Structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from streptococcus suis: Crystal structures of the substrate-free and quaternary complex enzymes

Protein Science

Volumn 18, Issue 2, 2009, Pages 294-303

  Zhang, Qiangmin ^a,b   Peng, Hao ^a   Gao, Feng ^a,c   Liu, Yiwei ^a   Cheng, Hao ^a,b   Thompson, John ^d   Gao, George F ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c CHINA AGRICULTURAL UNIVERSITY   (China)

^d NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Catalytic mechanism; Gluconate 5 dehydrogenase (Ga5DH); Quaternary complex; SDR enzymes; Streptococcus suis serotype 2

Indexed keywords

GLUCONATE 5 DEHYDROGENASE; OXIDOREDUCTASE; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; STREPTOCOCCUS SUIS;

AMINO ACID SEQUENCE; ARGININE; BACTERIAL PROTEINS; CALCIUM; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; GLUCONATES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NADP; OXIDOREDUCTASES; PROTEIN STRUCTURE, QUATERNARY; SEQUENCE ALIGNMENT; SERINE; STREPTOCOCCUS SUIS;

STREPTOCOCCUS SUIS;

EID: 59949089362     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.32     Document Type: Article

References (33)

1. Tang J, Wang C, Feng Y, Yang W, Song H, Chen Z, Yu H, Pan X, Zhou X, Wang H, Wu B, Wang H, Zhao H, Lin Y, Yue J, Wu Z, He X, Gao F, Khan AH, Wang J, Zhao GP, Wang Y, Wang X, Chen Z, Gao GF. (2006) Streptococcal toxic shock syndrome caused by Streptococcus suis serotype 2. PLos Med 3: e151.
2. Lun ZR, Wang QP, Chen XG, Li AX, Zhu XQ (2007) Streptococcus suis: an emerging zoonotic pathogen. Lancet Infect Dis 7: 201-209.
3. Adachi O, Shinagawa E, Matsushita K, Ameyama M (1979) Crystallization and properties of 5-keto-D-gluco- nate reductase from Gluconobacter suboxydans. Agric Biol Chem 43: 75-83.
4. Sweeney NJ, Laux DC, Cohen PS (1996) Escherichia coli F-18 and E. coli K-12 eda mutants do not colonize the streptomycin-treated mouse large intestine. Infect Immun 64: 3504-3511.
5. Klasen R, Bringer-Meyer S, Sahm H (1995) Biochemical characterization and sequence analysis of the gluconate: NADP 5-oxidoreductase gene from Gluconobacter oxy- dans. J Bacteriol 177: 2637-2643.
6. Bausch C, Peekhaus N, Utz C, Blais T, Murray E, Lowary T, Conway T (1998) Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli. J Bacteriol 180: 3704-3710.
7. Delarue M, Duclert-Savatier N, Miclet E, Haouz A, Giganti D, Ouazzani J, Lopez P, Nilges M, Stoven V (2007) Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei. J Mol Biol 366: 868-881.
8. Merfort M, Herrmann U, Bringer-Meyer S, Sahm H (2006) High-yield 5-keto-D-gluconic acid formation is mediated by soluble and membrane-bound gluconate-5- dehydrogenases of Gluconobacter oxydans. Appl Micro- biol Biotechnol 73: 443-451.
9. Ameyama M, Chiyonobu T, Adachi O (1974) Purification and properties of 5-ketogluconate reductase from Gluco- nobacter liquefaciens. Agric Biol Chem 38: 1377-1382.
10. Galante E, Lanzani GA, Sequi P (1966) Variations of 2- ketogluconate and 5-ketogluconate oxidoreductases during growth in Acetobacter suboxydans. Enzymologia 30: 257-264.
11. Tanaka N, Nonaka T, Nakanishi M, Deyashiki Y, Hara A (1995) Crystallization of mouse lung carbonyl reductase complexed with NADPH and analysis of symmetry of its tetrameric molecule. J Biochem 118: 871-873.
12. +. Biochemistry 35: 10702-10711.
