Crystal structure of dephospho-coenzyme A kinase from Haemophilus influenzae

Journal of Structural Biology

Volumn 136, Issue 2, 2001, Pages 119-125

  Obmolova, Galina ^a   Teplyakov, Alexey ^a   Bonander, Nicklas ^a   Eisenstein, Edward ^a   Howard, Andrew J ^b   Gilliland, Gary L ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b ILLINOIS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

CoA synthesis; Haemophilus influenzae; Kinase; Nucleotide binding fold

Indexed keywords

ADENOSINE TRIPHOSPHATE; BACTERIAL PROTEIN; COENZYME A; NUCLEOTIDE BINDING PROTEIN; PHOSPHOTRANSFERASE;

ALPHA HELIX; ARTICLE; BETA SHEET; BINDING SITE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; HAEMOPHILUS INFLUENZAE; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; STRUCTURE ANALYSIS;

HAEMOPHILUS; HAEMOPHILUS INFLUENZAE;

EID: 0035783037     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1006/jsbi.2001.4428     Document Type: Article

References (27)

1. 2+. Proteins 32, 276-288.
2. Briozzo, P., Golinelli-Pimpaneau, B., Gilles, A. M., Gaucher, J. F., Burlacu-Miron, S., Sakamoto, H., Janin, J., and Barzu, O. (1998) Structures of Escherichia coli CMP kinase alone and in complex with CDP: A new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity. Structure 6, 1517-1527.
3. Brown, D. G., Visse, R., Sandhu, G., Davies, A., Rizkallah, P. J., Melitz, C., Summers, W. C., and Sanderson, M. R. (1995) Crystal structures of the thymidine kinase from herpes simplex virus type-1 in complex with deoxythymidine and ganciclovir. Nat. Struct. Biol. 2, 876-881.
4. Bucurenci, N., Serina, L., Zaharia, C., Landais, S., Danchin, A., and Barzu, O. (1998) Mutational analysis of UMP kinase from Escherichia coli. J. Bacteriol. 180, 473-477.
5. Collaborative Computational Project, Number 4 (CCP4). (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. Sect. D 50, 760-763.
6. Dreusicke, D., Karplus, P. A., and Schulz, G. E. (1988) Refined structure of porcine cytosolic adenylate kinase at 2.1 Å resolution. J. Mol. Biol. 199, 359-371.
7. Holm, L., and Sander, C. (1998) Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26, 316-319.
8. Izard, T., and Ellis, J. (2000) The crystal structures of chloramphenicol phosphotransferase reveal a novel inactivation mechanism. EMBO J. 19, 2690-2700.
9. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for building models in electron density maps and the location of errors in these models. Acta Crystallogr. Sect. A 47, 110-119.
10. Kabsch, W., and Sander, C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22, 2577-2637.
11. Kraulis, P. J. (1991) MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
12. Krell, T., Coggins, J. R., and Lapthorn, A. J. (1998) The three-dimensional structure of shikimate kinase. J. Mol. Biol. 278, 983-997.
13. 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.
14. Lavie, A., Konrad, M., Brundiers, R., Goody, R. S., Schlichting, I., and Reinstein, J. (1998) Crystal structure of yeast thymidylate kinase complexed with the bisubstrate inhibitor P1-(5′-adenosyl) P5-(5′-thymidyl) pentaphosphate (TP5A) at 2.0 Å resolution: Implications for catalysis and AZT activation. Biochemistry 37, 3677-3686.
15. Merritt, E. A., and Bacon, D. J. (1997) Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277, 505-524.
16. Mishra, P., Park, P. K., and Drueckhammer, D. G. (2001) Identification of yacE (coaE) as the structural gene for dephosphocoenzyme A kinase in Escherichia coli K-12. J. Bacteriol. 183, 2774-2778.
17. Mueller-Dieckmann, H. J., and Schulz, G. E. (1995) Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase. J. Mol. Biol. 246, 522-530.
18. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by maximum-likelihood method. Acta Crystallogr. Sect. D 53, 240-255.
19. Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
20. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
21. Schulz, G. E. (1992) Binding of nucleotides by proteins. Curr. Opin. Struct. Biol. 2, 61-67.
22. Schulz, G. E., Mueller, C. W., and Diederichs, K. (1990) Inducedfit movements in adenylate kinases. J. Mol. Biol. 213, 627-630.
23. Stehle, T., and Schulz, G. E. (1992) Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 Å resolution. J. Mol. Biol. 224, 1127-1141.
24. Teplyakov, A., Sebastiao, P., Obmolova, G., Perrakis, A., Brush, G. S., Bessman, M. J., and Wilson, K. S. (1996) Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP. EMBO J. 15, 3487-3497.
25. Walker, J. E., Saraste, M., Runswick, M. J., and Gay, N. J. (1982) Distantly related sequences in the alpha- and beta-subunits of ATP synthase myosin kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1, 945-951.
26. Wild, K., Bohner, T., Folkers, G., and Schulz, G. E. (1997) The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue. Protein Sci. 6, 2097-2106.
27. Yan, H., and Tsai, M. D. (1999) Nucleoside monophosphate kinases: Structure, mechanism, and substrate specificity. Adv. Enzymol. Relat. Areas Mol. Biol. 73, 103-134.