NAD-binding mode and the significance of intersubunit contact revealed by the crystal structure of Mycobacterium tuberculosis NAD kinase-NAD complex

Biochemical and Biophysical Research Communications

Volumn 327, Issue 2, 2005, Pages 500-508

  Mori, Shigetarou ^a   Yamasaki, Masayuki ^a   Maruyama, Yukie ^a   Momma, Keiko ^a   Kawai, Shigeyuki ^a   Hashimoto, Wataru ^a   Mikami, Bunzo ^a   Murata, Kousaku ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

ATP; Mycobacterium tuberculosis; NAD; NAD kinase; Polyphosphate

Indexed keywords

NICOTINAMIDE ADENINE DINUCLEOTIDE KINASE;

ARTICLE; BINDING SITE; CATALYSIS; CHEMICAL STRUCTURE; CONTROLLED STUDY; CRYSTAL STRUCTURE; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; NAD; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN SUBUNITS; SEQUENCE ALIGNMENT;

MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS;

EID: 11144251556     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbrc.2004.11.163     Document Type: Article

References (39)

1. + synthesis Adv. Enzymol. Relat. Areas Mol. Biol. 73 1999 135 182
2. C.E. Outten, and V.C. Culotta A novel NADH kinase is the mitochondrial source of NADPH in Saccharomyces cerevisiae EMBO J. 22 2003 2015 2024
3. R. Vestin Enzymatic change from codehydrogenase I to codehydrogenase II Naturwissenschaften 25 1937 667 668
4. S. Kawai, S. Mori, T. Mukai, S. Suzuki, W. Hashimoto, T. Yamada, and K. Murata Inorganic polyphoshate/ATP-NAD kinase of Micrococcus flavus and Mycobacterium tuberculosis H37Rv Biochem. Biophys. Res. Commun. 276 2000 57 63
5. S. Kawai, S. Mori, T. Mukai, W. Hashimoto, and K. Murata Molecular characterization of Escherichia coli NAD kinase Eur. J. Biochem. 268 2001 4359 4365
6. S. Kawai, S. Mori, S. Suzuki, and K. Murata Molecular cloning and identification of UTR1 of a yeast Saccharomyces cerevisiae as a gene encoding an NAD kinase FEMS Microbiol. Lett. 200 2001 181 184
7. F. Lerner, M. Niere, A. Ludwing, and M. Ziegler Structural and functional characterization of human NAD kinase Biochem. Biophys. Res. Commun. 288 2001 69 74
8. S. Kawai, S. Mori, and K. Murata Primary structure of inorganic polyphosphate/ATP-NAD kinase from Micrococcus flavus, and occurrence of substrate inorganic polyphosphate for the enzyme Biosci. Biotechnol. Biochem. 67 2003 1751 1760
9. M.K. Strand, G.R. Stuart, M.J. Longley, M.A. Graziewicz, O.C. Dominick, and W.C. Copeland POS5 gene of Saccharomyces cerevisiae encodes a mitochondrial NADH kinase required for stability of mitochondrial DNA Eukaryot. Cell 2 2003 809 820
10. S. Garavaglia, A. Galizzi, and M. Rizzi Allosteric regulation of Bacillus subtilis NAD kinase by quinolinic acid J. Bacteriol. 185 2003 4844 4850
11. A. Ochiai, S. Mori, S. Kawai, and K. Murata Overexpression, purification, and characterization of ATP-NAD kinase of Sphingomonas sp. A1 Protein Expr. Purif. 36 2004 124 130
12. W.L. Turner, J.C. Waller, B. Vanderbeld, and W.A. Snedden Cloning and characterization of two NAD kinases from Arabidopsis. Identification of a calmodulin binding isoform Plant Physiol. 135 2004 1243 1255
13. N. Raffaelli, L. Finaurini, F. Mazzola, L. Pucci, L. Sorci, A. Amici, and G. Magni Characterization of Mycobacterium tuberculosis NAD kinase: functional analysis of the full-length enzyme by site-directed mutagenesis Biochemistry 43 2004 7610 7617
14. C.M. Sassetti, D.H. Boyd, and E.J. Rubin Genes required for mycobacterial growth defined by high density mutagenesis Mol. Microbiol. 48 2003 77 84
