Dimer Interface Migration in a Viral Sulfhydryl Oxidase

Journal of Molecular Biology

Volumn 391, Issue 4, 2009, Pages 758-768

  Hakim, Motti ^a   Fass, Deborah ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

disulfide bonds; DNA viruses; evolution; homooligomer; negative design

Indexed keywords

DIMER; DOUBLE STRANDED DNA; QUERCETIN; THIOL OXIDASE; VIRUS ENZYME;

AFRICAN SWINE FEVER VIRUS; ARTICLE; CONTROLLED STUDY; DIMERIZATION; DNA VIRUS; ENZYME BINDING; EUKARYOTE; FUNGUS; GENE MUTATION; MAMMAL; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGOMERIZATION; PLANT; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN FAMILY; SEQUENCE HOMOLOGY; VIRUS CELL INTERACTION;

AFRICAN SWINE FEVER VIRUS; DNA VIRUSES; EUKARYOTA; FUNGI; MAMMALIA; MIMIVIRUS;

EID: 68149178656     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.06.070     Document Type: Article

References (43)

1. Sevier C.S., and Kaiser C.A. Formation and transfer of disulfide bonds in living cells. Nat. Rev. Mol. Cell Biol. 3 (2002) 836-847
2. Mesecke N., Terziyska N., Kozany C., Baumann F., Neupert W., Hell K., and Herrmann J.M. A disulfide relay system in the intermembrane space of mitochondria that mediates protein import. Cell 121 (2005) 1059-1069
3. Paget M.S.B., and Buttner M.J. Thiol-based regulatory switches. Annu. Rev. Genet. 37 (2003) 91-121
4. Lillig C.H., and Holmgren A. Thioredoxin and related molecules-from biology to health and disease. Antioxid. Redox Signal. 9 (2007) 25-47
5. Senkevich T.G., Weisberg A.S., and Moss B. Vaccinia virus E10R protein is associated with the membranes of intracellular mature virions and has a role in morphogenesis. Virology 278 (2000) 244-252
6. Lewis T., Zsak L., Burrage T.G., Lu Z., Kutish G.F., Neilan J.G., and Rock D.L. An African swine fever virus ERV1-ALR homologue, 9GL, affects viral maturation and viral growth in macrophages and viral virulence in swine. J. Virol. 74 (2000) 1275-1285
7. Senkevich T.G., White C.L., Koonin E.V., and Moss B. A viral member of ERV1/ALR protein family participates in a cytoplasmic pathway of disulfide bond formation. Proc. Natl Acad. Sci. USA 97 (2000) 2068-12073
8. Senkevich T.G., White C.L., Koonin E.V., and Moss B. Complete pathway for protein disulfide bond formation encoded by poxviruses. Proc. Natl Acad. Sci. USA 99 (2002) 6667-6672
9. Rodríguez I., Redrejo-Rodríguez M., Rodríguez J.M., Alejo A., Salas J., and Salas M.L. African swine fever virus pB119L protein is a flavin adenine dinucleotide-linked sulfhydryl oxidase. J. Virol. 80 (2006) 3157-3166
10. Iyer L.M., Balaji S., Koonin E.V., and Aravind L. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res. 117 (2006) 156-184
11. Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., et al. Environmental genome shotgun sequencing of the Sargasso sea. Science 304 (2004) 66-74
12. Monier A., Larsen J.B., Sandaa R.A., Bratbak G., Claverie J.-M., and Ogata H. Marine mimivirus relatives are probably large algal viruses. Virol. J. 5 (2008) 12
13. Gross E., Sevier C.S., Vala A., Kaiser C.A., and Fass D. A new FAD-binding fold and intersubunit disulfide shuttle in the thiol oxidase Erv2p. Nat. Struct. Biol. 9 (2002) 61-67
14. Wu C.K., Dailey T.A., Dailey H.A., Wang B.C., and Rose J.P. The crystal structure of augmenter of liver regeneration: a mammalian FAD-dependent sulfhydryl oxidase. Protein Sci. 12 (2003) 1109-1118
15. Vitu E., Bentzur M., Lisowsky T., Kaiser C.A., and Fass D. Gain of function in an ERV/ALR sulfhydryl oxidase by molecular engineering of the shuttle disulfide. J. Mol. Biol. 362 (2006) 89-101
16. Lee J., Hofhaus G., and Lisowsky T. Erv1p from Saccharomyces cerevisiae is a FAD-linked sulfhydryl oxidase. FEBS Lett. 477 (2000) 62-66
