Crystal structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR

Proteins: Structure, Function and Genetics

Volumn 50, Issue 2, 2003, Pages 375-379

  Lim, Kap ^a   Tempczyk, Aleksandra ^a   Parsons, James F ^a   Bonander, Nicklas ^b   Toedt, John ^a,f   Kelman, Zvi ^a   Howard, Andrew ^c,d   Eisenstein, Edward ^a,e   Herzberg, Osnat ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

^c ARGONNE NATIONAL LABORATORY   (United States)

^d ILLINOIS INSTITUTE OF TECHNOLOGY   (United States)

^e UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^f EASTERN CONNECTICUT STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEIN YBAB; RECR PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING COMPETITION; CRYSTAL STRUCTURE; DNA REPAIR; DNA REPLICATION; HAEMOPHILUS INFLUENZAE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN STRUCTURE;

BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DNA; DNA REPAIR; ELECTROSTATICS; HAEMOPHILUS INFLUENZAE; MODELS, MOLECULAR; PROTEIN CONFORMATION; RECOMBINATION, GENETIC; SELENOMETHIONINE;

BACTERIA (MICROORGANISMS); HAEMOPHILUS; HAEMOPHILUS INFLUENZAE;

EID: 0037295566     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10297     Document Type: Article

References (27)

1. Courcelle J, Hanawalt PC. Participation of recombination proteins in rescue of arrested replication forks in UV-irradiated Escherichia coli need not involve recombination. Proc Natl Acad Sci U S A 2001;98:8196-8202.
2. Marians KJ. Replication and recombination intersect. Curr Op Genet Dev 2000;10:151-156.
3. Courcelle J, Carswell-Crumpton C, Hanawalt PC. recF and recR are required for the resumption of replication at DNA replication forks in Escherichia coli. Proc Natl Acad Sci U S A 1997;94:3714-3719.
4. Yeung T, Mullin DA, Chen KS, Craig EA, Bardwell JC, Walker JR. Sequence and expression of the Escherichia coli recR locus. J Bacteriol 1990;172:6042-6047.
5. Alonso JC, Shirahige K, Ogasawara N. Molecular cloning, genetic characterization and DNA sequence analysis of the recM region of Bacillus subtilis. Nucleic Acids Res 1990;18:6771-6777.
6. Pelaez AI, Ribas-Aparicio RM, Gomez A, Rodicio MR. Structural and functional characterization of the recR gene of Streptomyces. Mol Genet Genomics 2001;265:663-672.
7. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, McKenney K, Sutton GG, FitzHugh W, Fields CA, Gocayne JD, Scott JD, Shirley R, Liu LI, Goldek A, Kelley JM, Weidman JF, Phillips CA, Spriggs T, Hedblom E, Cotton MD, Utterback T, Hanna MC, Nguyen DT, Sandek DM, Brandon, RC, Fine LD, Fritchman JL, Fukrmann JL, Geoghagen NS, Gnehm CL, McDonald LA, Small KV, Fraser CM, Smith HO, Venter JC. Wholegenome random sequencing and assembly of Haemophilas influenzae Rd. Science 1995;269:496-512.
8. Doublie S. Preparation of selenomethionyl proteins for phase determination. Methods Enzymol 1997;276:523-530.
9. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997;276:307-326.
10. Sheldrick GM. SHELX applications to macromolecules. In: Fortierr S, editor. Direct Methods for Solving Macromolecular Structures. Dordrecht, The Netherlands: Kluwer Academic; 1998. p 401-411.
11. Collaborative Computational Project N. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr 1994;D50:760-763.
12. Otwinowski Z. Maximum Likelihood Refinement of Heavy Atom Parameters. In: Wolf W, Evans PR, Leslie AGW, editors. Warrington, UK: Daresbury Laboratory; 1991. p 80-86.
13. Cowtan K. "DM": An automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM. Newsletter Prot Crystallogr 1994;31:34-38.
14. Perrakis A, Morris R, Lamzin VS. Automated protein model building combined with iterative structure refinement. Nat Struct Biol 1999;6:458-463.
15. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 1991;47:110-119.
16. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, GrosseKunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54:905-921.
17. Laskowski RA, MacArthur MW. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291.
18. Kraullis PJ. A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24:946-950.
19. Bacon DJ, Anderson WF. A fast algorithm for rendering spacefilling molecule pictures. J Mol Graph 1988;6:219-220.
20. Merrit EA, Bacon DJ. Raster3D: Photorealistic molecular graphics. Methods Enzymol 1997;277:505-524.
21. Nicholls A, Sharp KA, Honig B. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 1991;11:281-296.
22. Kelman Z, Lee JK, Hurwitz J. The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum DeltaH contains DNA helicase activity. Proc Natl Acad Sci U S A 1999;96:14783-14788.
23. McEntee K, Weinstock GM, Lehman IR. recA protein-catalyzed strand assimilation: Stimulation by Escherichia coli singlestranded DNA-binding protein. Proc Natl Acad Sci U S A 1980;77:857-861.
24. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-138.
25. Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol 1996;6:377-385.
26. Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D. Rosetta in CASP4: Progress in ab initio protein structure prediction. Proteins 2001;45(Suppl 5):119-126.
27. Moult J, Fidelis K, Zemla A, Hubbard T. Critical assessment of methods of protein structure prediction (CASP): Round IV. Proteins 2001;45(Suppl 5):2-7.