The crystal structure of l-sorbose reductase from gluconobacter frateurii complexed with NADPH and l-sorbose

Journal of Molecular Biology

Volumn 407, Issue 4, 2011, Pages 543-555

  Kubota, Keiko ^a   Nagata, Koji ^a   Okai, Masahiko ^a   Miyazono, Ken Ichi ^a   Soemphol, Wichai ^b   Ohtsuka, Jun ^a   Yamamura, Akihiro ^a   Saichana, Natsaran ^b   Toyama, Hirohide ^b,c   Matsushita, Kazunobu ^b   Tanokura, Masaru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b YAMAGUCHI UNIVERSITY   (Japan)

^c UNIVERSITY OF THE RYUKYUS   (Japan)

Author keywords

4 morpholineethanesulfonic acid; EDTA; ethylenediaminetetraacetic acid; l sorbose reductase from Gluconobacter frateurii; Mes; PDB; PEG; polyethylene glycol; Protein Data Bank; SDR; short chain dehydrogenase reductase; SR

Indexed keywords

HYDROXYL GROUP; OXIDOREDUCTASE; PROTON; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; SORBITOL; SORBOSE; SORBOSE OXIDOREDUCTASE; TETRAMER; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ARTICLE; BINDING SITE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME CONFORMATION; ENZYME SPECIFICITY; ENZYME SUBSTRATE COMPLEX; GLUCONOBACTER; GLUCONOBACTER FRATEURII; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; SITE DIRECTED MUTAGENESIS;

GLUCONOBACTER FRATEURII;

EID: 79952439552     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.01.008     Document Type: Article

References (35)

