PDBsum entry 3wxf

Hydrolase/protein binding

PDB id: 3wxf

Contents

Protein chains

299 a.a.

148 a.a.

Ligands

SO4 ×2

Waters ×147

PDB id:

3wxf

Name:

Hydrolase/protein binding

Title:

Crystal structure of cyld usp domain (c596s e674q) in complex with met1-linked diubiquitin

Structure:

Uncharacterized protein. Chain: a, c. Fragment: usp domain, unp residues 578-780, linker, 850-951. Synonym: cyld protein. Engineered: yes. Mutation: yes. Ubiquitin. Chain: b, d. Synonym: m1-linked diubiquitin.

Source:

Danio rerio. Zebra fish. Organism_taxid: 7955. Gene: cyld, cylda. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606.

Resolution:

2.30Å R-factor: 0.189 R-free: 0.229

Authors:

Y.Sato,S.Fukai

Key ref:

Y.Sato et al. (2015). Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity. Nat Struct Mol Biol, 22, 222-229. PubMed id: 25686088 DOI: 10.1038/nsmb.2970

Date:

30-Jul-14 Release date: 11-Feb-15

Protein chains

E7FEV5  (E7FEV5_DANRE) -  Ubiquitin carboxyl-terminal hydrolase CYLD from Danio rerio

Seq: 951 a.a.

Struc: 299 a.a.*

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 148 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, C: 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 3: Chains B, D: 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.

DOI no: 10.1038/nsmb.2970

Nat Struct Mol Biol 22:222-229 (2015)

PubMed id: 25686088

Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.

Y.Sato, E.Goto, Y.Shibata, Y.Kubota, A.Yamagata, S.Goto-Ito, K.Kubota, J.Inoue, M.Takekawa, F.Tokunaga, S.Fukai.

ABSTRACT

The tumor suppressor CYLD belongs to a ubiquitin (Ub)-specific protease (USP) family and specifically cleaves Met1- and Lys63-linked polyubiquitin chains to suppress inflammatory signaling pathways. Here, we report crystal structures representing the catalytic states of zebrafish CYLD for Met1- and Lys63-linked Ub chains and two distinct precatalytic states for Met1-linked chains. In both catalytic states, the distal Ub is bound to CYLD in a similar manner, and the scissile bond is located close to the catalytic residue, whereas the proximal Ub is bound in a manner specific to Met1- or Lys63-linked chains. Further structure-based mutagenesis experiments support the mechanism by which CYLD specifically cleaves both Met1- and Lys63-linked chains and provide insight into tumor-associated mutations of CYLD. This study provides new structural insight into the mechanisms by which USP family deubiquitinating enzymes recognize and cleave Ub chains with specific linkage types.