Crystal Structure of ATVORF273, a New Fold for a Thermo- and Acido-Stable Protein from the Acidianus Two-Tailed Virus

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Felisberto Rodrigues, Catarina ^a   Blangy, Stéphanie ^a   Goulet, Adeline ^a,c   Vestergaard, Gisle ^b   Cambillau, Christian ^a   Garrett, Roger A ^b   Ortiz Lombardía, Miguel ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

METHIONINE; OLIGOMER; VIRUS PROTEIN;

ACIDIANUS; ACIDIANUS TWO TAILED VIRUS; AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIOPHAGE; CIRCULAR DICHROISM; CONTROLLED STUDY; CRYSTAL STRUCTURE; GEL PERMEATION CHROMATOGRAPHY; NONHUMAN; OPEN READING FRAME; PH; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN PURIFICATION; PROTEIN STABILITY; VIRION; VIRUS ENVELOPE; X RAY CRYSTALLOGRAPHY;

ACIDIANUS; CIRCULAR DICHROISM; CRYSTALLOGRAPHY, X-RAY; DNA VIRUSES; HOT TEMPERATURE; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; PROTEIN MULTIMERIZATION; PROTEIN STABILITY; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; SCATTERING, SMALL ANGLE; SOLUTIONS; VIRAL STRUCTURAL PROTEINS; X-RAY DIFFRACTION;

EID: 84867285874     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0045847     Document Type: Article

References (57)

