PDBsum entry 4uf6

Hydrolase

PDB id: 4uf6

Contents

Protein chains

292 a.a.

76 a.a.

50 a.a.

PDB id:

4uf6

Name:

Hydrolase

Title:

Uch-l5 in complex with ubiquitin-propargyl bound to an activating fragment of ino80g

Structure:

Ubiquitin carboxyl-terminal hydrolase isozyme l5. Chain: a, d, g, j. Synonym: uch-l5, ubiquitin c-terminal hydrolase uch37, ubiquitin thioesterase l5, uch-l5. Engineered: yes. Other_details: active site cys88 covalently linked to ubiquitin- propargyl. Polyubiquitin-b. Chain: b, e, h, k.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: rosetta 2. Synthetic: yes.

Resolution:

3.69Å R-factor: 0.240 R-free: 0.269

Authors:

D.D.Sahtoe,W.J.Van Dijk,F.El Oualid,R.Ekkebus,H.Ovaa,T.K.Sixma

Key ref:

D.D.Sahtoe et al. (2015). Mechanism of UCH-L5 activation and inhibition by DEUBAD domains in RPN13 and INO80G. Mol Cell, 57, 887-900. PubMed id: 25702870 DOI: 10.1016/j.molcel.2014.12.039

Date:

23-Dec-14 Release date: 04-Mar-15

Protein chains

Q9Y5K5  (UCHL5_HUMAN) -  Ubiquitin carboxyl-terminal hydrolase isozyme L5 from Homo sapiens

Seq: 329 a.a.

Struc: 292 a.a.

Protein chains

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 76 a.a.*

Protein chains

Q6P4R8  (NFRKB_HUMAN) -  Nuclear factor related to kappa-B-binding protein from Homo sapiens

Seq: 1299 a.a.

Struc: 50 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, D, G, J: 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).

DOI no: 10.1016/j.molcel.2014.12.039

Mol Cell 57:887-900 (2015)

PubMed id: 25702870

Mechanism of UCH-L5 activation and inhibition by DEUBAD domains in RPN13 and INO80G.

D.D.Sahtoe, W.J.van Dijk, F.El Oualid, R.Ekkebus, H.Ovaa, T.K.Sixma.

ABSTRACT

Deubiquitinating enzymes (DUBs) control vital processes in eukaryotes by hydrolyzing ubiquitin adducts. Their activities are tightly regulated, but the mechanisms remain elusive. In particular, the DUB UCH-L5 can be either activated or inhibited by conserved regulatory proteins RPN13 and INO80G, respectively. Here we show how the DEUBAD domain in RPN13 activates UCH-L5 by positioning its C-terminal ULD domain and crossover loop to promote substrate binding and catalysis. The related DEUBAD domain in INO80G inhibits UCH-L5 by exploiting similar structural elements in UCH-L5 to promote a radically different conformation, and employs molecular mimicry to block ubiquitin docking. In this process, large conformational changes create small but highly specific interfaces that mediate activity modulation of UCH-L5 by altering the affinity for substrates. Our results establish how related domains can exploit enzyme conformational plasticity to allosterically regulate DUB activity. These allosteric sites may present novel insights for pharmaceutical intervention in DUB activity.