Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses

Virology Journal

Volumn 4, Issue , 2007, Pages

  Keller, Jenny ^a   Leulliot, Nicolas ^a   Cambillau, Christian ^b   Campanacci, Valérie ^b   Porciero, Stéphanie ^b   Prangishvilli, David ^c   Forterre, Patrick ^c   Cortez, Diego ^c   Quevillon Cheruel, Sophie ^a   Van Tilbeurgh, Herman ^a  

^a INSTITUTE FOR INTEGRATIVE BIOLOGY OF THE CELL I2BC   (France)

^b AIX MARSEILLE UNIVERSITY   (France)

^c INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; PROTEIN AFV3 109; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ARTICLE; BETA SHEET; CRENARCHAEAL VIRUS; CRYSTAL STRUCTURE; FLUORESCENCE ANALYSIS; GENOME ANALYSIS; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PHOTOCHEMICAL QUENCHING; PROPHAGE; PROTEIN DATA BANK; PROTEIN DNA INTERACTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; VIRUS STRAIN;

AMINO ACID SEQUENCE; ARCHAEAL VIRUSES; CAPSID PROTEINS; CONSERVED SEQUENCE; CRENARCHAEOTA; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; SEQUENCE ALIGNMENT;

ACIDIANUS; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; EUKARYOTA; FIRMICUTES; LIPOTHRIXVIRIDAE; RUDIVIRIDAE; SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS;

EID: 33846987202     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-4-12     Document Type: Article

References (38)

