PDBsum entry 4v3k

Ligase

PDB id: 4v3k

Contents

Protein chains

146 a.a.

77 a.a.

75 a.a.

70 a.a.

Ligands

EDO ×5

Metals

_ZN ×4

_CL ×6

Waters ×368

PDB id:

4v3k

Name:

Ligase

Title:

Rnf38-ubch5b-ub complex

Structure:

Ubiquitin-conjugating enzyme e2 d2. Chain: a, d. Fragment: residues 2-147. Synonym: ubiquitin carrier protein d2, ubiquitin-conjugating enzyme e2(17)kb 2, ubiquitin-conjugating enzyme e2-17 kda 2, ubiquitin- protein ligase d2, p53-regulated ubiquitin-conjugating enzyme 1, ubch5b. Engineered: yes. Mutation: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.04Å R-factor: 0.183 R-free: 0.223

Authors:

L.Buetow,M.Gabrielsen,N.G.Anthony,H.Dou,A.Patel,H.Aitkenhead, G.J.Sibbet,B.O.Smith,D.T.Huang

Key ref:

L.Buetow et al. (2015). Activation of a primed RING E3-E2-ubiquitin complex by non-covalent ubiquitin. Mol Cell, 58, 297-310. PubMed id: 25801170 DOI: 10.1016/j.molcel.2015.02.017

Date:

20-Oct-14 Release date: 08-Apr-15

Protein chains

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

Seq: 147 a.a.

Struc: 146 a.a.*

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 77 a.a.

Protein chain

Q9H0F5  (RNF38_HUMAN) -  E3 ubiquitin-protein ligase RNF38 from Homo sapiens

Seq: 515 a.a.

Struc: 75 a.a.

Protein chain

Q9H0F5  (RNF38_HUMAN) -  E3 ubiquitin-protein ligase RNF38 from Homo sapiens

Seq: 515 a.a.

Struc: 70 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, D: 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 2: Chains A, D: 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
• Enzyme class 3: Chains B, E: E.C.?
• Enzyme class 4: Chains C, F: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[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: 10.1016/j.molcel.2015.02.017

Mol Cell 58:297-310 (2015)

PubMed id: 25801170

Activation of a primed RING E3-E2-ubiquitin complex by non-covalent ubiquitin.

L.Buetow, M.Gabrielsen, N.G.Anthony, H.Dou, A.Patel, H.Aitkenhead, G.J.Sibbet, B.O.Smith, D.T.Huang.

ABSTRACT

RING ubiquitin ligases (E3) recruit ubiquitin-conjugate enzymes (E2) charged with ubiquitin (Ub) to catalyze ubiquitination. Non-covalent Ub binding to the backside of certain E2s promotes processive polyUb formation, but the mechanism remains elusive. Here, we show that backside bound Ub (Ub(B)) enhances both RING-independent and RING-dependent UbcH5B-catalyzed donor Ub (Ub(D)) transfer, but with a more prominent effect in RING-dependent transfer. Ub(B) enhances RING E3s' affinities for UbcH5B-Ub, and RING E3-UbcH5B-Ub complex improves Ub(B)'s affinity for UbcH5B. A comparison of the crystal structures of a RING E3, RNF38, bound to UbcH5B-Ub in the absence and presence of Ub(B), together with molecular dynamics simulation and biochemical analyses, suggests Ub(B) restricts the flexibility of UbcH5B's α1 and α1β1 loop. Ub(B) supports E3 function by stabilizing the RING E3-UbcH5B-Ub complex, thereby improving the catalytic efficiency of Ub transfer. Thus, Ub(B) serves as an allosteric activator of RING E3-mediated Ub transfer.