15. S.Y. Gerdes, M.D. Scholle, M. D'Souza, A. Bernal, M.V. Baev, M. Farrell, O.V. Kurnasov, M.D. Daugherty, F. Mseeh, B.M. Polanuyer, J.W. Campbell, S. Anantha, K.Y. Shatalin, S.A. Chowdhury, M.Y. Fonstein, and A.L. Osterman From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways J. Bacteriol. 184 2002 4555 4572
16. S. Mori, S. Kawai, B. Mikami, and K. Murata Crystallization and preliminary X-ray analysis of NAD kinase from Mycobacterium tuberculosis H37Rv Acta Crystallogr. D 57 2001 1319 1320
17. S. Garavaglia, N. Raffaelli, L. Finaurini, G. Magni, and M. Rizzi A novel fold revealed by Mycobacterium tuberculosis NAD kinase, a key allosteric enzyme in NADP biosynthesis J. Biol. Chem. 279 2004 40980 40986
18. A. Kornberg Inorganic polyphosphate: a molecule of many functions Prog. Mol. Subcell. Biol. 23 1999 1 18
19. S. Mori, M. Yamasaki, Y. Maruyama, K. Momma, S. Kawai, W. Hashimoto, B. Mikami, and K. Murata Crystallographic studies of Mycobacterium tuberculosis polyphosphate/ATP-NAD kinase complexed with NAD J. Biosci. Bioeng. 98 2004 391 393
20. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
21. D.E. McRee XtalView/Xfit-a versatilt program for manipulating atomic coordinates and electron density J. Struct. Biol. 125 1999 156 165
22. W. Furey, and S. Swaminathan PHASE-95, a program pack for processing and analyzing diffraction data from macromolecules Methods Enzymol. 277 1997 590 620
23. B.C. Wang Resolution of phase ambiguity in macromolecular crystallography Methods Enzymol. 115 1985 90 112
24. A.T. Brünger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, N. Nilges, N.S. Pannu, R.J. Read, L.M. Rice, T. Simonson, and G.L. Warren Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr. D 54 1998 905 921
25. G.M. Sheldrick, and T.R. Schneider Substructure solution with SHELXD Methods Enzymol. 277 2002 319 343
26. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291
27. R.W. Hooft, G. Vriend, C. Sander, and E. Abola Errors in protein structures Nature 381 1996 272
28. P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24 1991 946 950
29. E.A. Merrit, and M.E.P. Murphy Raster3D version 2.0: a program for photorealistic molecular graphics Acta Crystallogr. D 50 1994 869 873
30. A. Nicholls, K. Sharp, and B. Honing Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons Proteins Struct. Funct. Genet. 11 1991 281 296
31. U.K. Laemmli Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Nature 227 1970 680 685
32. J.D. Thompson, D.G. Higgins, and T.J. Gibson 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 1994 4673 4680
33. G.N. Ramachandran, and V. Sasisekharan Conformation of polypeptides and proteins Adv. Protein Chem. 23 1968 283 438
34. M.G. Rossmann, D. Moras, and K.W. Olsen Chemical and biological evolution of nucleotide-binding protein Nature 250 1974 194 199
35. A.M. Lesk NAD-binding domains of dehydrogenases Curr. Opin. Struct. Biol. 5 1995 775 783
36. L. Mao, Y. Wang, Y. Liu, and X. Hu Molecular determinants for ATP-binding in proteins: a data mining and quantum chemical analysis J. Mol. Biol. 336 2004 787 807
37. G. Labesse, D. Douguet, L. Assairi, and A.M. Gilles Diacylglyceride kinases, sphingosine kinases and NAD kinases: distant relatives of 6-phosphofructokinases Trends Biochem. Sci. 27 2002 273 275
38. Y. Shirakihara, and P.R. Evans Crystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction products J. Mol. Biol. 204 1988 973 994
39. S.M. Pitson, P.A. Moretti, J.R. Zebol, R. Zareie, C.K. Derian, A.L. Darrow, J. Qi, R.J. D'Andrea, C.J. Bagley, M.A. Vadas, and B.W. Wattenberg The nucleotide-binding site of human sphingosine kinase 1 J. Biol. Chem. 277 2002 49545 49553