Crystal structure of dissimilatory sulfite reductase D (DsrD) protein - Possible interaction with B- and Z-DNA by its winged-helix motif

Structure

Volumn 11, Issue 9, 2003, Pages 1133-1140

  Mizuno, Nobuhiro ^a   Voordouw, Gerrit ^b   Miki, Kunio ^a   Sarai, Akinori ^c   Higuchi, Yoshiki ^d,e  

^a KYOTO UNIVERSITY   (Japan)

^b UNIVERSITY OF CALGARY   (Canada)

^c RIKEN TSUKUBA INSTITUTE   (Japan)

^d UNIVERSITY OF HYOGO   (Japan)

^e RIKEN Harima Institute/SPring 8 ^*  (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; DISSIMILATORY SULFITE REDUCTASE D; DNA B; DNA BINDING PROTEIN; DNA Z; OXIDOREDUCTASE; SULFATE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; DESULFOVIBRIO VULGARIS; ENZYME STRUCTURE; GENETIC TRANSCRIPTION; HYDROPHOBICITY; MOLECULAR INTERACTION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN MOTIF; REDUCTION; RNA TRANSLATION; STRUCTURAL HOMOLOGY;

BACTERIA (MICROORGANISMS); DESULFOVIBRIO; DESULFOVIBRIO VULGARIS; DESULFOVIBRIO VULGARIS SUBSP. VULGARIS STR. HILDENBOROUGH;

EID: 0042835773     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(03)00156-4     Document Type: Article

References (25)

1. Brünger 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.et al. Crystallography and NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921.
2. CCP4 The (Collaborative Computational Project, Number 4) CCP4 suite. programs for protein crystallography Acta Crystallogr. D Biol Crystallogr. 50:1994;760-763.
3. Clark K.L., Halay E.D., Lai E., Burley S.K. Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. Nature. 364:1993;412-420.
4. Cook W.J., Kar S.R., Taylor K.B., Hall L.M. Crystal structure of the cyanobacterial metallothionein repressor SmtB. a model for metalloregulatory proteins J. Mol. Biol. 275:1998;337-346.
5. Fogh R.H., Ottleben G., Ruterjans H., Schnarr M., Boelens R., Kaptein R. Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy. EMBO J. 13:1994;3936-3944.
6. Gajiwala K.S., Chen H., Cornille F., Roques B.P., Reith W., Mach B., Burley S.K. Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature. 403:2000;916-921.
7. Hittel, D.S. (1998). Overexpression of dsvD gene of Desulfovibrio vulgaris Hildenborough and characterization of the DsvD protein. MSc Thesis, University of Calgary, Alberta, Canada.
8. Hittel D.S., Voordouw G. Overexpression, purification and immunodetection of DsrD from Desulfovibrio vugaris Hildenborough. Antonie Van Leeuwenhoek. 77:2000;13-22.
9. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
10. Jin C., Marsden I., Chen X., Liao X. Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex. J. Mol. Biol. 289:1999;683-690.
11. Karkhoff-Schweizer R.R., Huber D.P., Voordouw G. Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR. Appl. Environ. Microbiol. 61:1995;290-296.
12. Laue H., Friedrich M., Ruff J., Cook A.M. Dissimilatory sulfite reductase (desulfoviridin) of the taurine-degrading, non-sulfate-reducing bacterium Bilophila wadsworthia RZATAU contains a fused DsrB-DsrD subunit. J. Bacteriol. 183:2001;1727-1733.
13. Lee J.P., LeGall J., Peck H.D. Jr. Isolation of assimilatory- and dissimilatory-type sulfite reductases from Desulfovibrio vulgaris. J. Bacteriol. 115:1973;529-542.
14. Mer G., Bochkarev A., Gupta R., Bochkareva E., Frappier L., Ingles C.J., Edwards A.M., Chazin W.J. Structural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor RPA. Cell. 103:2000;449-456.
15. Mizuno N., Hittel D.S., Miki K., Voordouw G., Higuchi Y. Preliminary X-ray crystallographic study of DsrD protein from the sulfate-reducing bacterium Desulfovibrio vulgaris. Acta Crystallogr. D Biol. Crystallogr. 56:2000;754-755.
16. Morris A.L., MacArthur M.W., Hutchinson E.G., Thornton J.M. Stereochemical quality of protein structure coordinates. Proteins. 12:1992;345-364.
17. Nicholls A., Sharp K.A., Honig B. Protein folding and association. insights from the interfacial and thermodynamic properties of hydrocarbons Proteins. 11:1991;281-296.
18. Ramakrishnan V., Finch J.T., Graziano V., Lee P.L., Sweet R.M. Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature. 362:1993;219-223.
19. Rossmann M.G., van Beek C.G. Data processing. Acta Crystallogr. D Biol. Crystallogr. 55:1999;1631-1640.
20. Roussel, A., and Cambillau, C. (1989). Turbo-Frodo. In Silicon Graphics Geometry Partners Directory (Mountain View, California: Silicon Graphics) 77-78.
21. Schwartz T., Rould M.A., Lowenhaupt K., Herbert A., Rich A. Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science. 284:1999;1841-1845.
22. Schwartz T., Behlke J., Lowenhaupt K., Heinemann U., Rich A. Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z-DNA-binding proteins. Nat. Struct. Biol. 8:2001;761-765.
23. Sheldrick G.M., Schneider T.R. Shelxl. high-resolution refinement Methods Enzymol. 277:1997;319-343.
24. Tan J., Helms L.R., Swenson R.P., Cowan J.A. Primary structure of the assimilatory-type sulfite reductase from Desulfovibrio vulgaris (Hildenborough). cloning and nucleotide sequence of the reductase gene Biochemistry. 30:1991;9900-9907.
25. Zubieta C., He X.Z., Dixon R.A., Noel J.P. Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases. Nat. Struct. Biol. 8:2001;271-279.