Crystal structure of binary and ternary complexes of archaeal UDP-galactose 4-epimerase-like L-threonine dehydrogenase from Thermoplasma volcanium

Journal of Biological Chemistry

Volumn 287, Issue 16, 2012, Pages 12966-12974

  Yoneda, Kazunari ^a   Sakuraba, Haruhiko ^b   Araki, Tomohiro ^a   Ohshima, Toshihisa ^c  

^a TOKAI UNIVERSITY   (Japan)

^b KAGAWA UNIVERSITY   (Japan)

^c KYUSHU UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARCHAEAL; ARCHAEON; CATALYTIC DOMAINS; CATALYTIC MECHANISMS; CATALYTIC RESIDUE; FLAVOBACTERIUM; ION PAIRS; MOLECULAR BASIS; MOLECULAR REPLACEMENTS; PSYCHROPHILIC BACTERIA; PYRUVATES; SITE DIRECTED MUTAGENESIS; STRUCTURAL BASIS; SUBSTRATE BINDING MODEL; SUBSTRATE RECOGNITION; TERNARY COMPLEX;

ESCHERICHIA COLI; GENE ENCODING; HYDROGEN; QUANTUM CHEMISTRY;

AMINO ACIDS;

3 HYDROXYNORVALINE; NICOTINAMIDE ADENINE DINUCLEOTIDE; OXIDOREDUCTASE; PYRUVIC ACID; THREONINE; UNCLASSIFIED DRUG; URIDINE DIPHOSPHATE GALACTOSE 4 EPIMERASE LIKE THREONINE DEHYDROGENASE;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME KINETICS; ENZYME PURIFICATION; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; FLAVOBACTERIUM; FLAVOBACTERIUM FRIGIDIMARIS; INCUBATION TEMPERATURE; INCUBATION TIME; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTON TRANSPORT; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS; SPECIES COMPARISON; THERMOPLASMA; THERMOPLASMA VOLCANIUM; THERMOSTABILITY;

ALCOHOL OXIDOREDUCTASES; ARCHAEAL PROTEINS; CRYSTALLOGRAPHY; ESCHERICHIA COLI; FLAVOBACTERIUM; MUTAGENESIS, SITE-DIRECTED; NAD; SUBSTRATE SPECIFICITY; THERMOPLASMA; THREONINE; UDPGLUCOSE 4-EPIMERASE;

ARCHAEA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; FLAVOBACTERIUM FRIGIDIMARIS; THERMOPLASMA VOLCANIUM;

EID: 84859759047     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.336958     Document Type: Article

References (39)