1. Bergh O, Borsheim KY, Bratbak G, Heldal M, (1989) High abundance of viruses found in aquatic environments. Nature 340: 467-468.
2. Suttle CA, (2007) Marine viruses-major players in the global ecosystem. Nat Rev Microbiol 5: 801-812.
3. Torsvik T, Dundas ID, (1974) Bacteriophage of Halobacterium salinarium. Nature 248: 680-681.
4. Zillig W, Kletzin A, Schleper C, Holz I, Janekovic D, et al. (1994) Screening for Sulfolobales, their plasmids and their viruses in Icelandic solfataras. Syst Appl Microbiol 16: 609-628.
5. Mochizuki T, Krupovic M, Pehau-Arnaudet G, Sako Y, Forterre P, et al. (2012) Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome. Proc Natl Acad Sci USA 109: 13386-13391.
6. Prangishvili D, Garrett RA, Koonin EV, (2006) Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res 117: 52-67.
7. Abrescia NGA, Bamford DH, Grimes JM, Stuart DI, (2012) Structure unifies the viral universe. Annu Rev Biochem 81: 795-822.
8. Prangishvili D, Krupovic M, (2012) A new proposed taxon for double-stranded DNA viruses, the order "Ligamenvirales". Arch Virol 157: 791-795.
9. Goulet A, Blangy S, Redder P, Prangishvili D, Felisberto-Rodrigues C, et al. (2009) Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage. Proc Natl Acad Sci USA 106: 21155-21160.
10. Goulet A, Vestergaard G, Felisberto-Rodrigues C, Campanacci V, Garrett RA, et al. (2010) Getting the best out of long-wavelength X-rays: de novo chlorine/sulfur SAD phasing of a structural protein from ATV. Acta Crystallogr D Biol Crystallogr 66: 304-308.
11. Goulet A, Pina M, Redder P, Prangishvili D, Vera L, et al. (2010) Orf157 from the archaeal virus Acidianus filamentous virus 1 defines a new class of nuclease. J Virol 84: 5025-5031.
12. Goulet A, Spinelli S, Blangy S, van Tilbeurgh H, Leulliot N, et al. (2009) The crystal structure of ORF14 from Sulfolobus islandicus filamentous virus. Proteins 76: 1020-1022.
13. Goulet A, Spinelli S, Blangy S, van Tilbeurgh H, Leulliot N, et al. (2009) The thermo- and acidostable ORF-99 from the archaeal virus AFV1. Protein Sci 18: 1316-1320.
14. Häring M, Vestergaard G, Rachel R, Chen L, Garrett RA, et al. (2005) Independent virus development outside a host. Nature 436: 1101-1102.
15. Prangishvili D, Vestergaard G, Häring M, Aramayo R, Basta T, et al. (2006) Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle. J Mol Biol 359: 1203-1216.
16. Xiang X, Chen L, Huang X, Luo Y, She Q, et al. (2005) Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features. J Virol 79: 8677-8686.
17. Buchan DWA, Ward SM, Lobley AE, Nugent TCO, Bryson K, et al. (2010) Protein annotation and modelling servers at University College London. Nucleic Acids Res 38: W563-568.
18. Hendlich M, Bergner A, Günther J, Klebe G, (2003) Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J Mol Biol 326: 607-620.
19. Hendlich M, Rippmann F, Barnickel G, (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model 15: 359-363, 389.
20. Jambon M, Imberty A, Deléage G, Geourjon C, (2003) A new bioinformatic approach to detect common 3D sites in protein structures. Proteins 52: 137-145.
21. Petsko GA, (2001) Structural basis of thermostability in hyperthermophilic proteins, or "there's more than one way to skin a cat". Methods Enzymol 334: 469-478.
22. Kumar S, Nussinov R, (2002) Relationship between ion pair geometries and electrostatic strengths in proteins. Biophys J 83: 1595-1612.
23. Holm L, Rosenström P, (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38: W545-549.
24. Krissinel E, Henrick K, (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60: 2256-2268.
25. Krissinel E, Henrick K (2005) Detection of protein assemblies in crystals. In: R Berthold M, Glen R, Diederichs K, Kohlbacher O, Fischer I, editors, Computational Life Sciences, Springer Berlin/Heidelberg, volume 3695 of Lecture Notes in Computer Science. pp. 163-174.
26. Mills JE, Dean PM, (1996) Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. J Comput Aided Mol Des 10: 607-622.
27. Lawrence MC, Colman PM, (1993) Shape complementarity at protein/protein interfaces. J Mol Biol 234: 946-950.
28. Petoukhov MV, Franke D, Shkumatov AV, Tria G, Kikhney AG, et al. (2012) New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr 45: 342-350.
29. Petoukhov MV, Svergun DI, (2005) Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys J 89: 1237-1250.
30. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ, (2005) Geometry-based exible and symmetric protein docking. Proteins 60: 224-231.
31. Svergun D, Barberato C, Koch MHJ, (1995) CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28: 768-773.
32. Compton LA, Johnson WC Jr, (1986) Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication. Anal Biochem 155: 155-167.
33. Whitmore L, Wallace BA, (2008) Protein secondary structure analyses from circular dichroism spectroscopy: methods and reference databases. Biopolymers 89: 392-400.
34. Scheele U, Erdmann S, Ungewickell EJ, Felisberto-Rodrigues C, Ortiz-Lombardía M, et al. (2011) Chaperone role for proteins P618 and P892 in the extracellular tail development of Acidianus two-tailed virus. J Virol 85: 4812-4821.
35. Studier FW, (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41: 207-234.
36. Konarev PV, Volkov VV, Sokolova AV, Koch MHJ, Svergun DI, (2003) PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J Appl Crystallogr 36: 1277-1282.
37. Konarev PV, Petoukhov MV, Volkov VV, Svergun DI, (2006) ATSAS 2.1, a program package for small-angle scattering data analysis. J Appl Crystallogr 39: 277-286.
38. Guinier A, (1939) La diffraction des rayons x aux très pétits angles: application à l'etude de phénomènes ultramicroscopiques. Ann Phys (Paris) 12: 161-237.
39. Svergun DI, (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr 25: 495-503.
40. Franke D, Svergun DI, (2009) DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J Appl Crystallogr 42: 342-346.
41. Volkov VV, Svergun DI, (2003) Uniqueness of ab initio shape determination in small-angle scattering. J Appl Crystallogr 36: 860-864.
42. Kozin MB, Svergun DI, (2001) Automated matching of high- and low-resolution structural models. J Appl Crystallogr 34: 33-41.
43. Wriggers W, (2010) Using Situs for the integration of multi-resolution structures. Biophys Rev 2: 21-27.
44. Kabsch W, (2010) XDS. Acta Crystallogr D Biol Crystallogr 66: 125-132.
45. Evans PR, (2011) An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta Crystallogr D Biol Crystallogr 67: 282-292.
46. Vonrhein C, Blanc E, Roversi P, Bricogne G, (2007) Automated structure solution with autoSHARP. Methods Mol Biol 364: 215-230.
47. Sheldrick GM, (2010) Experimental phasing with shelxc/d/e: combining chain tracing with density modification. Acta Crystallogr D Biol Crystallogr 66: 479-485.
48. Cowtan K, (2006) The buccaneer software for automated model building. 1. tracing protein chains. Acta Crystallogr D Biol Crystallogr 62: 1002-1011.
49. Emsley P, Lohkamp B, Scott WG, Cowtan K, (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66: 486-501.
50. Bricogne G, Blanc E, Brandl M, Flensburg C, Keller P, et al. (2011) BUSTER version 2.11.2. Cambridge, UK: Global Phasing Ltd.
51. Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, et al. (2011) Refmac5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 67: 355-367.
52. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658-674.
53. Smart OS, Womack TO, Flensburg C, Keller P, Paciorek W, et al. (2012) Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER. Acta Crystallogr D Biol Crystallogr 68: 368-380.
54. Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
55. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612.
56. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA, (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98: 10037-10041.
57. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, et al. (2007) Molprobity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35: W375-383.