The Crystal Structure of UMP Kinase from Bacillus anthracis (BA1797) Reveals an Allosteric Nucleotide-Binding Site

Journal of Molecular Biology

Volumn 381, Issue 5, 2008, Pages 1098-1105

  Meier, Christoph ^a   Carter, Lester G ^a   Sainsbury, Sarah ^a   Mancini, Erika J ^a   Owens, Raymond J ^a   Stuart, David I ^a   Esnouf, Robert M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

allostery; Gram positive bacteria; pyrH; regulation; uridylate kinase

Indexed keywords

PHOSPHOTRANSFERASE; URIDINE PHOSPHATE KINASE;

ARTICLE; BACILLUS ANTHRACIS; CRYSTAL STRUCTURE; GENE CONTROL; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROKARYOTIC CELL;

BACILLUS ANTHRACIS; BACTERIA (MICROORGANISMS); POSIBACTERIA; PROKARYOTA;

EID: 48749129111     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.06.078     Document Type: Article

References (30)

1. Yamanaka K., Ogura T., Niki H., and Hiraga S. Identification and characterization of the smbA gene, a suppressor of the mukB null mutant of Escherichia coli. J. Bacteriol. 174 (1992) 7517-7526
2. Fassy F., Krebs O., Lowinski M., Ferrari P., Winter J., Collard-Dutilleul V., and Salahbey Hocini K. UMP kinase from Streptococcus pneumoniae: evidence for co-operative ATP binding and allosteric regulation. Biochem. J. 384 (2004) 619-627
3. Briozzo P., Evrin C., Meyer P., Assairi L., Joly N., Barzu O., and Gilles A.M. Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation. J. Biol. Chem. 280 (2005) 25533-25540
4. Serina L., Blondin C., Krin E., Sismeiro O., Danchin A., Sakamoto H., et al. Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. Biochemistry 34 (1995) 5066-5074
5. Evrin C., Straut M., Slavova-Azmanova N., Bucurenci N., Onu A., Assairi L., et al. Regulatory mechanisms differ in UMP kinases from Gram-negative and Gram-positive bacteria. J Biol. Chem. 282 (2007) 7242-7253
6. Turnbull P.C. Anthrax history, disease and ecology. Curr. Top. Microbiol. Immunol. 271 (2002) 1-19
7. Mock M., and Fouet A. Anthrax. Annu. Rev. Microbiol. 55 (2001) 647-671
8. Serina L., Bucurenci N., Gilles A.M., Surewicz W.K., Fabian H., Mantsch H.H., et al. Structural properties of UMP-kinase from Escherichia coli: modulation of protein solubility by pH and UTP. Biochemistry 35 (1996) 7003-7011
9. Davis I.W., Murray L.W., Richardson J.S., and Richardson D.C. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res. 32 (2004) W615-W619
10. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
11. Alzari P.M., Berglund H., Berrow N.S., Blagova E., Busso D., Cambillau C., et al. Implementation of semi-automated cloning and prokaryotic expression screening: the impact of SPINE. Acta Crystallogr. Sect. D 62 (2006) 1103-1113
12. Ren J., Sainsbury S., Berrow N.S., Alderton D., Nettleship J.E., Stammers D.K., et al. Crystal structure of nitrogen regulatory protein IIANtr from Neisseria meningitidis. BMC Struct Biol. 5 (2005) 13
13. Walter T.S., Diprose J.M., Brown J., Pickford M., Owens R.J., Stuart D.I., and Harlos K. A procedure for setting up high-throughput nanolitre crystallization experiments: I. Protocol design and validation. J. Appl. Crystallogr. 36 (2003) 308-314
14. Walter T.S., Diprose J.M., Mayo C.J., Siebold C., Pickford M.G., Carter L., et al. A procedure for setting up high-throughput nanolitre crystallization experiments. Crystallization workflow for initial screening, automated storage, imaging and optimization. Acta Crystallogr. Sect. D 61 (2005) 651-657
15. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
16. Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. Sect. A 50 (1994) 157-163
17. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. Sect. D 60 (2004) 2126-2132
18. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Grose P.N., Grosse-Kunstleve R.W., et al. Crystallography and NMR System: a new software suite for macromolecular structure determination. Acta Crystallogr. Sect. D 54 (1998) 905-921
19. Roversi P., Blanc E., Vonrhein C.E.G., and Bricogne G. Modelling prior distributions of atoms for macromolecular refinement and completion. Acta Crystallogr. Sect. D 56 (2000) 1313-1323
20. Stuart D.I., Levine M., Muirhead H., and Stammers D.K. Crystal structure of cat muscle pyruvate kinase at a resolution of 2.6 Å. J Mol. Biol. 134 (1979) 109-142
21. DeLano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific, San Carlos, CA, USA
22. Gouet P., Courcelle E., Stuart D.I., and Metoz F. ESPript: multiple sequence alignments in PostScript. Bioinformatics 15 (1999) 305-308
23. Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
24. Hubbard S.J., Campbell S.F., and Thornton J.M. Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J. Mol. Biol. 220 (1991) 507-530
25. Marco-Marin C., Gil-Ortiz F., and Rubio V. The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis. J. Mol. Biol. 352 (2005) 438-454
26. Jensen K.S., Johansson E., and Jensen K.F. Structural and enzymatic investigation of the Sulfolobus solfataricus uridylate kinase shows competitive UTP inhibition and the lack of GTP stimulation. Biochemistry 46 (2007) 2745-2757
27. Yan H., and Tsai M.D. Nucleoside monophosphate kinases: structure, mechanism, and substrate specificity. Adv. Enzymol. Relat. Areas Mol. Biol. 73 (1999) 103-134
28. Eckstein F., Romaniuk P.J., Heideman W., and Storm D.R. Stereochemistry of the mammalian adenylate cyclase reaction. J. Biol. Chem. 256 (1981) 9118-9120
29. Fassy F., Krebs O., Lowinski M., Ferrari P., Winter J., Collard-Dutilleul V., and Salahbey Hocini K. UMP kinase from Streptococcus pneumoniae: evidence for co-operative ATP binding and allosteric regulation. Biochem J. 384 (2004) 619-627
30. Sakamoto H., Landais S., Evrin C., Laurent-Winter C., Bârzu O., and Kelln R.A. Structure-function relationships of UMP kinases from pyrH mutants of Gram-negative bacteria. Microbiology 150 (2004) 2153-2159