Structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domain-containing protease.
The attachment of ubiquitin (Ub) and the Ub-like (Ubl) molecule interferon-stimulated gene 15 (ISG15) to cellular proteins mediates important innate antiviral responses. Ovarian tumor (OTU) domain proteases from nairoviruses and arteriviruses were recently found to remove these molecules from host proteins, which inhibits Ub and ISG15-dependent antiviral pathways. This contrasts with the Ub-specific activity of known eukaryotic OTU-domain proteases. Here we describe crystal structures of a viral OTU domain from the highly pathogenic Crimean-Congo haemorrhagic fever virus (CCHFV) bound to Ub and to ISG15 at 2.5-Å and 2.3-Å resolution, respectively. The complexes provide a unique structural example of ISG15 bound to another protein and reveal the molecular mechanism of an ISG15 cross-reactive deubiquitinase. To accommodate structural differences between Ub and ISG15, the viral protease binds the β-grasp folds of Ub and C-terminal Ub-like domain of ISG15 in an orientation that is rotated nearly 75° with respect to that observed for Ub bound to a representative eukaryotic OTU domain from yeast. Distinct structural determinants necessary for binding either substrate were identified and allowed the reengineering of the viral OTU protease into enzymes with increased substrate specificity, either for Ub or for ISG15. Our findings now provide the basis to determine in vivo the relative contributions of deubiquitination and deISGylation to viral immune evasion tactics, and a structural template of a promiscuous deubiquitinase from a haemorrhagic fever virus that can be targeted for inhibition using small-molecule-based strategies.
Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
Terrence W
TW
James
Natalia
N
Frias-Staheli
John-Paul
JP
Bacik
Jesica M
JM
Levingston Macleod
Mazdak
M
Khajehpour
Adolfo
A
García-Sastre
Brian L
BL
Mark
D018360:Crystallography, X-Ray; D016207:Cytokines / Q000737:chemistry* / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D005260:Female; D003225:Hemorrhagic Fever Virus, Crimean-Congo / Q000201:enzymology* / Q000235:genetics / Q000276:immunology; D006801:Humans; D010051:Ovarian Neoplasms; D010447:Peptide Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D025801:Ubiquitin / Q000737:chemistry / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D014452:Ubiquitins / Q000737:chemistry* / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
D016207:Cytokines; D025801:Ubiquitin; D014452:Ubiquitins; D014764:Viral Proteins; C074034:ISG15 protein, human; D010447:Peptide Hydrolases
Nat Rev Mol Cell Biol. 2001 Mar;2(3):195-201
11265249
J Mol Biol. 1993 Jan 5;229(1):105-24
7678431
Chem Biol. 2002 Oct;9(10):1149-59
12401499
Nat Rev Mol Cell Biol. 2009 Aug;10(8):550-63
19626045
Nature. 1979 Jun 7;279(5713):523-5
571963
Biochem J. 2009 Mar 1;418(2):379-90
18954305
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
15572765
Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54
12393927
J Biol Chem. 1992 Apr 15;267(11):7806-13
1373138
J Mol Biol. 1984 Oct 25;179(2):233-56
6502713
EMBO J. 2001 Feb 1;20(3):362-71
11157743
Biochem J. 2008 Jan 1;409(1):77-85
17961127
Virology. 2004 Mar 30;321(1):29-35
15033562
J Virol. 2005 Dec;79(24):15199-208
16306591
Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64
15805601
Acta Crystallogr D Biol Crystallogr. 2006 Apr;62(Pt 4):439-50
16552146
Nat Rev Mol Cell Biol. 2005 Aug;6(8):599-609
16064136
Antiviral Res. 2004 Dec;64(3):145-60
15550268
Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3
15299374
J Virol. 2002 Jun;76(12):6323-31
12021365
Cell. 2010 Oct 15;143(2):187-90
20946978
Curr Opin Cell Biol. 2007 Apr;19(2):199-205
17303403
Trends Biochem Sci. 2000 Feb;25(2):50-2
10664582
Cell Host Microbe. 2007 Dec 13;2(6):404-16
18078692
Nature. 2004 Aug 5;430(7000):694-9
15258597
J Mol Biol. 2008 Feb 15;376(2):526-40
18164316
J Virol. 2010 May;84(9):4619-29
20181693
Science. 2007 Dec 7;318(5856):1628-32
17991829
J Mol Biol. 2007 Sep 21;372(3):774-97
17681537
Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1371-6
17227866
EMBO Rep. 2004 Aug;5(8):783-8
15258613
J Biol Chem. 2005 Jul 22;280(29):27356-65
15917233
Virology. 2004 Mar 30;321(1):23-8
15033561
Biochemistry. 1976 Aug 24;15(17):3731-8
952885
Nucleic Acids Res. 2010 Jan;38(Database issue):D227-33
19892822
J Biol Chem. 2008 Apr 18;283(16):11038-49
18270205
Nature. 2009 Mar 26;458(7237):430-7
19325622
J Virol. 2010 Aug;84(15):7832-46
20504922
J Biol Chem. 1995 Jul 14;270(28):16671-6
7622476
Nature. 2009 Mar 26;458(7237):422-9
19325621