Structural determinants of the β-selectivity of a bacterial

Journal of Biological Chemistry

Volumn 287, Issue 34, 2012, Pages 28495-28502

  Wybenga, Gjalt G ^a   Crismaru, Ciprian G ^a   Janssen, Dick B ^a   Dijkstra, Bauke W ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

2-OXOGLUTARATE; ACTIVE SITE; AMINOTRANSFERASE; BINDING MODES; BINDING POCKETS; CARBOXYLATE GROUPS; COFACTORS; ENANTIOPURE; MESORHIZOBIUM SP; MOLECULAR BASIS; REVERSE ORIENTATION; SIDE-CHAINS; STRUCTURAL DETERMINANTS; SYNTHETIC COMPOUNDS;

BINDING ENERGY; CARBOXYLATION; X RAY CRYSTALLOGRAPHY;

AMINO ACIDS;

2 OXOGLUTARIC ACID; 3 AMINO 5 METHYLHEXANOIC ACID; ALPHA AMINO ACID; AMINOOXYACETIC ACID; AMINOTRANSFERASE; BACTERIAL AMINOTRANSFERASE; BETA AMINO ACID; CARBOXYLIC ACID; HEXANOIC ACID; PYRIDOXAL 5 PHOSPHATE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; BINDING AFFINITY; CONTROLLED STUDY; ENANTIOSELECTIVITY; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; MESORHIZOBIUM; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ANALYSIS; WILD TYPE; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ENZYME INHIBITORS; KETOGLUTARIC ACIDS; MESORHIZOBIUM; PHENYLALANINE; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY; TRANSAMINASES;

EID: 84865275131     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M112.375238     Document Type: Article

References (41)

