Structural analysis of QdtB, an aminotransferase required for the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-α-D-glucose

Biochemistry

Volumn 48, Issue 7, 2009, Pages 1553-1561

  Thoden, James B ^a   Schäffer, Christina ^b   Messner, Paul ^b   Holden, Hazel M ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ACETAMIDO; ACTIVE SITES; AMINO NITROGENS; AMINOTRANSFERASE; ASPARTATE AMINOTRANSFERASE; COFACTOR; D GALACTOSE; D GLUCOSE; ELECTRON DENSITIES; GRAM-NEGATIVE BACTERIA; GRAM-POSITIVE BACTERIA; S-LAYERS; SCHIFF-BASE; SIDE CHAINS; THERMOANAEROBACTERIUM;

AMINATION; AMINES; AMINO ACIDS; BACTERIOLOGY; BINDING SITES; BIOCHEMICAL ENGINEERING; BIOCHEMISTRY; ENZYMES; GLUCOSE; ORGANIC ACIDS; STRUCTURAL ANALYSIS; SUGAR (SUCROSE);

BACTERIA;

ASPARTATE AMINOTRANSFERASE; NITROGEN; PROTEIN SUBUNIT; THYMIDINE DIPHOSPHATE; AMINOTRANSFERASE; DEOXYSUGAR; DTDP 3 ACETAMIDO 3,6 DIDEOXYGLUCOSE; DTDP-3-ACETAMIDO-3,6-DIDEOXYGLUCOSE; PYRIMIDINE NUCLEOTIDE; SCHIFF BASE;

ARTICLE; BIOSYNTHESIS; CATALYSIS; ENZYME ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; THERMOANAEROBACTERIUM; CHEMICAL STRUCTURE; CHEMISTRY; CRYSTALLIZATION; ELECTROSPRAY MASS SPECTROMETRY; ENZYMOLOGY; HYDROGEN BOND; METABOLISM; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DEOXY SUGARS; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN CONFORMATION; SCHIFF BASES; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; THERMOANAEROBACTERIUM; THYMINE NUCLEOTIDES; TRANSAMINASES;

NEGIBACTERIA; POSIBACTERIA; THERMOANAEROBACTERIUM THERMOSACCHAROLYTICUM;

EID: 61749087768     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi8022015     Document Type: Article

References (25)

