Crystal structure and enantiomer selection by D-alanyl carrier protein ligase DltA from Bacillus cereus

Biochemistry

Volumn 47, Issue 44, 2008, Pages 11473-11480

  Du, Liqin ^a   He, Yujiong ^a   Luo, Yu ^a  

^a UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDS; BACTERIA; BACTERIOLOGY; BIOCHEMISTRY; CHIRALITY; CIVIL AVIATION; ENANTIOMERS; ENZYMES; POWDERS; PROTEINS; TURBULENT FLOW;

ADENYLATE; ADENYLATION; BACILLUS CEREUSES; CARRIER PROTEINS; DO-MAINS; LIGAND BINDINGS; LIPOTEICHOIC ACIDS; METHICILLIN; MUTANT PROTEINS; NONCOVALENT INTERACTIONS; POSITIVE CELLS; RESISTANT STAPHYLOCOCCUS AUREUS; SEQUENCE SIMILARITIES; SIDE CHAINS; SYNTHETASE; TEICHOIC ACIDS;

CRYSTAL STRUCTURE;

ALANINE; CYSTEINE; DEXTRO ALANINE; DEXTRO ALANYL CARRIER PROTEIN LIGASE; LIGASE; LIPOTEICHOIC ACID; PROTEIN LIGASE DLTA; UNCLASSIFIED DRUG;

ANTIBIOTIC SENSITIVITY; ARTICLE; BACILLUS CEREUS; CRYSTAL STRUCTURE; ENANTIOMER; ENZYME SPECIFICITY; LIGAND BINDING; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; NONHUMAN; PRIORITY JOURNAL;

ALANINE; AMINO ACID SEQUENCE; BACILLUS CEREUS; BACTERIAL PROTEINS; BASE SEQUENCE; CARBON-OXYGEN LIGASES; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DNA, BACTERIAL; GENES, BACTERIAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; STEREOISOMERISM; SUBSTRATE SPECIFICITY;

BACILLUS CEREUS; BACTERIA (MICROORGANISMS); METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; POSIBACTERIA;

EID: 55249096220     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi801363b     Document Type: Article

References (39)