1. Viruses of hyperthermophilic Crenarchaea. D Prangishvili RA Garrett, Trends Microbiol 2005 13 11 535 542 16154357 10.1016/j.tim.2005.08.013
2. Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life. D Prangishvili RA Garrett EV Koonin, Virus Res 2006 117 1 52 67 16503363 10.1016/j.virusres.2006.01.007
3. Biochemical and phylogenetic characterization of the dUTPase from the archaeal virus SIRV. D Prangishvili HP Klenk G Jakobs A Schmiechen C Hanselmann I Holz W Zillig, J Biol Chem 1998 273 11 6024 6029 9497317 10.1074/jbc.273.11. 6024
4. TTV1, TTV2 and TTV3, a family of viruses of the extremely thermophilic, anaerobic sulfur reducing archaebacterium Thermoproteus tenax. D Janekovic S Wunderl I Holz W Zillig A Gierl H Neumann, Mol Gen Genet 1983 192 39 45 10.1007/BF00327644
5. SNDV, a novel virus of the extremely thermophilic and acidophilic archaeon Sulfolobus. HP Arnold U Ziese W Zillig, Virology 2000 272 2 409 416 10873785 10.1006/viro.2000.0375
6. AFV1, a novel virus infecting hyperthermophilic archaea of the genus acidianus. M Bettstetter X Peng RA Garrett D Prangishvili, Virology 2003 315 1 68 79 14592760 10.1016/S0042-6822(03)00481-1
7. Viral diversity in hot springs of Pozzuoli, Italy, and characterization of a unique archaeal virus, Acidianus bottle-shaped virus, from a new family, the Ampullaviridae. M Haring R Rachel X Peng RA Garrett D Prangishvili, J Virol 2005 79 15 9904 9911 16014951 10.1128/JVI.79.15.9904-9911.2005
8. The particle SSV1 from the extremely thermophilic archaeon Sulfolobus is a virus: demonstration of infectivity and of transfection with viral DNA. C Schleper K Kubo W Zillig, Proc Natl Acad Sci U S A 1992 89 16 7645 7649 1502176 10.1073/pnas.89.16.7645
9. Relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2. KM Stedman Q She H Phan HP Arnold I Holz RA Garrett W Zillig, Res Microbiol 2003 154 4 295 302 12798235 10.1016/S0923-2508(03)00074-3
10. Comparative genomic analysis of hyperthermophilic archaeal Fuselloviridae viruses. B Wiedenheft K Stedman F Roberto D Willits AK Gleske L Zoeller J Snyder T Douglas M Young, J Virol 2004 78 4 1954 1961 14747560 10.1128/JVI.78.4.1954-1961.2004
11. A novel lipothrixvirus, SIFV, of the extremely thermophilic crenarchaeon Sulfolobus. HP Arnold W Zillig U Ziese I Holz M Crosby T Utterback JF Weidmann JK Kristjanson HP Klenk KE Nelson CM Fraser, Virology 2000 267 2 252 266 10662621 10.1006/viro.1999.0105
12. Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae. M Haring X Peng K Brugger R Rachel KO Stetter RA Garrett D Prangishvili, Virology 2004 323 2 233 242 15193919 10.1016/j.virol.2004.03.002
13. Ttsv1, a novel globuloviridae family virus isolated from the hyperthermophilic crenarchaeote Thermoproteus tenax. DG Ahn SI Kim JK Rhee KP Kim JW Oh, GenBank Accession: NC_006556 2004 [http://www.ncbi.nlm.nih.gov/ entrez/viewer.fcgi?db=nucleotide&val=56692997]
14. Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures. M Haring G Vestergaard K Brugger R Rachel RA Garrett D Prangishvili, J Bacteriol 2005 187 11 3855 3858 15901711 10.1128/JB.187.11.3855-3858.2005
15. Virology: independent virus development outside a host. M Haring G Vestergaard R Rachel L Chen RA Garrett D Prangishvili, Nature 2005 436 7054 1101 1102 16121167 10.1038/4361101a
16. The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life. G Rice L Tang K Stedman F Roberto J Spuhler E Gillitzer JE Johnson T Douglas M Young, Proc Natl Acad Sci U S A 2004 101 20 7716 7720 15123802 10.1073/pnas.0401773101
17. Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features. X Xiang L Chen X Huang Y Luo Q She L Huang, J Virol 2005 79 14 8677 8686 15994761 10.1128/JVI.79.14.8677-8686.2005
18. Observation of virus-like particles in high temperature enrichment cultures from deep-sea hydrothermal vents. C Geslin M Le Romancer M Gaillard G Erauso D Prieur, Res Microbiol 2003 154 4 303 307 12798236 10.1016/S0923- 2508(03)00075-5
19. Holliday junction resolving enzymes of archaeal viruses SIRV1 and SIRV2. RP Birkenbihl K Neef D Prangishvili B Kemper, J Mol Biol 2001 309 5 1067 1076 11399079 10.1006/jmbi.2001.4761
20. SSV1-encoded site-specific recombination system in Sulfolobus shibatae. G Muskhelishvili P Palm W Zillig, Mol Gen Genet 1993 237 3 334 342 8483447
21. Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses. R Khayat L Tang ET Larson CM Lawrence M Young JE Johnson, Proc Natl Acad Sci U S A 2005 102 52 18944 18949 16357204 10.1073/pnas.0506383102
22. Structure of A197 from Sulfolobus Turreted Icosahedral Virus: a Crenarchaeal Viral Glycosyltransferase Exhibiting the GT-A Fold. ET Larson D Reiter M Young CM Lawrence, J Virol 2006 80 15 7636 7644 16840342 10.1128/JVI.00567-06
23. Crystallization and preliminary X-ray diffraction analysis of protein 14 from Sulfolobus islandicus filamentous virus (SIFV). A Goulet S Spinelli V Campanacci S Porciero S Blangy R Garrett H Herman van Tilbeurgh N Leulliot T Basta D Prangishvilid C Cambillau, Acta Crystallograph Sect F Struct Biol Cryst Commun 2006 62 884 6 10.1107/S1744309106029150 16946470
24. The atomic structure of protein-protein recognition sites. L Lo Conte C Chothia J Janin, J Mol Biol 1999 285 5 2177 2198 9925793 10.1006/jmbi.1998.2439
25. Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein, EBNA1, bound to DNA. A Bochkarev JA Barwell RA Pfuetzner E Bochkareva L Frappier AM Edwards, Cell 1996 84 5 791 800 8625416 10.1016/S0092-8674(00)81056-9
26. Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. RS Hegde SR Grossman LA Laimins PB Sigler, Nature 1992 359 6395 505 512 1328886 10.1038/359505a0
27. The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells. P Forterre, Biochimie 2005 87 9-10 793 803 16164990 10.1016/j.biochi.2005.03.015
28. Evolution of complexity in the viral world: the dawn of a new vision. EV Koonin VV Dolja, Virus Res 2006 117 1 1 4 16497406 10.1016/j.virusres.2006.01. 018
29. A Leslie, Joint CCP4 and EACMB Newsletter Protein Crystallography, Daresbury Laboratory, Warrington, United Kingdom 1992
30. Scaling and assessment of data quality. P Evans, Acta Crystallogr D Biol Crystallogr 2006 62 Pt 1 72 82 16369096
31. Substructure solution with SHELXD. TR Schneider GM Sheldrick, Acta Crystallogr D Biol Crystallogr 2002 58 Pt 10 Pt 2 1772 1779 12351820 10.1107/S0907444902011678
32. SOLVE and RESOLVE: automated structure solution, density modification and model building. T Terwilliger, J Synchrotron Radiat 2004 11 Pt 1 49 52 14646132
33. Automated protein model building combined with iterative structure refinement. A Perrakis RJ Morris VS Lamzin, Nature Struct Biol 1999 6 458 463 10331874 10.1038/8263
34. Refinement of macromolecular structures by the maximum-likelihood method. G Murshudov A Vagin E Dodson, Acta Cryst D 1997 53 240 255 10.1107/ S0907444996012255
35. TURBO-FRODO, Silicon Graphics Applications Directory. A Roussel C Cambillau, Silicon Graphics, Mountain View, CA 1991
36. PROCHECK: a program to check stereochemical quality of protein structures. RA Laskowski MW MacArthur DS Moss JM Thornton, J Appl Crystallogr 1993 26 283 291 10.1107/S0021889892009944
37. Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps. AA Vagin MN Isupov, Acta Crystallogr D Biol Crystallogr 2001 57 Pt 10 1451 1456 11567159 10.1107/S0907444901012409
38. ESPript: analysis of multiple sequence alignments in PostScript. P Gouet E Courcelle DI Stuart F Metoz, Bioinformatics 1999 15 4 305 308 10320398 10.1093/bioinformatics/15.4.305