressor. Nature 341, 705-710 (1989).
11. Murayama, K., Orth, P., de la Hoz, A.B., Alonso, J.C. & Saenger, W. Crystal structure of omega transcriptional repressor encoded by Streptococcus pyogenes plasmid pSM19035 at 1.5 Å resolution. J. Mol. Biol. 314, 789-796 (2001).
12. Doukov, T.I., Iverson, T.M., Seravalli, J., Ragsdale, S.W. & Drennan, C.L. A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Science 298, 567-572 (2002).
13. Chipman, D.M. & Shaanan, B. The ACT domain family. Curr. Opin. Struct. Biol. 11, 694-700 (2001).
14. Schuller, D.J., Grant, G.A. & Banaszak, L.J. The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Nat. Struct. Biol. 2, 69-76 (1995).
15. Cho, Y., Sharma, V. & Sacchettini, J.C. Crystal structure of ATP phosphoribosyltransferase from Mycobacterium tuberculosis. J. Biol. Chem. 278, 8333-8339 (2003).
16. Kobe, B. et al. Structural basis of autoregulation of phenylalanine hydroxylase. Nat. Struct. Biol. 6, 442-448 (1999).
17. Leonard, P.M. et al. Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus. EMBO J. 20, 990-997 (2001).
18. Ettema, T.J., Brinkman, A.B., Tani, T.H., Rafferty, J.B. & Van Der Oost, J. A novel ligand-binding domain involved in regulation of amino acid metabolism in prokaryotes. J. Biol. Chem. 277, 37464-37468 (2002).
19. Schneider, T.R. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta Crystallogr. D 58, 195-208 (2002).
20. Sheldrick, G.M. & Schneider, T.R. SHELXL: high-resolution refinement. Methods Enzymol. 277, 319-343 (1997).
21. Nicholls, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296 (1991).
22. 15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type. Biochemistry 24, 7263-7268 (1985).
23. Hunt, J.B., Neece, S.H. & Ginsburg, A. The use of 4-(2-pyridylazo)resorcinol in studies of zinc release from Escherichia coli aspartate transcarbamoylase. Anal. Biochem. 146, 150-157 (1985).
24. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
25. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
26. Cowtan, K.D. & Main, P. Phase combination and cross validation in iterated density-modification calculations. Acta Crystallogr. D 52, 43-48 (1996).
27. McRee, D.E. XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156-165 (1999).
28. Lamzin, V.S. & Wilson, K.S. Automated refinement of protein models. Acta Crystallogr. D49, 129-147 (1993).
29. Terwilliger, T.C. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. D 55, 1174-1178 (1999).
30. Carson, M. Ribbons. Methods Enzymol. 277, 493-505 (1997).
31. Raumann, B.E., Rould, M.A., Pabo, C.O. & Sauer, R.T. DNA recognition by β-sheets in the Arc repressor-operator crystal structure. Nature 367, 754-757 (1994).