Crystal structure of the conserved hypothetical protein TTHA1606 from Thermus thermophilus HB8

Proteins: Structure, Function and Bioinformatics

Volumn 76, Issue 1, 2009, Pages 244-248

  Tomoike, Fumiaki ^a   Wakamatsu, Taisuke ^a   Nakagawa, Noriko ^a,b   Kuramitsu, Seiki ^a,b   Masui, Ryoji ^a,b  

^a OSAKA UNIVERSITY   (Japan)

^b RIKEN SPring 8 Center   (Japan)

Author keywords

Conserved hypothetical protein; DNA binding; Nif3; Troidal structure; YbgI

Indexed keywords

BACTERIAL PROTEIN; DNA BINDING PROTEIN; PROTEIN TTHA 1606; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CRYSTAL STRUCTURE; DNA BINDING; GEL MOBILITY SHIFT ASSAY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FUNCTION; THERMUS THERMOPHILUS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA; ESCHERICHIA COLI; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; THERMUS THERMOPHILUS;

THERMUS THERMOPHILUS;

EID: 66249123238     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22397     Document Type: Article

References (19)

1. Martens JA, Genereaux J, Saleh A, Brandl CJ. Transcriptional activation by yeast PDR1p is inhibited by its association with NGG1p/ADA3p. J Biol Chem 1996;271:15884-15890. (Pubitemid 26236196)
2. Tascou S, Uedelhoven J, Dixkens C, Nayernia K, Engel W, Burfeind P. Isolation and characterization of a novel human gene. NIF3L1, and its mouse ortholog Nif3l1, highly conserved from bacteria to mammals. Cytogenet Cell Genet 2000;90:330-336.
3. Akiyama H, Fujisawa N, Tashiro Y, Takanabe N, Sugiyama A, Tashiro F. The role of transcriptional corepressor Nif3l1 in early stage of neural differentiation via cooperation with Trip15/CSN2. J Biol Chem 2003;278:10752-10762. (Pubitemid 36800347)
4. Gifford CM, Wallace SS. The genes encoding endonuclease VIII and endonuclease III in Escherichia coli are transcribed as the terminal genes in operons. Nucleic Acids Res 2000;28:762-769. (Pubitemid 30068260)
5. Khil PP, Camerini-Otero RD. Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol Microbiol 2002;44:89-105. (Pubitemid 34429767)
6. Ladner JE, Obmolova G, Teplyakov A, Howard AJ, Khil PP, Camerini-Otero RD, Gilliland GL. Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site. BMC Struct Biol 2003;3:7. (Pubitemid 38809174)
7. Saikatendu KS, Zhang X, Kinch L, Leybourne M, Grishin NV, Zhang H. Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center. BMC Struct Biol 2006;6:27. (Pubitemid 46306078)
8. Godsey MH, Minasov G, Shucaloca L, Brunzelle JS, Vorontsov II, Collart FR, Anderson WF. The 2.2 A resolution crystal structure of Bacillus cereus Nif3-family protein YqfO reveals a conserved dimetal-binding motif and a regulatory domain. Protein Sci 2007;16:1285-1293. (Pubitemid 46984863)
9. E holoenzyme from Thermus thermophilus HB8. J Bacteriol 2007;23:8758-8764.
10. Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku Y, Miki K, Masui R, Kuramitsu S. Structural genomics projects in Japan. Nat Struct Biol 2000;7:943-945.
11. Iino H, Naitow H, Nakamura Y, Nakagawa N, Agari Y, Kanagawa M, Ebihara A, Shikai A, Sugahara M, Miyano M, Kamiya N, Yokoyama S, Hirotsu K, Kuramitsu S. Crystallization screening test for the whole-cell project on Thermus thermophilus HB8. Acta Cryst 2008;F64:487-491.
12. Ueno G, Kanda H, Hirose R, Ida K, Kumasaka T, Yamamoto M. RIKEN structural genomics beamlines at the SPring-8; high throughput protein crystallography with automated beamline operation. J Struct Funct Genomics 2006;7:15-22. (Pubitemid 44273859)
13. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997;276:307-326. (Pubitemid 27085611)
14. Vagin A, Teplyakov A. MOLREP: an automated program for molecular replacement. J Appl Cryst 1997;30:1022-1025. (Pubitemid 127485985)
15. Morris RJ, Perrakis A, Lamzin VS. ARP/wARP and automatic interpretation of protein electron density maps. Methods Enzymol 2003;374:229-244. (Pubitemid 37531812)
16. McRee DE. A visual protein crystallographic software system for X11/XView. J Mol Graph 1992;10:44-46.
17. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54:905-921. (Pubitemid 28443603)
18. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283-291.
19. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 2005;33:W299-W302. (Pubitemid 44529930)