Crystal structure of UDP-galactose 4-epimerase-like l -threonine dehydrogenase belonging to the intermediate short-chain dehydrogenase-reductase superfamily

FEBS Journal

Volumn 277, Issue 24, 2010, Pages 5124-5132

  Yoneda, Kazunari ^a   Sakuraba, Haruhiko ^b   Muraoka, Ikuo ^c   Oikawa, Tadao ^c   Ohshima, Toshihisa ^d  

^a TOKAI UNIVERSITY   (Japan)

^b KAGAWA UNIVERSITY   (Japan)

^c KANSAI UNIVERSITY   (Japan)

^d KYUSHU UNIVERSITY   (Japan)

Author keywords

crystal structure; l threonine dehydrogenase; psychrophilic bacterium Flavobacterium frigidimaris KUC 1

Indexed keywords

GLYCEROL; NICOTINAMIDE ADENINE DINUCLEOTIDE; OXIDOREDUCTASE; RIBOSE; SERINE; THREONINE 3 DEHYDROGENASE; TYROSINE; UNCLASSIFIED DRUG; URIDINE DIPHOSPHATE GLUCOSE 4 EPIMERASE;

ACCURACY; ARTICLE; CARBOHYDRATE ANALYSIS; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; FLAVOBACTERIUM; FLAVOBACTERIUM FRIGIDIMARIS; HUMAN VERSUS NONHUMAN DATA; MOLECULAR MODEL; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTON TRANSPORT; PSYCHROPHILIC BACTERIUM; QUALITY CONTROL; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

ALCOHOL OXIDOREDUCTASES; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; FLAVOBACTERIUM; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; THREONINE; UDPGLUCOSE 4-EPIMERASE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; FLAVOBACTERIUM FRIGIDIMARIS;

EID: 78650014982     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2010.07916.x     Document Type: Article

References (29)

1. Elliott WH, (1958) A new threonine metabolite. Biochim Biophys Acta 29, 446-447.
2. McGilvray D, &, Morris JG, (1969) Utilization of L-threonine by a species of Arthrobacter. A novel catabolic role for 'aminoacetone synthase'. Biochem J 112, 657-671.
3. Aoyama Y, &, Motokawa Y, (1981) L-Threonine dehydrogenase of chicken liver. Purification, characterization, and physiological significance. J Biol Chem 256, 12367-12373.
4. Ohshima T, &, Soda K, (2000) Amino Acid Dehydrogenases and Their Applications. In Stereoselective Biocatalysis (, Patel RN, ed), pp. 877-902. Marcel Dekker Inc, New York.
5. Shimizu Y, Sakuraba H, Kawakami R, Goda S, Kawarabayasi Y, &, Ohshima T, (2005) L-Threonine dehydrogenase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3: gene cloning and enzymatic characterization. Extremophiles 9, 317-324. (Pubitemid 41187700)
6. Higashi N, Tanimoto K, Nishioka M, Ishikawa K, &, Taya M, (2008) Investigating a catalytic mechanism of hyperthermophilic L-threonine dehydrogenase from Pyrococcus horikoshii. J Biochem 144, 77-85.
7. Higashi N, Fukada H, &, Ishikawa K, (2005) Kinetic study of thermostable L-threonine dehydrogenase from an archaeon Pyrococcus horikoshii. J Biosci Bioeng 99, 175-180.
8. Bashir Q, Rashid N, Jamil F, Imanaka T, &, Akhtar M, (2009) Highly thermostable L-threonine dehydrogenase from the hyperthermophilic archaeon Thermococcus kodakaraensis. J Biochem 146, 95-102.
9. Aronson BD, Somerville RL, Epperly BR, &, Dekker EE, (1989) The primary structure of Escherichia coli L-threonine dehydrogenase. J Biol Chem 264, 5226-5232.
10. Ishikawa K, Higashi N, Nakamura T, Matsuura T, &, Nakagawa A, (2007) The first crystal structure of L-threonine dehydrogenase. J Mol Biol 366, 857-867.
11. Bowyer A, Mikolajek H, Stuart JW, Wood SP, Jamil F, Rashid N, Akhtar M, &, Cooper JB, (2009) Structure and function of the L-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis. J Struct Biol 168, 294-304.
12. Kazuoka T, Takigawa S, Arakawa N, Hizukuri Y, Muraoka I, Oikawa T, &, Soda K, (2003) Novel psychrophilic and thermolabile L-threonine dehydrogenase from psychrophilic Cytophaga sp. strain KUC-1. J Bacteriol 185, 4483-4489.
13. Matthews BW, (1968) Solvent content of protein crystals. J Mol Biol 33, 491-497.
14. Liu Y, Thoden JB, Kim J, Berger E, Gulick AM, Ruzicka FJ, Holden HM, &, Frey PA, (1997) Mechanistic roles of tyrosine 149 and serine 124 in UDP-galactose 4-epimerase from Escherichia coli. Biochemistry 36, 10675-10684.
15. Thoden JB, Frey PA, &, Holden HM, (1996) Molecular structure of the NADH/UDP-glucose abortive complex of UDP-galactose 4-epimerase from Escherichia coli: implications for the catalytic mechanism. Biochemistry 35, 5137-5144.
16. Thoden JB, Frey PA, &, Holden HM, (1996) Crystal structures of the oxidized and reduced forms of UDP-galactose 4-epimerase isolated from Escherichia coli. Biochemistry 35, 2557-2566.
17. Thoden JB, Wohlers TM, Fridovich-Keil JL, &, Holden HM, (2000) Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase. Biochemistry 39, 5691-5701.
18. Cho H, (2006) Structural study of 15-hydroxyprostaglandin dehydrogenase for drug design. Appl Chem 10, 196-199.
19. Thoden JB, Frey PA, &, Holden HM, (1996) High-resolution X-ray structure of UDP-galactose 4-epimerase complexed with UDP-phenol. Protein Sci 5, 2149-2161.
20. Otwinowski Z, &, Minor W, (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276, 307-326.
21. Terwilliger TC, &, Berendzen J, (1999) Automated MAD and MIR structure solution. Acta Crystallogr 55, 849-861.
22. Terwilliger TC, (2000) Maximum-likelihood density modification. Acta Crystallogr D 56, 965-972.
23. Emsley P, &, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr 60, 2126-2132.
24. Murshudov GN, Vagin AA, &, Dodson EJ, (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr 53, 240-255.
25. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, et al. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr 54, 905-921.
26. Potterton E, McNicholas S, Krissinel E, Cowtan K, &, Noble M, (2002) The CCP4 molecular-graphics project. Acta Crystallogr 58, 1955-1957.
27. Rodriguez R, Chinea G, Lopez N, Pons T, &, Vriend G, (1998) Homology modeling, model and software evaluation: three related resources. Bioinformatics 14, 523-528.
28. Laskowski RA, MacArthur MW, Moss DS, &, Thornton JM, (1993) PROCHECK: a program to check the stereochemical quality of protein structure. J Appl Crystallogr 26, 283-291.
29. Lovell SC, Davis IW, Arendall WBIII, De Bakker PIW, Word JM, Prisant MG, Richardson JS, &, Richardson DC, (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50, 437-450.