17. Fass D. The Erv family of sulfhydryl oxidases. Biochim. Biophys. Acta 1783 (2008) 557-566
18. Lawrence M.C., and Colman P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234 (1993) 946-950
19. 2 transport protein. Nature 458 (2009) 305-310
20. Dasgupta S., Iyer G.H., Bryant S.H., Lawrence C.E., and Bell J.A. Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins 28 (1997) 494-514
21. Aloy P., Ceulmans H., Stark A., and Russell R. The relationship between sequence and interaction divergence in proteins. J. Mol. Biol. 332 (2003) 989-998
22. Higa R.H., Oliveira A.G., Horita L.G., Miura R.T., Inoue M.K., Kuser P.R., et al. Defining 3D residue environment in protein structures using SCORPION and FORMIGA. Bioinformatics 20 (2004) 1989-1991
23. Krissinel E., and Henrick K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372 (2007) 774-797
24. Levy E.D. PiQSi: protein quaternary structure investigation. Structure 15 (2007) 364-1367
25. Sinha S., Gupta G., Vijayan M., and Surolia A. Subunit assembly of plant lectins. Curr. Opin. Struct. Biol. 17 (2007) 498-505
26. Caillat C., Topalis D., Agrofoglio L.A.., Pochet S., Balzirini J., Deville-Bonne D., et al. Crystal structure of poxvirus thymidylate kinase: an unexpected dimerization has implications for antiviral therapy. Proc. Natl Acad. Sci. USA 105 (2008) 16900-16905
27. Farrell S.R., and Thorpe C. Augmenter of liver regeneration: a flavin-dependent sulfhydryl oxidase with cytochrome c reductase activity. Biochemistry 44 (2005) 1532-1541
28. Vala A., Sevier C.S., and Kaiser C.A. Structural determinants of substrate access to the disulfide oxidase Erv2p. J. Mol. Biol. 354 (2005) 952-966
29. Frand A.R., and Kaiser C.A. Ero1p oxidizes protein disulfide isomerase in a pathway for disulfide bond formation in the endoplasmic reticulum. Mol. Cell 4 (1999) 469-477
30. Lukatsky D.B., Shakhnovich B.E., Mintseris J., and Shakhnovich E.I. Structural similarity enhances interaction propensity of proteins. J. Mol. Biol. 365 (2007) 1596-1606
31. Levy E.D., Boeri Erba E., Robinson C.V., and Teichmann S.A. Assembly reflects evolution of protein complexes. Nature 453 (2008) 1262-1265
32. Hughes A.L. Origin and evolution of viral interleukin-10 and other DNA virus genes with vertebrate homologues. J. Mol. Evol. 54 (2002) 90-101
33. Belshaw R., Gardner A., Rambaut A., and Pybus O.G. Pacing a small cage: mutation and RNA viruses. Trends Ecol. Evol. 23 (2008) 188-193
34. Van Duyne G.D., Standaert R.T., Karplus P.A., Schreiber S.L., and Clardy J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229 (2001) 105-124
35. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
36. Terwilliger T.C., and Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr. Sect. D 55 (1999) 849-861
37. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. Sect. D 60 (2005) 2126-2132
38. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Gross-Kunstleve R.W.C., et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. Sect. D 54 (1998) 905-921
39. Lovell S.C., Davis I.W., Arendallll III W.B., de Bakker P.I., Word J.M., Prisant M.G., et al. Structure validation by Calpha geometry: phi, psi, and Cbeta deviation. Proteins 50 (2003) 437-450
40. McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., and Read R.J. Phaser crystallographic software. J. Appl. Crystallogr. 40 (2007) 658-674
41. Canutescu A.A., Shelenkov A.A., and Dunbrack Jr. R.L. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12 (2003) 2001-2014
42. Demeler B., Saber H., and Hansen J.C. Identification and interpretation of complexity in sedimentation velocity boundaries. Biophys. J. 72 (1997) 397-407
43. Sali A., and Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234 (1993) 779-815