1. Kowalik D., Haller F., Adamski J., and Moeller G. In search for function of two human orphan SDR enzymes: hydroxysteroid dehydrogenase like 2 (HSDL2) and short-chain dehydrogenase/reductase-orphan (SDR-O) J. Steroid Biochem. Mol. Biol. 117 2009 117 124
2. Kavanagh K., Jörnvall H., Persson B., and Oppermann U. Medium- and short-chain dehydrogenase/reductase gene and protein families: the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes Cell. Mol. Life. Sci. 65 2008 3895 3906
3. Oppermann U., Filling C., Hult M., Shafqat N., Wu X., and Lindh M. Short-chain dehydrogenases/reductases (SDR): the 2002 update Chem. Biol. Interact. 143-144 2003 247 253 (Pubitemid 36253589)
4. Persson B., Kallberg Y., Oppermann U., and Jörnvall H. Coenzyme-based functional assignments of short-chain dehydrogenases/reductases (SDRs) Chem. Biol. Interact. 143-144 2003 271 278 (Pubitemid 36253590)
5. Jörnvall H., Persson B., Krook M., Atrian S., Gonzàlez-Duarte R., Jeffery J., and Ghosh D. Short-chain dehydrogenases/reductases (SDR) Biochemistry 34 1995 6003 6013
6. El-Kabbani O., Ishikura S., Darmanin C., Carbone V., Chung R., Usami N., and Hara A. Crystal structure of human l-xylulose reductase holoenzyme: probing the role of Asn107 with site-directed mutagenesis Proteins 55 2004 724 732 (Pubitemid 38655911)
7. Benach J., Filling C., Oppermann U., Roversi P., Bricogne G., and Berndt K. Structure of bacterial 3β/17β-hydroxysteroid dehydrogenase at 1.2 Å resolution: a model for multiple steroid recognition Biochemistry 41 2002 14659 14668 (Pubitemid 35476868)
8. Filling C., Berndt K., Benach J., Knapp S., Prozorovski T., and Nordling E. Critical residues for structure and catalysis in short-chain dehydrogenases/reductases J. Biol. Chem. 277 2002 25677 25684 (Pubitemid 34959957)
9. Philippsen A., Schirmer T., Stein M., Giffhorn F., and Stetefeld J. Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 Å resolution Acta Crystallogr. Sect. D 61 2005 374 379 (Pubitemid 43934596)
10. Ehrensberger A., Elling R., and Wilson D. Structure-guided engineering of xylitol dehydrogenase cosubstrate specificity Structure 14 2006 567 575 (Pubitemid 43363489)
11. Yamamoto K., Kurisu G., Kusunoki M., Tabata S., Urabe I., and Osaki S. Crystal structure of glucose dehydrogenase from Bacillus megaterium IWG3 at 1.7 Å resolution J. Biochem. 129 2001 303 312 (Pubitemid 32176181)
12. Yasutake Y., Nishiya Y., Tamura N., and Tamura T. Structural insights into unique substrate selectivity of Thermoplasma acidophilum d-aldohexose dehydrogenase J. Mol. Biol. 367 2007 1034 1046 (Pubitemid 46386068)
13. + binary complex from Agaricus bisporus J. Biol. Chem. 276 2001 27555 27561
14. Soemphol W., Toyama H., Moonmangmee D., Adachi O., and Matsushita K. l-Sorbose reductase and its transcriptional regulator involved in l-sorbose utilization of Gluconobacter frateurii J. Bacteriol. 189 2007 4800 4808 (Pubitemid 47025592)
15. Greenberg J., Price N., Oliver R., Sherman F., and Rustchenko E. Candida albicans SOU1 encodes a sorbose reductase required for l-sorbose utilization Yeast 22 2005 957 969 (Pubitemid 41387712)
16. Gross W., Seipold P., and Schnarrenberger C. Characterization and purification of an aldose reductase from the acidophilic and thermophilic red alga Galdieria sulphuraria Plant Physiol. 114 1997 231 236 (Pubitemid 28117797)
17. Kallberg Y., Oppermann U., Jörnvall H., and Persson B. Short-chain dehydrogenases/reductases (SDRs) Eur. J. Biochem. 269 2002 4409 4417
18. Zhang Q., Peng H., Gao F., Liu Y., Cheng H., Thompson J., and Gao G. 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 2009 294 303
19. Brünger A., Adams P., Clore G., DeLano W., Gros P., and Grosse-Kunstleve R. Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr. Sect. D 54 1998 905 921
20. Adachi O., Ano Y., Moonmangmee D., Shinagawa E., Toyama H., and Theeragool G. Crystallization and properties of NADPH-dependent l-sorbose reductase from Gluconobacter melanogenus IFO 3294 Biosci. Bacteriol. Biochem. 63 1999 2137 2143 (Pubitemid 129549036)
21. Kubota K., Nagata K., Miyazono K., Toyama H., Matsushita K., and Tanokura M. Purification, crystallization and preliminary X-ray analysis of l-sorbose reductase from Gluconobacter frateurii complexed with l-sorbose or NADPH Acta Crystallogr. Sect. F. 65 2009 562 564
22. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326 (Pubitemid 27085611)
23. Kabsch W. Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector J. Appl. Crystallogr. 21 1988 916 924
24. Matthews B. Solvent content of protein crystals J. Mol. Biol. 33 1968 491 497
25. Vagin A., and Teplyakov A. MOLREP: an automated program for molecular replacement J. Appl. Crystallogr. 30 1997 1022 1025 (Pubitemid 127485985)
26. Collaborative Computational Project Number 4 The CCP4 suite: programs for protein crystallography Acta Crystallogr. Sect. D 50 1994 760 763
27. Höffken H., Duong M., Friedrich T., Breuer M., Hauer B., and Reinhardt R. Crystal structure and enzyme kinetics of the (S)-specific 1-phenylethanol dehydrogenase of the denitrifying bacterium strain EbN1 Biochemistry 45 2006 82 93 (Pubitemid 43054085)
28. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr. Sect. D 53 1997 240 255 (Pubitemid 27235885)
29. McRee D.E. XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 125 1999 156 165 (Pubitemid 29402600)
30. Perrakis A., Morris R., and Lamzin V. Automated protein model building combined with iterative structure refinement Nat. Struct. Biol. 6 1999 458 463 (Pubitemid 29218016)
31. Guex N., and Peitsch M. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling Electrophoresis 18 1997 2714 2723 (Pubitemid 28059943)
32. Krissinel E., and Henrick K. Inference of macromolecular assemblies from crystalline state J. Mol. Biol. 372 2007 774 797 (Pubitemid 47321791)
33. DeLano W.L. The PyMOL Molecular Graphics System on World Wide Web http://www.pymol.org 2002
34. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
35. Dulley J., and Grieve P. A simple technique for eliminating interference by detergents in the Lowry method of protein determination Anal. Biochem. 64 1975 136 141