Crystal structures of Streptococcus suis mannonate dehydratase (ManD) and its complex with substrate: Genetic and biochemical evidence for a catalytic mechanism

Journal of Bacteriology

Volumn 191, Issue 18, 2009, Pages 5832-5837

  Zhang, Qiangmin ^a,b   Gao, Feng ^a   Peng, Hao ^a   Cheng, Hao ^a,b   Liu, Yiwei ^a   Tang, Jiaqi ^c   Thompson, John ^d   Wei, Guohua ^e   Zhang, Jingren ^f   Du, Yuguo ^e   Yan, Jinghua ^a   Gao, George F ^a,b,g  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c Research Institute for Medicine of Nanjing Command   (China)

^d NATIONAL INSTITUTE OF DENTAL AND CRANIOFACIAL RESEARCH   (United States)

^e RESEARCH CENTER FOR ECO ENVIRONMENTAL SCIENCES   (China)

^f ALBANY MEDICAL COLLEGE   (United States)

^g INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; CARBOHYDRATE DERIVATIVE; DEXTRO MANNONATE; HISTIDINE; HOMODIMER; MANGANESE; MANNONATE DEHYDRATASE; TYROSINE; UNCLASSIFIED DRUG; XYLOSE ISOMERASE;

AMINO ACID SEQUENCE; ARTICLE; ATOMIC EMISSION SPECTROMETRY; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME PURIFICATION; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ENZYME SUBUNIT; ENZYME SYNTHESIS; FOURIER TRANSFORM MASS SPECTROMETRY; GENE OVEREXPRESSION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; SITE DIRECTED MUTAGENESIS; STREPTOCOCCUS SUIS;

CATALYSIS; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; HYDRO-LYASES; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; STREPTOCOCCUS SUIS; SUGAR ACIDS;

BACTERIA (MICROORGANISMS); STREPTOCOCCUS SUIS;

EID: 69949111845     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00599-09     Document Type: Article

References (26)

