PDBsum entry 4ldt

Hydrolase regulator

PDB id: 4ldt

Contents

Protein chains

255 a.a.

76 a.a.

148 a.a.

Ligands

EDO ×4

Metals

_MG

Waters ×316

PDB id:

4ldt

Name:

Hydrolase regulator

Title:

The structure of h/ceotub1-ubiquitin aldehyde-ubch5b~ub

Structure:

Ubiquitin thioesterase otubain-like. Chain: a. Fragment: see remark 999. Synonym: deubiquitinating enzyme otub1, otu domain-containing ubiquitin aldehyde-binding protein 1, otubain-1, hotu1, ubiquitin- specific-processing protease otub1, deubiquitinating enzyme otubain- like, ubiquitin-specific-processing protease otubain-like. Engineered: yes. Ubiquitin aldehyde.

Source:

Homo sapiens, caenorhabditis elegans. Human, nematode. Organism_taxid: 9606, 6239. Gene: otub1, otb1, otu1, hspc263, c25d7.8, otub-1. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606.

Resolution:

1.90Å R-factor: 0.193 R-free: 0.223

Authors:

R.Wiener,A.T.Dibello,P.M.Lombardi,C.M.Guzzo,X.Zhang,M.J.Matunis, C.Wolberger

Key ref:

R.Wiener et al. (2013). E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1. Nat Struct Biol, 20, 1033-1039. PubMed id: 23955022 DOI: 10.1038/nsmb.2655

Date:

25-Jun-13 Release date: 14-Aug-13

Protein chain

Q96FW1  (OTUB1_HUMAN) -  Ubiquitin thioesterase OTUB1 from Homo sapiens

Seq: 271 a.a.

Struc: 255 a.a.*

Protein chain

Q9XVR6  (OTUBL_CAEEL) -  Ubiquitin thioesterase otubain-like from Caenorhabditis elegans

Seq: 284 a.a.

Struc: 255 a.a.*

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.*

Protein chain

P62837  (UB2D2_HUMAN) -  Ubiquitin-conjugating enzyme E2 D2 from Homo sapiens

Seq: 147 a.a.

Struc: 148 a.a.*

* PDB and UniProt seqs differ at 168 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: 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 3: Chains B, D: E.C.?
• Enzyme class 4: Chain C: E.C.2.3.2.23 - E2 ubiquitin-conjugating enzyme.
• Reaction: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L- cysteine
• Enzyme class 5: Chain C: E.C.2.3.2.24 - (E3-independent) E2 ubiquitin-conjugating enzyme.
• Reaction: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E1 ubiquitin-activating enzyme]-L-cysteine + N₆- monoubiquitinyl-[acceptor protein]-L-lysine

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.2655

Nat Struct Biol 20:1033-1039 (2013)

PubMed id: 23955022

E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1.

R.Wiener, A.T.DiBello, P.M.Lombardi, C.M.Guzzo, X.Zhang, M.J.Matunis, C.Wolberger.

ABSTRACT

OTUB1 is a Lys48-specific deubiquitinating enzyme that forms a complex in vivo with E2 ubiquitin (Ub)-conjugating enzymes including UBC13 and UBCH5. OTUB1 binds E2~Ub thioester intermediates and prevents ubiquitin transfer, thereby noncatalytically inhibiting accumulation of polyubiquitin. We report here that a second role of OTUB1-E2 interactions is to stimulate OTUB1 cleavage of Lys48 polyubiquitin. This stimulation is regulated by the ratio of charged to uncharged E2 and by the concentration of Lys48-linked polyubiquitin and free ubiquitin. Structural and biochemical studies of human and worm OTUB1 and UBCH5B show that the E2 enzyme stimulates binding of the Lys48 polyubiquitin substrate by stabilizing folding of the OTUB1 N-terminal ubiquitin-binding helix. Our results suggest that OTUB1-E2 complexes in the cell are poised to regulate polyubiquitin chain elongation or degradation in response to changing levels of E2 charging and available free ubiquitin.