PDBsum entry 3phx

Hydrolase/protein binding

PDB id: 3phx

Contents

Protein chains

162 a.a. *

77 a.a. *

Ligands

ACY ×2

NEH

Metals

_ZN ×12

Waters ×192

* Residue conservation analysis

PDB id:

3phx

Name:

Hydrolase/protein binding

Title:

Otu domain of crimean congo hemorrhagic fever virus in complex with isg15

Structure:

RNA-directed RNA polymerase l. Chain: a. Fragment: unp residues 1-183. Synonym: protein l, large structural protein, replicase, transcriptase, ubiquitin thiolesterase, RNA-directed RNA polymerase. Engineered: yes. Ubiquitin-like protein isg15. Chain: b. Fragment: unp residues 79-156.

Source:

Crimean-congo hemorrhagic fever virus. Cchfv. Organism_taxid: 652961. Strain: nigeria/ibar10200/1970. Gene: l. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human.

Resolution:

1.60Å R-factor: 0.142 R-free: 0.192

Authors:

M.Akutsu,Y.Ye,S.Virdee,D.Komander

Key ref:

M.Akutsu et al. (2011). Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains. Proc Natl Acad Sci U S A, 108, 2228-2233. PubMed id: 21266548

Date:

04-Nov-10 Release date: 02-Feb-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: 162 a.a.

Protein chain

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

Seq: 165 a.a.

Struc: 77 a.a.

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.- - ?????

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 108:2228-2233 (2011)

PubMed id: 21266548

Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains.

M.Akutsu, Y.Ye, S.Virdee, J.W.Chin, D.Komander.

ABSTRACT

Crimean Congo hemorrhagic fever virus (CCHFV) is a deadly human pathogen that evades innate immune responses by efficiently interfering with antiviral signaling pathways mediated by NF-κB, IRF3, and IFNα/β. These pathways rely on protein ubiquitination for their activation, and one outcome is the modification of proteins with the ubiquitin (Ub)-like modifier interferon-stimulated gene (ISG)15. CCHFV and related viruses encode a deubiquitinase (DUB) of the ovarian tumor (OTU) family, which unlike eukaryotic OTU DUBs also targets ISG15 modifications. Here we characterized the viral OTU domain of CCHFV (vOTU) biochemically and structurally, revealing that it hydrolyzes four out of six tested Ub linkages, but lacks activity against linear and K29-linked Ub chains. vOTU cleaved Ub and ISG15 with similar kinetics, and we were able to understand vOTU cross-reactivity at the molecular level from crystal structures of vOTU in complex with Ub and ISG15. An N-terminal extension in vOTU not present in eukaryotic OTU binds to the hydrophobic Ile44 patch of Ub, which results in a dramatically different Ub orientation compared to a eukaryotic OTU-Ub complex. The C-terminal Ub-like fold of ISG15 (ISG15-C) adopts an equivalent binding orientation. Interestingly, ISG15-C contains an additional second hydrophobic surface that is specifically contacted by vOTU. These subtle differences in Ub/ISG15 binding allowed the design of vOTU variants specific for either Ub or ISG15, which will be useful tools to understand the relative contribution of ubiquitination vs. ISGylation in viral infection. Furthermore, the crystal structures will allow structure-based design of antiviral agents targeting this enzyme.