1. Allard, S. T., W. W. Cleland, and H. M. Holden. 2004. High resolution X-ray structure of dTDP-glucose 4,6-dehydratase from Streptomyces venezuelae. J. Biol. Chem. 279:2211-2220.
2. Banner, D. W., A. C. Bloomer, G. A. Petsko, D. C. Phillips, C. I. Pogson, I. A. Wilson, P. H. Corran, A. J. Furth, J. D. Milman, R. E. Offord, J. D. Priddle, and S. G. Waley. 1975. Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 Å resolution using amino acid sequence data. Nature 255:609-614.
3. Chen, C., J. Tang, W. Dong, C. Wang, Y. Feng, J. Wang, F. Zheng, X. Pan, D. Liu, M. Li, Y. Song, X. Zhu, H. Sun, T. Feng, Z. Guo, A. Ju, J. Ge, Y. Dong, W. Sun, Y. Jiang, J. Wang, J. Yan, H. Yang, X. Wang, G. F. Gao, R. Yang, J. Wang, and J. Yu. 2007. A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolates. PLoS ONE 2:e315.
4. DeLano, W. L. 2002. The PyMOL molecular graphics system. DeLano Scientific, Palo Alto, CA.
5. Dreyer, J. L. 1987. The role of iron in the activation of mannonic and altronic acid hydratases, two Fe-requiring hydro-lyases. Eur. J. Biochem. 166:623-630.
6. Emsley, P., and K. Cowtan. 2004. COOT: model-building tools for molecular graphics. Acta Crystallogr. D 60:2126-2132. (Pubitemid 41742764)
7. Evans, P. R. 1997. SCALA. Joint CCP4/ESF-EACBM Newsl. Protein Crystallogr. 33:22-24.
8. Koster, S., G. Stier, R. Ficner, M. Holzer, H. C. Curtius, D. Suck, and S. Ghisla. 1996. Location of the active site and proposed catalytic mechanism of pterin-4a-carbinolamine dehydratase. Eur. J. Biochem. 241:858-864.
9. Laskowski, R. A., M. W. MacArthur, D. S. Moss, and J. M. Thornton. 1993. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:283-291.
10. Leesong, M., B. S. Henderson, J. R. Gillig, J. M. Schwab, and J. L. Smith. 1996. Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site. Structure 4:253-264. (Pubitemid 3036547)
11. Leslie, A. G. W. 1992. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4/ESF-EAMCB Newsl. Protein Crystallogr. 26:27-33.
12. Linster, C. L., and E. Van Schaftingen. 2004. A spectrophotometric assay of D-glucuronate based on Escherichia coli uronate isomerase and mannonate dehydrogenase. Protein Expr. Purif. 37:352-360.
13. Lundqvist, T., J. Rice, C. N. Hodge, G. S. Basarab, J. Pierce, and Y. Lindqvist. 1994. Crystal structure of scytalone dehydratase - a disease determinant of the rice pathogen, Magnaporthe grisea. Structure 2:937-944. (Pubitemid 2154301)
14. Mekjian, K. R., E. M. Bryan, B. W. Beall, and C. P. Moran, Jr. 1999. Regulation of hexuronate utilization in Bacillus subtilis. J. Bacteriol. 181:426-433.
15. Murshudov, G. N., A. A. Vagin, and E. J. Dodson. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53:240-255.
16. Otwinowski, Z., W. Minor, and Charles W. Carter, Jr. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:307-326.
17. Rakus, J. F., A. A. Fedorov, E. V. Fedorov, M. E. Glasner, B. K. Hubbard, J. D. Delli, P. C. Babbitt, S. C. Almo, and J. A. Gerlt. 2008. Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Biochemistry 47:9944-9954.
18. Rakus, J. F., A. A. Fedorov, E. V. Fedorov, M. E. Glasner, J. E. Vick, P. C. Babbitt, S. C. Almo, and J. A. Gerlt. 2007. Evolution of enzymatic activities in the enolase superfamily: D-mannonate dehydratase from Novosphingobium aromaticivorans. Biochemistry 46:12896-12908.
19. Robert-Baudouy, J., J. Jimeno-Abendano, and F. Stoeber. 1982. D-Mannonate and D-altronate dehydratases of Escherichia coli K12. Methods Enzymol. 90:288-294.
20. Shulami, S., O. Gat, A. L. Sonenshein, and Y. Shoham. 1999. The glucuronic acid utilization gene cluster from Bacillus stearothermophilus T-6. J. Bacteriol. 181:3695-3704.
21. Sonnhammer, E. L., S. R. Eddy, and R. Durbin. 1997. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28:405-420.
22. Tang, J., C. Wang, Y. Feng, W. Yang, H. Song, Z. Chen, H. Yu, X. Pan, X. Zhou, H. Wang, B. Wu, H. Wang, H. Zhao, Y. Lin, J. Yue, Z. Wu, X. He, F. Gao, A. H. Khan, J. Wang, G.-P. Zhao, Y. Wang, X. Wang, Z. Chen, and G. F. Gao. 2006. Streptococcal toxic shock syndrome caused by Streptococcus suis serotype 2. PLoS Med. 3:e151.
23. Vagin, A., and A. Teplyakov. 1997. MolRep: an automated program for molecular replacement. J. Appl. Crystallogr. 30:1022-1025.
24. Yew, W. S., A. A. Fedorov, E. V. Fedorov, J. F. Rakus, R. W. Pierce, S. C. Almo, and J. A. Gerlt. 2006. Evolution of enzymatic activities in the enolase superfamily: L-fuconate dehydratase from Xanthomonas campestris. Biochemistry 45:14582-14597.
25. Yu, H., H. Jing, Z. Chen, H. Zheng, X. Zhu, H. Wang, S. Wang, L. Liu, R. Zu, L. Luo, N. Xiang, H. Liu, X. Liu, Y. Shu, S. S. Lee, S. K. Chuang, Y. Wang, J. Xu, and W. Yang. 2006. Human Streptococcus suis outbreak, Sichuan, China. Emerg. Infect. Dis. 12:914-920.
26. Zhang, Q., H. Peng, F. Gao, Y. Liu, H. Cheng, J. Thompson, and G. F. Gao. 2009. Structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from Streptococcus suis: crystal structures of the substrate-free and quaternary complex enzymes. Protein Sci. 18:294-303.