PDBsum entry 3pse

Hydrolase/protein binding

PDB id: 3pse

Contents

Protein chains

164 a.a. *

150 a.a. *

Ligands

4LJ

GOL

Waters ×139

* Residue conservation analysis

PDB id:

3pse

Name:

Hydrolase/protein binding

Title:

Structure of a viral otu domain protease bound to interferon- stimulated gene 15 (isg15)

Structure:

RNA polymerase. Chain: a. Fragment: otu domain (unp residues 1-169). Engineered: yes. Ubiquitin-like protein isg15. Chain: b. Synonym: interferon-induced 15 kda protein, interferon-induced 17 kda protein, ip17, ubiquitin cross-reactive protein, hucrp. Engineered: yes.

Source:

Crimean-congo hemorrhagic fever virus. Organism_taxid: 11593. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606. Gene: isg15, g1p2, ucrp. Expression_system_taxid: 562

Resolution:

2.30Å R-factor: 0.167 R-free: 0.224

Authors:

J.P.Bacik,T.W.James,N.Frias-Staheli,A.Garcia-Sastre,B.L.Mark

Key ref:

T.W.James et al. (2011). Structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domain-containing protease. Proc Natl Acad Sci U S A, 108, 2222-2227. PubMed id: 21245344

Date:

01-Dec-10 Release date: 19-Jan-11

Protein chain

Q6TQR6  (L_CCHFI) -  RNA-directed RNA polymerase L from Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)

Seq: 3945 a.a.

Struc: 164 a.a.

Protein chain

P05161  (ISG15_HUMAN) -  Ubiquitin-like protein ISG15 from Homo sapiens

Seq: 165 a.a.

Struc: 150 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain A: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: Chain A: E.C.3.1.-.-
• Enzyme class 4: Chain A: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
• Enzyme class 5: Chain A: E.C.3.4.22.- - ?????
• Enzyme class 6: Chain B: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Proc Natl Acad Sci U S A 108:2222-2227 (2011)

PubMed id: 21245344

Structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domain-containing protease.

T.W.James, N.Frias-Staheli, J.P.Bacik, J.M.Levingston Macleod, M.Khajehpour, A.García-Sastre, B.L.Mark.

ABSTRACT

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.