PDBsum entry 3n3k

Hydrolase

PDB id: 3n3k

Contents

Protein chains

355 a.a. *

74 a.a. *

Metals

_ZN

Waters ×112

* Residue conservation analysis

PDB id:

3n3k

Name:

Hydrolase

Title:

The catalytic domain of usp8 in complex with a usp8 specific inhibitor

Structure:

Ubiquitin carboxyl-terminal hydrolase 8. Chain: a. Fragment: catalytic domain. Synonym: ubiquitin thioesterase 8, ubiquitin-specific-processing protease 8, deubiquitinating enzyme 8, ubiquitin isopeptidase y, hubpy. Engineered: yes. Ubiquitin. Chain: b.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: kiaa0055, ubpy, usp8. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rps27a, uba52, uba80, ubb, ubc, ubcep1, ubcep2, ubq.

Resolution:

2.60Å R-factor: 0.181 R-free: 0.242

Authors:

J.R.Walker,G.V.Avvakumov,S.Xue,Y.Li,A.Allali-Hassani,R.Lam,A.Ernst, S.Sidhu,J.Weigelt,C.Bountra,C.H.Arrowsmith,A.M.Edwards,A.Bochkarev, S.Dhe-Paganon,Structural Genomics Consortium (Sgc)

Key ref:

A.Ernst et al. (2013). A strategy for modulation of enzymes in the ubiquitin system. Science, 339, 590-595. PubMed id: 23287719

Date:

20-May-10 Release date: 23-Jun-10

Protein chain

P40818  (UBP8_HUMAN) -  Ubiquitin carboxyl-terminal hydrolase 8 from Homo sapiens

Seq: 1118 a.a.

Struc: 355 a.a.

Protein chain

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 74 a.a.*

* PDB and UniProt seqs differ at 12 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).

Science 339:590-595 (2013)

PubMed id: 23287719

A strategy for modulation of enzymes in the ubiquitin system.

A.Ernst, G.Avvakumov, J.Tong, Y.Fan, Y.Zhao, P.Alberts, A.Persaud, J.R.Walker, A.M.Neculai, D.Neculai, A.Vorobyov, P.Garg, L.Beatty, P.K.Chan, Y.C.Juang, M.C.Landry, C.Yeh, E.Zeqiraj, K.Karamboulas, A.Allali-Hassani, M.Vedadi, M.Tyers, J.Moffat, F.Sicheri, L.Pelletier, D.Durocher, B.Raught, D.Rotin, J.Yang, M.F.Moran, S.Dhe-Paganon, S.S.Sidhu.

ABSTRACT

The ubiquitin system regulates virtually all aspects of cellular function. We report a method to target the myriad enzymes that govern ubiquitination of protein substrates. We used massively diverse combinatorial libraries of ubiquitin variants to develop inhibitors of four deubiquitinases (DUBs) and analyzed the DUB-inhibitor complexes with crystallography. We extended the selection strategy to the ubiquitin conjugating (E2) and ubiquitin ligase (E3) enzymes and found that ubiquitin variants can also enhance enzyme activity. Last, we showed that ubiquitin variants can bind selectively to ubiquitin-binding domains. Ubiquitin variants exhibit selective function in cells and thus enable orthogonal modulation of specific enzymatic steps in the ubiquitin system.