PDBsum entry 5lrv

Hydrolase

PDB id: 5lrv

Contents

Protein chains

286 a.a.

71 a.a.

76 a.a.

Ligands

PO4

GOL ×4

Waters ×3

PDB id:

5lrv

Name:

Hydrolase

Title:

Structure of cezanne/otud7b otu domain bound to lys11-linked diubiquitin

Structure:

Otu domain-containing protein 7b. Chain: a. Synonym: cellular zinc finger anti-nf-kappa-b protein,zinc finger a20 domain-containing protein 1,zinc finger protein cezanne. Engineered: yes. Polyubiquitin-b. Chain: b. Engineered: yes. Mutation: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: otud7b, za20d1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606

Resolution:

2.80Å R-factor: 0.209 R-free: 0.244

Authors:

T.E.T.Mevissen,Y.Kulathu,M.P.C.Mulder,P.P.Geurink,S.L.Maslen, M.Gersch,P.R.Elliott,J.E.Burke,B.D.M.Van Tol,M.Akutsu,F.El Oualid, M.Kawasaki,S.M.V.Freund,H.Ovaa,D.Komander

Key ref:

T.E.T.Mevissen et al. (2016). Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne. Nature, 538, 402-405. PubMed id: 27732584

Date:

22-Aug-16 Release date: 19-Oct-16

Protein chain

Q6GQQ9  (OTU7B_HUMAN) -  OTU domain-containing protein 7B from Homo sapiens

Seq: 843 a.a.

Struc: 286 a.a.*

Protein chain

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 71 a.a.*

Protein chain

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 76 a.a.*

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

Enzyme reactions

• Enzyme class: 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).

Nature 538:402-405 (2016)

PubMed id: 27732584

Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne.

T.E.T.Mevissen, Y.Kulathu, M.P.C.Mulder, P.P.Geurink, S.L.Maslen, M.Gersch, P.R.Elliott, J.E.Burke, B.D.M.van Tol, M.Akutsu, F.E.Oualid, M.Kawasaki, S.M.V.Freund, H.Ovaa, D.Komander.

ABSTRACT

The post-translational modification of proteins with polyubiquitin regulates virtually all aspects of cell biology. Eight distinct chain linkage types co-exist in polyubiquitin and are independently regulated in cells. This 'ubiquitin code' determines the fate of the modified protein. Deubiquitinating enzymes of the ovarian tumour (OTU) family regulate cellular signalling by targeting distinct linkage types within polyubiquitin, and understanding their mechanisms of linkage specificity gives fundamental insights into the ubiquitin system. Here we reveal how the deubiquitinase Cezanne (also known as OTUD7B) specifically targets Lys11-linked polyubiquitin. Crystal structures of Cezanne alone and in complex with monoubiquitin and Lys11-linked diubiquitin, in combination with hydrogen-deuterium exchange mass spectrometry, enable us to reconstruct the enzymatic cycle in great detail. An intricate mechanism of ubiquitin-assisted conformational changes activates the enzyme, and while all chain types interact with the enzymatic S1 site, only Lys11-linked chains can bind productively across the active site and stimulate catalytic turnover. Our work highlights the plasticity of deubiquitinases and indicates that new conformational states can occur when a true substrate, such as diubiquitin, is bound at the active site.