1. Cole, D. C. (1994) Recent stereoselective synthetic approaches to β-aminoacids. Tetrahedron 50, 9517-9582
2. Weiner, B., Szymański, W., Janssen, D. B., Minnaard, A. J., and Feringa, B. L. (2010) Recent advances in the catalytic asymmetric synthesis of β-aminoacids. Chem. Soc. Rev. 39, 1656-1691
3. Liljeblad, A., and Kanerva, L. T. (2006) Biocatalysis as a profound tool in the preparation of highly enantiopure β-amino acids. Tetrahedron 62, 5831-5854
4. Koeller, K. M., and Wong, C. H. (2001) Enzymes for chemical synthesis. Nature 409, 232-240
5. Taylor, P. P., Pantaleone, D. P., Senkpeil, R. F., and Fotheringham, I. G. (1998) Novel biosynthetic approaches to the production of unnatural amino acids using transaminases. Trends Biotechnol. 16, 412-418
6. 6 coenzyme in the catalytic center of aspartate transaminase. Vitam. Horm. 22, 451-484
7. Bea, H. S., Park, H. J., Lee, S. H., and Yun, H. (2011) Kinetic resolution of aromatic β-amino acids by ω-transaminase. Chem. Commun. 47, 5894-5896
8. Kim, J., Kyung, D., Yun, H., Cho, B. K., Seo, J. H., Cha, M., and Kim, B. G. (2007) Cloning and characterization of a novel β-transaminase from Mesorhizobium sp. strain LUK: a new biocatalyst for the synthesis of enantiomerically pure β-amino acids. Appl. Environ. Microbiol. 73, 1772-1782
9. Kim, B., Park, O. K., Bae, J. Y., Jang, T. H., Yoon, J. H., Do, K. H., Kim, B. G., Yun, H., and Park, H. H. (2011) Crystallization and preliminary x-ray crystallographic studies of β-transaminase from Mesorhizobium sp. strain LUK. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67, 231-233
10. Kim, J., Kyung, D., Yun, H., Cho, B. K., and Kim, B. G. (2006) Screening and purification of a novel transaminase catalyzing the transamination of aryl β-amino acid from Mesorhizobium sp. LUK. J. Microbiol. Biotechnol. 16, 1832-1836
11. Oue, S., Okamoto, A., Nakai, Y., Nakahira, M., Shibatani, T., Hayashi, H., and Kagamiyama, H. (1997) Paracoccus denitrificans aromatic amino acid aminotransferase: a model enzyme for the study of dual substrate recognition mechanism. J. Biochem. 121, 161-171
12. Barth, S., Huhn, M., Matthey, B., Klimka, A., Galinski, E. A., and Engert, A. (2000) Compatible-solute-supported periplasmic expression of functional recombinant proteins under stress conditions. Appl. Environ. Microbiol. 66, 1572-1579
13. Evans, P. (2006) Scaling and assessment of data quality. Acta Crystallogr.D Biol. Crystallogr. 62, 72-82
14. Kabsch, W. (2010) Integration, scaling, space group assignment, and postrefinement. Acta Crystallogr. D Biol. Crystallogr. 66, 133-144
15. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763
16. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., and Read, R. J. (2007) Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674
17. Jaroszewski, L., Rychlewski, L., Li, Z., Li, W., and Godzik, A. (2005) FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res. 33, W284-W288
18. Storici, P., De Biase, D., Bossa, F., Bruno, S., Mozzarelli, A., Peneff, C., Silverman, R. B., and Schirmer, T. (2004) Structures of γ- aminobutyricacid (GABA) aminotransferase, a pyridoxal 5′-phosphate, and [2Fe-2S] cluster-containing enzyme, complexed with γ-ethynyl-GABA and withthe antiepilepsy drug vigabatrin. J. Biol. Chem. 279, 363-373
19. Langer, G., Cohen, S. X., Lamzin, V. S., and Perrakis, A. (2008) Automated macromolecular model building for x-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171-1179
20. Emsley, P., Lohkamp, B., Scott, W. G., and Cowtan, K. (2010) Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501
21. 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
22. Chen, V. B., Arendall, W. B., 3rd, Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., and Richardson, D. C. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12-21
23. Schuttelkopf, A. W., and van Aalten, D. M. (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 60, 1355-1363
24. Claude, J. B., Suhre, K., Notredame, C., Claverie, J. M., and Abergel, C. (2004) CaspR: a web server for automated molecular replacement using homology modeling. Nucleic Acids Res. 32, W606-W609
25. Holm, L., and Rosenström, P. (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, W545-W549
26. Krissinel, E., and Henrick, K. (2007) Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774-797
27. Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L. W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C., and Zwart, P. H. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221
28. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, San Carlos, CA
29. Grishin, N. V., Phillips, M. A., and Goldsmith, E. J. (1995) Modeling of the spatial structure of eukaryotic ornithine decarboxylases. Protein Sci. 4, 1291-1304
30. 6-dependent enzymes. Structure 8, R1-R6
31. Okamoto, A., Nakai, Y., Hayashi, H., Hirotsu, K., and Kagamiyama, H. (1998) Crystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: a substrate recognition site constructed by rearrangement of hydrogen bond network. J. Mol. Biol. 280, 443-461
32. Soda, K., Yoshimura, T., and Esaki, N. (2001) Stereospecificity for the hydrogen transfer of pyridoxal enzyme reactions. Chem. Rec. 1, 373-384
33. Eliot, A. C., and Kirsch, J. F. (2004) Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. Annu. Rev. Biochem. 73, 383-415
34. Tipton, K. F. (1996) in Enzymology LabFax (Engel, P. C., ed) pp. 115-174, Academic Press, San Diego, CA
35. John, R. A., and Charteris, A. (1978) The reaction of amino oxyacetate with pyridoxal phosphate-dependent enzymes. Biochem. J. 171, 771-779
36. Marcotte, P., and Walsh, C. (1975) Active site-directed inactivation of cystathionine γ-synthetase and glutamic pyruvic transaminase by propargylglycine.Biochem. Biophys. Res. Commun. 62, 677-682
37. Tanase, S., and Morino, Y. (1976) Irreversible inactivation of aspartate aminotransferases during transamination with L-propargylglycine. Biochem. Biophys. Res. Commun. 68, 1301-1308
38. Marković-Housley, Z., Schirmer, T., Hohenester, E., Khomutov, A. R., Khomutov, R. M., Karpeisky, M. Y., Sandmeier, E., Christen, P., and Jansonius, J. N. (1996) Crystal structures and solution studies of oxime adducts of mitochondrial aspartate aminotransferase. Eur. J. Biochem. 236, 1025-1032
39. Kirsch, J. F., Eichele, G., Ford, G. C., Vincent, M. G., Jansonius, J. N., Gehring, H., and Christen, P. (1984) Mechanism of action of aspartate aminotransferase proposed on the basis of its spatial structure. J. Mol. Biol. 174, 497-525
40. Shin, J. S., and Kim, B. G. (2002) Exploring the active site of amine:pyruvate aminotransferase on the basis of the substrate structure-reactivity relationship: how the enzyme controls substrate specificity and stereoselectivity. J. Org. Chem. 67, 2848-2853
41. Toney, M. D. (2011) Controlling reaction specificity in pyridoxal phosphate enzymes. Biochim. Biophys. Acta 1814, 1407-1418