X-ray analysis of Mycobacterium smegmatis Dps and a comparative study involving other Dps and Dps-like molecules

Journal of Molecular Biology

Volumn 339, Issue 5, 2004, Pages 1103-1113

  Roy, Siddhartha ^a   Gupta, Surbhi ^a   Das, Satyabrata ^a   Sekar, K ^a   Chatterji, Dipankar ^a   Vijayan, M ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

AtDps, A. tumefaciens Dps; DNA binding protein; Dps, DNA binding protein from starved cells; EcDps, E. coli Dps; ferroxidation; molecular plasticity; MsDps, M. smegmatis Dps; quaternary assembly

Indexed keywords

AMINO ACID; BACTERIAL DNA; BACTERIAL PROTEIN; DNA BINDING PROTEIN; FERRIC ION; PROTEIN SUBUNIT; DPS PROTEIN, BACTERIA; IRON;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA BINDING; ESCHERICHIA COLI; MOLECULAR MODEL; MOLECULE; MYCOBACTERIUM SMEGMATIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; RHIZOBIUM RADIOBACTER; X RAY CRYSTALLOGRAPHY; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

AGROBACTERIUM; AGROBACTERIUM TUMEFACIENS; ESCHERICHIA COLI; MYCOBACTERIUM; MYCOBACTERIUM SMEGMATIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA-BINDING PROTEINS; IRON; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM SMEGMATIS; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; SEQUENCE ALIGNMENT;

EID: 3042582299     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.04.042     Document Type: Article

References (40)

