The 2.2 Å resolution crystal structure of Bacillus cereus Nif3-family protein YqfO reveals a conserved dimetal-binding motif and a regulatory domain

Protein Science

Volumn 16, Issue 7, 2007, Pages 1285-1293

  Godsey, Michael H ^a   Minasov, George ^b   Shuvalova, Ludmilla ^b   Brunzelle, Joseph S ^c   Vorontsov, Ivan I ^b   Collart, Frank R ^d   Anderson, Wayne F ^b  

^a Concordia University ^*  (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

^c ARGONNE NATIONAL LABORATORY   (United States)

^d ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

Cocatalytic site; Cuta; Dimetal; Nif3; PII; Structural genomics; YqfO

Indexed keywords

BACTERIAL PROTEIN; CUTA PROTEIN; NGG1P INTERACTING FACTOR 3 PROTEIN; NITROGEN REGULATORY PROTEIN; PEPTIDES AND PROTEINS; REGULATOR PROTEIN; UNCLASSIFIED DRUG; YQFO PROTEIN; METAL;

AMINO ACID SEQUENCE; ARTICLE; BACILLUS CEREUS; BINDING AFFINITY; CRYSTAL STRUCTURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN FAMILY; PROTEIN MOTIF; STRUCTURAL GENOMICS; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

BACILLUS CEREUS; BACTERIA (MICROORGANISMS);

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BACILLUS CEREUS; BACTERIAL PROTEINS; BINDING SITES; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; METALS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 34250850376     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062674007     Document Type: Article

References (33)

