B. subtilis ykuD protein at 2.0 Å resolution: Insights into the structure and function of a novel, ubiquitous family of bacterial enzymes

Proteins: Structure, Function and Genetics

Volumn 62, Issue 1, 2006, Pages 144-151

  Bielnicki, Jakub ^a   Devedjiev, Yancho ^a   Derewenda, Urszula ^a   Dauter, Zbigniew ^b   Joachimiak, Andrzej ^b   Derewenda, Zygmunt S ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

Catalytic triad; Crystal structure; Hydrolase; Protein crystallization; Structural genomics

Indexed keywords

ARGININE; BACTERIAL ENZYME; CYSTINE; HYDROLASE; LYSINE; SORTASE;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; BACILLUS SUBTILIS; BACTERIAL CELL WALL; CATALYSIS; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME SPECIFICITY; GENOME ANALYSIS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE; STEREOCHEMISTRY; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BACTERIAL PROTEINS; CONSENSUS SEQUENCE; CRYSTALLIZATION; DIPEPTIDES; ENZYMES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; POSIBACTERIA; PROKARYOTA;

EID: 30344465753     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20702     Document Type: Article

References (33)

1. Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P. SMART 4.0: towards genomic data integration. Nucleic Acids Res 2004;32:D142-D144.
2. Bateman A, Bycroft M. The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD). J Mol Biol 2000;299:1113-1119.
3. Spaink HP. Specific recognition of bacteria by plant LysM domain receptor kinases. Trends Microbiol 2004;12:201-204.
4. Derewenda ZS. Rational protein crystallization by mutational surface engineering. Structure 2004;12:529-535.
5. Stols L, Gu M, Dieckman L, Raffen R, Collart FR, Donnelly MI. A new vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site. Protein Expr Purif 2002;25:8-15.
6. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997;276:307-326.
7. Schneider TR, Sheldrick GM. Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr 2002;58:1772-1779.
8. de la Fortelle E, Bricogne G. Maximum-likelihood heavy atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol 1997;276:472-494.
9. Terwilliger TC. Automated side-chain model building and sequence assignment by template matching. Acta Crystallogr D Biol Crystallogr 2003;59:45-49.
10. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for binding protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 1991;47:110-119.
11. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004;60:2126-2132.
12. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 1997;53:240-255.
13. Laskowski RA, McArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:282-291.
14. Holm L, Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 1997;25:231-234.
15. Dodson G, Wlodawer A. Catalytic triads and their relatives. Trends Biochem Sci 1998;23:347-352.
16. Lewis SD, Johnson FA, Shafer JA. Effect of cysteine-25 on the ionization of histidine-159 in papain as determined by proton nuclear magnetic resonance spectroscopy: evidence for a his-159-Cys-25 ion pair and its possible role in catalysis. Biochemistry 1981;20:48-51.
17. Huang C, Wei P, Fan K, Liu Y, Lai L. 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism. Biochemistry 2004;43:4568-4574.
18. Sprang S, Standing T, Fletterick RJ, Stroud RM, Finer-Moore J, Xuong NH, Hamlin R, Rutter WJ, Craik CS. The three-dimensional structure of Asn102 mutant of trypsin: role of Asp102 in serine protease catalysis. Science 1987;237:905-909.
19. Schrag JD, Li Y, Wu S, Cygler M. Ser-His-Glu triad forms the catalytic site of the lipase from Geotrichum candidum. Nature 1991;351:761-764.
20. Wei Y, Contreras JA, Sheffield P, Osterlund T, Derewenda U, Kneusel RE, Matern U, Holm C, Derewenda ZS. Crystal structure of brefeldin A esterase, a bacterial homolog of the mammalian hormone-sensitive lipase. Nat Struct Biol 1999;6:340-345.
21. Serre L, Verbree EC, Dauter Z, Stuitje AR, Derewenda ZS. The Escherichia coli malonyl-CoA:ACP transacylase at 1.5Å resolution. J Biol Chem 1995;270:12961-12964.
22. Wenig K, Chatwell L, von Pawel-Rammingen U, Bjorck L, Huber R, Sondermann P. Structure of the streptococcal endopeptidase IdeS, a cysteine proteinase with strict specificity for IgG. Proc Natl Acad Sci USA 2004;101:17371-17376.
23. Johnston SC, Larsen CN, Cook WJ, Wilkinson KD, Hill CP. Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 Å resolution. EMBO J 1997;16:3787-3796.
24. Matthews DA, Alden RA, Birktoft JJ, Freer ST, Kraut J. X-ray crystallographic study of boronic acid adducts with subtilisin BPN′ (Novo): a model for the catalytic transition state. J Biol Chem 1975;250:7120-7126.
25. Martinez C, Nicolas A, van Tilbeurgh H, Egloff MP, Cudrey C, Verger R, Cambillau C. Cutinase, a lipolytic enzyme with a preformed oxyanion hole. Biochemistry 1994;33:83-89.
26. Novick RP. Sortase: the surface protein anchoring transpeptidase and the LPXTG motif. Trends Microbiol 2000;8:148-151.
27. Zhang R, Wu R, Joachimiak G, Mazmanian SK, Missiakas DM, Gornicki P, Schneewind O, Joachimiak A. Structures of sortase B from Staphylococcus aureus and Bacillus anthracis reveal catalytic amino acid triad in the active site. Structure 2004;12:1147-1156.
28. Zong Y, Bice TW, Ton-That H, Schneewind O, Narayana SV. Crystal structures of Staphylococcus aureus sortase A and its substrate complex. J Biol Chem 2004;279:31383-31389.
29. Zong Y, Mazmanian SK, Schneewind O, Narayana SV. The structure of sortase B, a cysteine transpeptidase that tethers surface protein to the Staphylococcus aureus cell wall. Structure 2004;12:105-112.
30. Dessen A. A new catalytic dyad regulates anchoring of molecules to the Gram-positive cell wall by sortases. Structure 2004;12:6-7.
31. Marraffini LA, Ton-That H, Zong Y, Narayana SV, Schneewind O. Anchoring of surface proteins to the cell wall of Staphylococcus aureus: a conserved arginine residue is required for efficient catalysis of sortase A. J Biol Chem 2004;279:37763-37770.
32. Kodama T, Takamatsu H, Asai K, Ogasawara N, Sadaie Y, Watabe K. Synthesis and characterization of the spore proteins of Bacillus subtilis YdhD, YkuD, and YkvP, which carry a motif conserved among cell wall binding proteins. J Biochem 2000;128: 655-663.
33. Devedjiev Y, Surendranath Y, Derewenda U, Gabrys A, Cooper DR, Zhang RG, Lezondra L, Joachimiak A, Derewenda ZS. The structure and ligand binding properties of the B.subtilis YkoF gene product, a member of a novel family of thiamin/HMP-binding proteins. J Mol Biol 2004;343:395-406.