13. Tanaka N, Nonaka T, Nakanishi M, Deyashiki Y, Hara A, Mitsui Y (1996) Crystal structure of the ternary complex of mouse lung carbonyl reductase at 1.8 Å resolution: the structural origin of coenzyme specificity in the short-chain dehydrogenase/reductase family. Structure 4: 33-45.
14. Tanaka N, Nonaka T, Tanabe T, Yoshimoto T, Tsuru D, Mitsui Y (1996) Crystal structures of the binary and ternary complexes of 7 α- hydroxysteroid dehydrogenase from Escherichia coli. Biochemistry 35: 7715-7730.
15. + and pseudotropine at 1.9 Å resolution: implication for stereospecific substrate binding and catalysis. Biochemistry 38: 7630-7637.
16. Laskowski RA, MacArthur MW, Moss DS, Thorton JM (1993) J Appl Crystallogr 26: 283-291.
17. Ghosh D, Weeks CM, Grochulski P, Duax WL, Erman M, Rimsay RL, Orr JC (1991) Three-dimensional structure of holo 3α,20β-hydroxysteroid dehydrogenase: a member of a short-chain dehydrogenase family. Proc Natl Acad Sci USA 88: 10064-10068.
18. Andersson A, Jordan D, Schneider G, Lindqvist Y (1996) Crystal structure of the ternary complex of 1,3,8-trihy- droxynaphthalene reductase from Magnaporthe grisea with NADPH and an active-site inhibitor. Structure 4: 1161-1170.
19. Yasutake Y, Nishiya Y, Tamura N, Tamura T (2007) Structural insights into unique substrate selectivity of Thermoplasma acidophilumd-aldohexose dehydrogenase. J Mol Biol 367: 1034-1046.
20. Thompson JD, Higgins DG, Gibson TJ (1994) CLUS-TALW: 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.
21. Gouet P, Courcelle E, Stuart DI, Metoz F (1999) ESPript: multiple sequence alignments in PostScript. Bioinfor- matics 15: 305-308.
22. Jörnvall H, Persson B, Krook M, Atrian S, Gonzalez- Duarte R, Jeffery J, Ghosh D (1995) Short-chain dehy- drogenases/reductases (SDR). Biochemistry 34: 6003-6013.
23. Oppermann UC, Filling C, Berndt KD, Persson B, Benach J, Ladenstein R, Joornvall H (1997) Active site directed mutagenesis of 3β/17 β-hydroxysteroid dehydrogenase establishes differential effects on short-chain dehydrogen- ase/reductase reactions. Biochemistry 36: 34-40.
24. Chen Z, Jiang JC, Lin ZG, Lee WR, Baker ME, Chang SH (1993) Site-specific mutagenesis of Drosophila alcohol dehydrogenase: evidence for involvement of tyrosine-152 and lysine-156 in catalysis. Biochemistry 32: 3342-3346.
25. Hwang CC, Chang YH, Hsu CN, Hsu HH, Li CW, Pon HI (2005) Mechanistic roles of Ser-114, Tyr-155, and Lys-159 in 3α-hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni. J Biol Chem 280: 3522-3528.
26. 2+-dependent phospho-α-gluco- sidase from Bacillus subtilis. Structure 12: 1619-1629.
27. Matsushita K, Shinagawa E, Ameyama M (1982) D-Gluco- nate dehydrogenase from bacteria, 2-keto-D-gluconate- yielding, membrane-bound. Methods Enzymol 89 (Part D): 187-193.
28. Leslie AGW (1992) Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newsletter. Protein Crystallogr 26: 27-33.
29. 4/ESF-EACBM Newsletter. Protein Crystallogr 33: 22-24.
30. Vagin A, Teplyakov A (1997) MOLREP: an automated program for molecular replacement. J Appl Crystallogr 30: 1022-1025.
31. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D 53: 240-255.
32. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D 60: 2126-2132.
33. DeLano WL (2002)The PyMOL molecular graphics sys- tem.Palo Alto, CA: DeLano Scientific.