1. Akiyama, H., Fujisawa, N., Tashiro, Y., Takanabe, N., Sugiyama, A., and Tashiro, F. 2003. The role of transcriptional corepressor Nif3l1 in early stage of neural differentiation via cooperation with Trip15/CSN2. J. Biol. Chem. 278: 10752-10762.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. Arnesano, F., Banci, L., Benvenuti, M., Bertini, I., Calderone, V., Mangani, S., and Viezzoli, M.S. 2003. The evolutionarily conserved trimeric structure of CutA1 proteins suggests a role in signal transduction. J. Biol. Chem. 278: 45999-46006.
4. Auld, D.S. 2001. Zinc coordination sphere in biochemical zinc sites. Biometals 14: 271-313.
5. Barton, G.J. 1993. ALSCRIPT: A tool to format multiple sequence alignments. Protein Eng. 6: 37-40.
6. Cheah, E., Carr, P.D., Suffolk, P.M., Vasudevan, S.G., Dixon, N.E., and Ollis, D.L. 1994. Structure of the Escherichia coli signal transducing protein PII. Structure 2: 981-990.
7. Cho, Y., Sharma, V., and Sacchettini, J.C. 2003. Crystal structure of ATP phosphoribosyltransferase from Mycobacterium tuberculosis. J. Biol. Chem. 278: 8333-8339.
8. Fong, S.T., Camakaris, J., and Lee, B.T. 1995. Molecular genetics of a chromosomal locus involved in copper tolerance in Escherichia coli K-12. Mol. Microbiol. 15: 1127-1137.
9. Galperin, M.Y. and Koonin, E.V. 2004. "Conserved hypothetical" proteins: Prioritization of targets for experimental study. Nucleic Acids Res. 32: 5452-5463.
10. Grosse-Kunstleve, R.W. and Adams, P.D. 2003. Substructure search procedures for macromolecular structures. Acta Crystallogr. D Biol. Crystallogr. 59: 1966-1973.
11. Hingorani, M.M. and O'Donnell, M. 1998. Toroidal proteins: Running rings around DNA. Curr. Biol. 8: R83-R86.
12. Holm, L. and Sander, C. 1996. Mapping the protein universe. Science 273: 595-603.
13. Jiang, P., Zucker, P., Atkinson, M.R., Kamberov, E.S., Tirasophon, W., Chandran, P., Schefke, B.R., and Ninfa, A.J. 1997. Structure/function analysis of the PII signal transduction protein of Escherichia coli: Genetic separation of interactions with protein receptors. J. Bacteriol. 179: 4342-4353.
14. Jones, T.A. 1985. Diffraction methods for biological macromolecules. Interactive computer graphics: FRODO. Methods Enzymol. 115: 157-171.
15. Kabsch, W. 1993. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26: 795-800.
16. Ladner, J.E., Obmolova, G., Teplyakov, A., Howard, A.J., Khil, P.P., Camerini-Otero, R.D., and Gilliland, G.L. 2003. Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site. BMC Struct. Biol. 3: 7.
17. La Fortelle, E. and Bricogne, G. 1997. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multi-wavelength anomalous diffraction methods, pp. 472-494, Academic Press, New York.
18. 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. Crystallogr. 26: 283-291.
19. Martens, J.A., Genereaux, J., Saleh, A., and Brandl, C.J. 1996. Transcriptional activation by yeast PDR1p is inhibited by its association with NGG1p/ADA3p. J. Biol. Chem. 271: 15884-15890.
20. Murshudov, G.N., Vagin, A.A., and Dodson, E.J. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53: 240-255.
21. Ninfa, A.J. and Jiang, P. 2005. PII signal transduction proteins: Sensors of a-ketoglutarate that regulate nitrogen metabolism. Curr. Opin. Microbiol. 8: 168-173.
22. Perrakis, A., Harkiolaki, M., Wilson, K.S., and Lamzin, V.S. 2001. ARP/wARP and molecular replacement. Acta Crystallogr. D Biol. Crystallogr. 57: 1445-1450.
23. Sakai, H., Wang, H., Takemoto-Hori, C., Kaminishi, T., Yamaguchi, H., Kamewari, Y., Terada, T., Kuramitsu, S., Shirouzu, M., and Yokoyama, S. 2005. Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8. J. Struct. Biol. 149: 99-110.
24. Savchenko, A., Skarina, T., Evdokimova, E., Watson, J.D., Laskowski, R., Arrowsmith, C.H., Edwards, A.M., Joachimiak, A., and Zhang, R.G. 2004. X-ray crystal structure of CutA from Thermotoga maritima at 1.4 Å resolution. Proteins 54: 162-165.
25. Schwarzenbacher, R., von Delft, F., Abdubek, P., Ambing, E., Biorac, T., Brinen, L.S., Canaves, J.M., Cambell, J., Chiu, H.J., Dai, X., et al. 2004. Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 Å resolution. Proteins 54: 810-813.
26. Stols, L., Gu, M., Dieckman, L., Raffen, R., Collart, F.R., and Donnelly, M.I. 2002. A new vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site. Protein Expr. Purif. 25: 8-15.
27. Tascou, S., Uedelhoven, J., Dixkens, C., Nayernia, K., Engel, W., and Burfeind, P. 2000. Isolation and characterization of a novel human gene, NIF3L1, and its mouse ortholog, Nif3l1, highly conserved from bacteria to mammals. Cytogenet. Cell Genet. 90: 330-336.
28. Tascou, S., Kang, T.W., Trappe, R., Engel, W., and Burfeind, P. 2003. Identification and characterization of NIF3L1 BP1, a novel cytoplasmic interaction partner of the NIF3L1 protein. Biochem. Biophys. Res. Commun. 309: 440-448.
29. Tatusov, R.L., Galperin, M.Y., Natale, D.A., and Koonin, E.V. 2000. The COG database: A tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28: 33-36.
30. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
31. Xu, Y., Cheah, E., Carr, P.D., van Heeswijk, W.C., Westerhoff, H.V., Vasudevan, S.G., and Ollis, D.L. 1998. GlnK, a PII-homologue: Structure reveals ATP binding site and indicates how the T-loops may be involved in molecular recognition. J. Mol. Biol. 282: 149-165.
32. Xu, Y., Carr, P.D., Clancy, P., Garcia-Dominguez, M., Forchhammer, K., Florencio, F., Vasudevan, S.G., Tandeau de Marsac, N., and Ollis, D.L. 2003. The structures of the PII proteins from the cyanobacteria Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803. Acta Crystallogr. D Biol. Crystallogr. 59: 2183-2190.
33. Ye, Y. and Godzik, A. 2003. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19: II246-II255.