1. Elliott, W. H. (1958) A new threonine metabolite. Biochim. Biophys. Acta 29, 446-447
2. McGilvray, D., and Morris, J. G. (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., and Motokawa, Y. (1981) L-Threonine dehydrogenase of chicken liver. Purification, characterization, and physiological significance. J. Biol. Chem. 256, 12367-12373
4. Ohshima, T., and Soda, K. (2000) in Stereoselective Biocatalysis (R. N. Patel, ed.) pp. 877-902, Marcel Dekker Inc., New York
5. Shimizu, Y., Sakuraba, H., Kawakami, R., Goda, S., Kawarabayasi, Y., and Ohshima, T. (2005) L-Threonine dehydrogenase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3. Gene cloning and enzymatic characterization. Extremophiles 9, 317-324
6. Higashi, N., Tanimoto, K., Nishioka, M., Ishikawa, K., and Taya, M. (2008) Investigating a catalytic mechanism of hyperthermophilic L-threonine dehydrogenase from Pyrococcus horikoshii. J. Biochem. 144, 77-85 (Pubitemid 351957476)
7. Higashi, N., Fukada, H., and 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., and Akhtar, M. (2009) Highly thermostable L-threonine dehydrogenase from the hyperthermophilic archaeon Thermococcus kodakaraensis. J. Biochem. 146, 95-102
9. Aronson, B. D., Somerville, R. L., Epperly, B. R., and Dekker, E. E. (1989) The primary structure of Escherichia coli L-threonine dehydrogenase. J. Biol. Chem. 264, 5226-5232 (Pubitemid 19092940)
10. Ishikawa, K., Higashi, N., Nakamura, T., Matsuura, T., and Nakagawa, A. (2007) The first crystal structure of L-threonine dehydrogenase. J. Mol. Biol. 366, 857-867 (Pubitemid 46175867)
11. Bowyer, A., Mikolajek, H., Stuart, J. W., Wood, S. P., Jamil, F., Rashid, N., Akhtar, M., and Cooper, J. B. (2009) Structure and function of the L-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis. J. Struct. Biol. 168, 294-304
12. Yoneda, K., Sakuraba, H., Muraoka, I., Oikawa, T., and Ohshima, T. (2010) Crystal structure of UDP-galactose 4-epimerase-like L-threonine dehydrogenase belonging to the intermediate short-chain dehydrogenase-reductase superfamily. FEBS J. 277, 5124-5132
13. Kazuoka, T., Takigawa, S., Arakawa, N., Hizukuri, Y., Muraoka, I., Oikawa, T., and Soda, K. (2003) Novel psychrophilic and thermolabile L-threonine dehydrogenase from psychrophilic Cytophaga sp. strain KUC-1. J. Bacteriol. 185, 4483-4489 (Pubitemid 36890495)
14. Liu, Y., Thoden, J. B., Kim, J., Berger, E., Gulick, A. M., Ruzicka, F. J., Holden, H. M., and Frey, P. A. (1997) Mechanistic roles of tyrosine 149 and serine 124 in UDP-galactose 4-epimerase from Escherichia coli. Biochemistry 36, 10675-10684 (Pubitemid 27382557)
15. Thoden, J. B., Frey, P. A., and Holden, H. M. (1996) Crystal structures of the oxidized and reduced forms of UDP-galactose 4-epimerase isolated from Escherichia coli. Biochemistry 35, 2557-2566 (Pubitemid 26098763)
16. Thoden, J. B., Wohlers, T. M., Fridovich-Keil, J. L., and Holden, H. M. (2000) Crystallographic evidence for Tyr-157 functioning as the active site base in human UDP-galactose 4-epimerase. Biochemistry 39, 5691-5701 (Pubitemid 30307957)
17. Murray, M. G., and Thompson, W. F. (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8, 4321-4325
18. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254
19. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685
20. Ohshima, T., Misono, H., and Soda, K. (1978) Properties of crystalline leucine dehydrogenase from Bacillus sphaericus. J. Biol. Chem. 253, 5719-5725 (Pubitemid 8403706)
21. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (Pubitemid 27085611)
22. Collaborative Computational Project, Number 4 (1994) The CCP4 suite. Programs for protein crystallography. Acta Crystallogr.DBiol. Crystallogr. 50, 760-763
23. Emsley, P., and Cowtan, K. (2004) Coot. Model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132 (Pubitemid 41742764)
24. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240-255 (Pubitemid 27235885)
25. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography and NMR system. A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905-921
26. Lovell, S. C., Davis, I. W., Arendall, W. B., 3rd, de Bakker, P. I., Word, J. M., Prisant, M. G., Richardson, J. S., and Richardson, D. C. (2003) Structure validation by Cα geometry. ≲Πηι∀, ≲πσι∀, and Cβ deviation. Proteins 50, 437-450
27. Potterton, E., McNicholas, S., Krissinel, E., Cowtan, K., and Noble, M. (2002) The CCP4 molecular graphics project. Acta Crystallogr. D Biol. Crystallogr. 58, 1955-1957
28. Barlow, D. J., and Thornton, J. M. (1983) Ion pairs in proteins. J. Mol. Biol. 168, 867-885
29. Rodriguez, R., Chinea, G., Lopez, N., Pons, T., and Vriend, G. (1998) Homology modeling, model, and software evaluation. Three related resources. Bioinformatics 14, 523-528 (Pubitemid 28416766)
30. Ueatrongchit, T., and Asano, Y. (2011) Highly selective L-threonine 3-dehydrogenase from Cupriavidus necator and its use in determination of L-threonine. Anal. Biochem. 410, 44-56
31. Matthews, B. W. (1968) Solvent content of protein crystals. J. Mol. Biol. 33, 491-497
32. Hennig, M., Darimont, B., Sterner, R., Kirschner, K., and Jansonius, J. N. (1995) 2.0 Å structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus. Possible determinants of protein stability. Structure 3, 1295-1306 (Pubitemid 3012260)
33. DeDecker, B. S., O'Brien, R., Fleming, P. J., Geiger, J. H., Jackson, S. P., and Sigler, P. B. (1996) The crystal structure of a hyperthermophilic archaeal TATA-box binding protein. J. Mol. Biol. 264, 1072-1084 (Pubitemid 27019493)
34. Lim, J. H., Yu, Y. G., Han, Y. S., Cho, S., Ahn, B. Y., Kim, S. H., and Cho, Y. (1997) The crystal structure of an Iron-superoxide dismutase from the hyperthermophile Aquifex pyrophilus at 1.9 A resolution. Structural basis for thermostability. J. Mol. Biol. 270, 259-274 (Pubitemid 27296686)
35. Kavanagh, K. L., Jörnvall, H., Persson, B., and Oppermann, U. (2008) 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, 3895-3906
36. Thoden, J. B., Frey, P. A., and Holden, H. M. (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
37. Thoden, J. B., Frey, P. A., and Holden, H. M. (1996) High resolution x-ray structure of UDP-galactose 4-epimerase complexed with UDP-phenol. Protein Sci. 5, 2149-2161 (Pubitemid 26384454)
38. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST. A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (Pubitemid 27359211)
39. Holm, L., and Sander, C. (1998) Touring protein fold space with Dali/ FSSP. Nucleic Acids Res. 26, 316-319 (Pubitemid 28291549)