1. Armstrong, J. J., Baddiley, J., Buchanan, J. G., Davision, A. L., Kelemen, M. V., and Neuhaus, F. C. (1959) Composition of teichoic acids from a number of bacterial walls. Nature 184, 247-248.
2. Hyyrylainen, H. L., Vitikainen, M., Thwaite, J., Wu, H., Sarvas, M., Harwood, C. R., Kontinen, V. P., and Stephenson, K. (2000) D-Alanine substitution of teichoic acids as a modulator of protein folding and stability at the cytoplasmic membrane/cell wall interface of Bacillus subtilis. J. Biol. Chem. 275, 26696-26703.
3. Fischer, W. (1988) Physiology of lipoteichoic acids in bacteria. Adv. Microb. Physiol. 29, 233-302.
4. Perego, M., Glaser, P., Minutello, A., Strauch, M. A., Leopold, K., and Fischer, W. (1995) Incorporation of D-alanine into lipoteichoic acid and wall teichoic acid in Bacillus subtilis. Identification of genes and regulation. J. Biol. Chem. 270, 15598-15606.
5. Neuhaus, F. C., and Baddiley, J. (2003) A continuum of anionic charge: structures and functions of D-alanyl-teichoic acids in gram-positive bacteria. Microbiol. Mol. Biol. Rev. 67, 686-723.
6. Wecke, J., Perego, M., and Fischer, W. (1996) D-alanine deprivation of Bacillus subtilis teichoic acids is without effect on cell growth and morphology but affects the autolytic activity. Microb. Drug Resist. 2, 123-129.
7. Peschel, A., Otto, M., Jack, R. W., Kalbacher, H., Jung, G., and Gotz, F. (1999) Inactivation of the dit operon in Staphylococcus aureus confers sensitivity to defensins, protegrins, and other antimicrobial peptides. J. Biol. Chem. 274, 8405-8410.
8. Kristian, S. A., Lauth, X., Nizet, V., Goetz, F., Neumeister, B., Peschel, A., and Landmann, R. (2003) Alanylation of teichoic acids protects Staphylococcus aureus against Toll-like receptor 2-dependent host defense in a mouse tissue cage infection model. J. Infect. Dis. 188, 414-423.
9. Gross, M., Cramton, S. E., Gotz, F., and Peschel, A. (2001) Key role of teichoic acid net charge in Staphylococcus aureus colonization of artificial surfaces. Infect. Immun. 69, 3423-3426.
10. Gotz, F. (2002) Staphylococcus and biofilms. Mol. Microbiol. 43, 1367-1378.
11. Stachelhaus, T., Mootz, H. D., and Marahiel, M. A. (1999) The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem. Biol. 6, 493-505.
12. Conti, E., Franks, N. P., and Brick, P. (1996) Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes. Structure 4, 287-298.
13. Debabov, D. V., Kiriukhin, M. Y., and Neuhaus, F. C. (2000) Biosynthesis of lipoteichoic acid in Lactobacillus rhamnosus: role of DltD in D-alanylation. J. Bacteriol. 182, 2855-2864.
14. May, J. J., Finking, R., Wiegeshoff, F., Weber, T. T., Bandur, N., Koert, U., and Marahiel, M. A. (2005) Inhibition of the D-alanine: D-alanyl carrier protein ligase from Bacillus subtilis increases the bacterium's susceptibility to antibiotics that target the cell wall. FEBS J. 272, 2993-3003.
15. Zheng, L., Baumann, U., and Reymond, J. L. (2004) An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res. 32, e115.
16. Wu, Y., He, Y., Moya, I. A., Qian, X., and Luo, Y. (2004) Crystal structure of archaeal recombinase RadA; A snapshot of its extended conformation. Mol. Cell 15, 423-435.
17. Conti, E., Stachelhaus, T., Marahiel, M. A., and Brick, P. (1997) Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. EMBO J. 16, 4174-4183.
18. Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. F., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M. (1977) The Protein Data Bank. A computer-based archival file for macromolecular structures. Eur. J. Biochem. 80, 319-324.
19. Berman, H., Henrick, K., and Nakamura, H. (2003) Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 10, 980.
20. Navaza, J. (2001) Implementation of molecular replacement in AMoRe. Acta Crystallogr., Sect. D: Biol. Crystallogr. 57, 1367-1372.
21. Perrakis, A., Morris, R., and Lamzin, V. S. (1999) Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458-463.
22. McRee, D. E. (1999) XtalView/Xfit - A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156-165.
23. Brunger, 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 & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 54, 905-921.
24. Kraulis, P. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
25. Bacon, D. J., and Anderson, W. F. (1988) A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graphics 6, 219-220.
26. Itaya, K., and Ui, M. (1966) A new micromethod for the colorimetric determination of inorganic phosphate. Clin. Chim. Acta 14, 361-366.
27. Chang, K. H., Xiang, H., and Dunaway-Mariano, D. (1997) Acyl-adenylate motif of the acyl-adenylate/thioester-forming enzyme superfamily: a site-directed mutagenesis study with the Pseudomonas sp. strain CBS3 4-chlorobenzoate:coenzyme A ligase. Biochemistry 36, 15650-15659.
28. Stuible, H., Buttner, D., Ehlting, J., Hahlbrock, K., and Kombrink, E. (2000) Mutational analysis of 4-coumarate:CoA ligase identifies functionally important amino acids and verifies its close relationship to other adenylate-forming enzymes. FEBS Lett. 467, 117-122.
29. Horswill, A. R., and Escalante-Semerena, J. C. (2002) Characterization of the propionyl-CoA synthetase (PrpE) enzyme of Salmonella enterica: residue Lys592 is required for propionyl-AMP synthesis. Biochemistry 41, 2379-2387.
30. Walker, J. E., Saraste, M., Runswick, M. J., and Gay, N. J. (1982) Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1, 945-951.
31. Gulick, A. M., Starai, V. J., Horswill, A. R., Homick, K. M., and Escalante-Semerena, J. C. (2003) The 1.75 Åcrystal structure of acetyl-CoA synthetase bound to adenosine-5′-propylphosphate and coenzyme A. Biochemistry 42, 2866-2873.
32. Reger, A. S., Carney, J. M., and Gulick, A. M. (2007) Biochemical and crystallographic analysis of substrate binding and conformational changes in acetyl-CoA synthetase. Biochemistry 46, 6536-6546.
33. Laskowski, R. A., Watson, J. D., and Thornton, J. M. (2005) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res. 33, W89-93.
34. Linne, U., Schafer, A., Stubbs, M. T., and Marahiel, M. A. (2007) Aminoacyl-coenzyme A synthesis catalyzed by adenylation domains. FEBS Lett. 581, 905-910.
35. May, J. J., Kessler, N., Marahiel, M. A., and Stubbs, M. T. (2002) Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases. Proc. Natl. Acad. Sci. U.S.A. 99, 12120-12125.
36. Jogl, G., and Tong, L. (2004) Crystal structure of yeast acetyl-coenzyme A synthetase in complex with AMP. Biochemistry 43, 1425-1431.
37. Manning, J. M., Merrifield, N. E., Jones, W. M., and Gotschlich, E. C. (1974) Inhibition of bacterial growth by beta-chloro-D-alanine. Proc. Natl. Acad. Sci. U.S.A. 71, 417-421.
38. Pearson, W. R., and Lipman, D. J. (1988) Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85, 2444-2448.
39. Barton, G. J. (1993) ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng. 6, 37-40.