1. Almiron M., Link A.J., Furlong D., Kolter R. A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev. 6:1992;2646-2654
2. Grant R.A., Filman D.J., Finkel S.E., Kolter R., Hogle J.M. The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nature Struct. Biol. 5:1998;294-303
3. 2+ derivatives. J. Mol. Biol. 307:2001;587-603
4. Carrondo M.A. Ferritins, iron uptake and storage from the bacterioferritin viewpoint. EMBO J. 22:2003;1959-1968
5. Ilari A., Ceci P., Ferrari D., Rossi G.L., Chiancone E. Iron incorporation into Escherichia coli Dps gives rise to a ferritin-like microcrystalline core. J. Biol. Chem. 277:2002;37619-37623
6. Wolf S.G., Frenkiel D., Arad T., Finkel S.E., Kolter R., Minsky A. DNA protection by stress-induced biocrystallization. Nature. 400:1999;83-85
7. Ilari A., Stefanini S., Chiancone E., Tsernoglou D. The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site. Nature Struct. Biol. 7:2000;38-43
8. Bozzi M., Mignogna G., Stefanini S., Barra D., Longhi C., Valenti P., Chiancone E. A novel non-heme iron-binding Ferritin related to the DNA-binding proteins of the Dps family in Listeria innocua. J. Biol. Chem. 272:1997;3259-3265
9. Papinutto E., Dundon W.G., Pitulis N., Battistutta R., Montecucco C., Zanotti G. Structure of two iron binding proteins from Bacillus anthracis. J. Biol. Chem. 277:2002;15093-15098
10. Zanotti G., Papinutto E., Dundon W.G., Battistutta R., Seveso M., DelGiudice G., et al. Structure of the Neutrophil-activating protein from Helicobacter pylori. J. Mol. Biol. 323:2002;125-130
11. Ren B., Tibbelin G., Kajino T., Asami O., Ladenstein R. The multi-layered structure of Dps with a novel di-nuclear ferroxidase centre. J. Mol. Biol. 329:2003;467-477
12. Ceci P., Ilari A., Falvo E., Chiancone E. The Dps protein of Agrobacterium tumefaciens does not bind to DNA but protects it toward oxidative cleavage: X-ray crystal structure, iron binding, and hydroxyl-radical scavenging properties. J. Biol. Chem. 278:2003;20319-20326
13. Gupta S., Pandit S.B., Srinivasan N., Chatterji D. Proteomics analysis of carbon-starved Mycobacterium smegmatis: induction of Dps-like protein. Protein Engng. 15:2002;503-511
14. Gupta S., Chatterji D. Bimodal protection of DNA by Mycobacterium smegmatis DNA-binding protein from stationary phase cells. J. Biol. Chem. 278:2003;5235-5341
15. Granier T., Comberton G., Gallois B., d'Estaitot B.L., Dautant A., Crichton R.R., Precigoux G. Evidence of new cadmium binding sites in recombinant horse L-chain ferritin by anomalous fourier difference map calculation. Proteins: Struct. Funct. Genet. 31:1998;477-485
16. Hempstead P.D., Yewdall S.J., Fernie A.R., Lawson D.M., Artymiuk P.J., Rice D.W., et al. Comparison of the three-dimensional structures of recombinant human H and horse L ferritins at high resolution. J. Mol. Biol. 268:1997;424-448
17. Granier T., Gallois B., d'Estaintot B.L., Dautant A., Chevalier J.M., Mellado J.M., et al. Structure of mouse L-chain ferritin at 1.6 Å resolution. Acta Crystallog. sect. D. 57:2001;1491-1597
18. Raghunathan S., Kozlov A.G., Lohman T.M., Waksman G. Structure of the DNA binding domain of E. coli SSB bound to SSDNA. Nature Struct. Biol. 7:2000;648-652
19. Yang C., Curth U., Urbanke C., Kang C. Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 Å resolution. Nature Struct. Biol. 4:1997;153-157
20. Matsumoto T., Morimoto Y., Shibata N., Kinebuchi T., Shimamoto N., Tsukihara T., Yasuoka N. Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-ray structure analysis. J. Biochem. 127:2000;329-335
21. Saikrishnan K., Jeyakanthan J., Venkatesh J., Acharya N., Sekar K., Varshney U., Vijayan M. Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in Quaternary Structure and Its Implications. J. Mol. Biol. 331:2003;385-393
22. Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J. Crystal structure of the nucleosome core particle particle at 2.8 Å resolution. Nature. 389:1997;251-260
23. Schneider T.R. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta Crystallog. sect. D. 58:2002;195-208
24. Biswal B.K., Sukumar N., Vijayan M. Hydration, mobility and accessibility of lysozyme: structures of a pH 6.5 orthorhombic form and its low-humidity variant and a comparative study involving 20 crystallographically independent molecules. Acta Crysallog. sect. D. 56:2000;1110-1119
25. Sadasivan C., Nagendra H.G., Vijayan M. Plasticity, hydration and accessibility in ribonuclease A. The structure of a new crystal form and its low-humidity variant. Acta Crystallog. sect. D. 54:1998;1343-1352
26. Natchiar S.K., Jeyaprakash A.A., Ramya T.N.C., Thomas C.J., Suguna K., Surolia A., Vijayan M. Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure. Acta Crystallog. sect. D. 60:2004;211-219
27. Roy S., Gupta S., Das S., Sekar K., Chatterji D., Vijayan M. Crystallization and preliminary X-ray diffraction analysis of Mycobacterium smegmatis Dps. Acta Crystallog. sect. D. 59:2003;2254-2256
28. Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallog. sect. A. 50:1994;445-449
29. Brunger A.T., Adams P.D., Clore G.M., Delano W.L., Gross P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D. 54:1998;905-921
30. Collaborative Computational Project, No. 4. Acta Crystallog. sect. D. 50:1994;760-763
31. Jones T.A. A graphics model building and refinement system for macromolecules. J. Appl. Crystallog. 11:1978;268-272
32. Vijayan M. On the Fourier refinement of protein structures. Acta Crystallog. sect. A. 36:1980;295-298
33. Laskowski R.A., Moss D.S., Thornton J.M. Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol. 231:1993;1049-1067
34. Cohen G.E. ALIGN: a program to superimpose protein coordinates, accounting for insertions and deletions. J. Appl. Crystallog. 30:1997;1160-1161
35. Hubbard, S. J., Thronton, J. M. (1993). NACCESS, Computer Program, Department of Biochemistry and Molecular Biology, University College, London.
36. McDonald I.K., Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238:1994;777-793
37. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950
38. Esnouf R. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graph. 15:1997;132-134
39. Merritt E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524
40. Farrugia L.J. ORTEP-3 for Windows- a version of ORTEP-III with a Graphical User Interface (GUI). J. Appl. Crystallog. 30:1997;565