1. Nedal, A., and Zotchev, S. B. (2004) Biosynthesis of deoxyaminosugars in antibiotic-producing bacteria. Appl. Microbiol. Biotechnol. 64, 7-15.
2. Schlunzen, F., Zarivach, R., Harms, J., Bashan, A., Tocilj, A., Albrecht, R., Yonath, A., and Franceschi, F. (2001) Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413, 814-821.
3. Hansen, J. L., Ippolito, J. A., Ban, N., Nissen, P., Moore, P. B., and Steitz, T. A. (2002) The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol. Cell 10, 117-128.
4. Raetz, C. R., and Whitfield, C. (2002) Lipopolysaccharide endotoxins. Annu. Rev. Biochem. 71, 635-700.
5. Messner, P., and Schaffer, C. (2003) Prokaryotic glycoproteins. Fortschr. Chem. Org. Naturst. 85, 51-124.
6. Timmons, S. C., and Thorson, J. S. (2008) Increasing carbohydrate diversity via amine oxidation: aminosugar, hydroxyaminosugar, nitrososugar, and nitrosugar biosynthesis in bacteria. Curr. Opin. Chem. Biol. 12, 297-305.
7. Eliot, A. C., and Kirsch, J. F. (2004) Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. Annu. Rev. Biochem. 73, 383-415.
8. Noland, B. W., Newman, J. M., Hendle, J., Badger, J., Christopher, J. A., Tresser, J., Buchanan, M. D., Wright, T. A., Rutter, M. E., Sanderson, W. E., Muller-Dieckmann, H. J., Gajiwala, K. S., and Buchanan, S. G. (2002) Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: a 4-amino-4-deoxy-L-arabi-nose lipopolysaccharide-modifying enzyme. Structure (Cambridge ) 10, 1569-1580.
9. Schoenhofen, I. C., Lunin, V. V., Julien, J. P., Li, Y., Ajamian, E., Matte, A., Cygler, M., Brisson, J. R., Aubry, A., Logan, S. M., Bhatia, S., Wakarchuk, W. W., and Young, N. M. (2006) Structural and functional characterization of PseC, an aminotransferase involved in the biosynthesis of pseudaminic acid, an essential flagellar modification in Helicobacter pylori. J. Biol. Chem. 281, 8907-8916.
10. Schoenhofen, I. C., McNally, D. J., Vinogradov, E., Whitfield, D., Young, N. M., Dick, S., Wakarchuk, W. W., Brisson, J. R., and Logan, S. M. (2006) Functional characterization of dehydratase/ aminotransferase pairs from Helicobacter and Campylobacter: enzymes distinguishing the pseudaminic acid and bacillosamine biosynthetic pathways. J. Biol. Chem. 281, 723-732.
11. Burgie, E. S., Thoden, J. B., and Holden, H. M. (2007) Molecular architecture of DesV from Streptomyces venezuelae: a PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine. Protein Sci. 16, 887-896.
12. Burgie, E. S., and Holden, H. M. (2007) Molecular architecture of DesI: a key enzyme in the biosynthesis of desosamine. Biochemistry 46, 8999-9006.
13. Cook, P. D., and Holden, H. M. (2008) GDP-perosamine synthase: structural analysis and production of a novel trideoxysugar. Biochemistry 47, 2833-2840.
14. Novotny, R., Pfoestl, A., Messner, P., and Schaffer, C. (2004) Genetic organization of chromosomal S-layer glycan biosynthesis loci of Bacillaceae. Glycoconjugate J. 20, 435-447.
15. Feng, L., Wang, W., Tao, J., Guo, H., Krause, G., Beutin, L., and Wang, L. (2004) Identification of Escherichia coli O114 O-antigen gene cluster and development of an O114 serogroup-specific PCR assay. J. Clin. Microbiol. 42, 3799-3804.
16. Pfostl, A., Zayni, S., Hofinger, A., Kosma, P., Schaffer, C., and Messner, P. (2008) Biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-glucose. Biochem. J. 410, 187-194.
17. Xue, Y., Zhao, L., Liu, H. W., and Sherman, D. H. (1998) A gene cluster for macrolide antibiotic biosynthesis in Streptomyces venezuelae: architecture of metabolic diversity. Proc. Natl. Acad. Sci. U.S.A. 95, 12111-12116.
18. Otwinowski, Z., and Minor, W. (1997) Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
19. Storoni, L. C., McCoy, A. J., and Read, R. J. (2004) Likelihoodenhanced fast rotation functions. Acta Crystallogr., Sect. D: Biol. Crystallogr. D60, 432-438.
20. Read, R. J. (2001) Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr., Sect. D: Biol. Crystallogr. D57, 1373-1382.
21. Tronrud, D. E., Ten Eyck, L. F., and Matthews, B. W. (1987) An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Crystallogr., Sect. A: Found. Crystallogr. A43, 489-501.
22. Cowtan, K., and Main, P. (1998) Miscellaneous algorithms for density modification. Acta Crystallogr., Sect. D: Biol. Crystallogr. D54, 487-493.
23. Emsley, P., and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr., Sect. D: Biol. Crystallogr. D60, 2126-2132.
24. Szu, P. H., He, X., Zhao, L., and Liu, H. W. (2005) Biosynthesis of TDP-D-desosamine: identification of a strategy for C4 deoxygenation. Angew. Chem., Int. Ed. Engl. 44, 6742-6746.
25. DeLano, W. L. (2002) The PyMOL Molecular Graphics System. , DeLano Scientific, San Carlos, CA.