PDBsum entry 5d1m

Ligase

PDB id: 5d1m

Contents

Protein chains

146 a.a.

110 a.a.

Ligands

OXL

PEG

EDO ×2

Metals

_ZN ×2

Waters ×384

PDB id:

5d1m

Name:

Ligase

Title:

Crystal structure of ubch5b in complex with the ring-u5br fragment of ao7 (p199a)

Structure:

Ubiquitin-conjugating enzyme e2 d2. Chain: a. 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. Engineered: yes. E3 ubiquitin-protein ligase rnf25. Chain: b. Fragment: unp residues 126-258.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ube2d2, pubc1, ubc4, ubc5b, ubch4, ubch5b. Expressed in: escherichia coli. Expression_system_taxid: 469008. Gene: rnf25.

Resolution:

1.58Å R-factor: 0.189 R-free: 0.223

Authors:

Y.-H.Liang,S.Li,A.M.Weissman,X.Ji

Key ref:

S.Li et al. (2015). Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B. J Biol Chem, 290, 30225-30239. PubMed id: 26475854 DOI: 10.1074/jbc.M115.685867

Date:

08-Oct-13 Release date: 28-Oct-15

Protein chain

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

Seq: 147 a.a.

Struc: 146 a.a.

Protein chain

Q96BH1  (RNF25_HUMAN) -  E3 ubiquitin-protein ligase RNF25 from Homo sapiens

Seq: 459 a.a.

Struc: 110 a.a.*

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

Enzyme reactions

• Enzyme class 1: Chain A: 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: Chain A: 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: Chain B: 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: 10.1074/jbc.M115.685867

J Biol Chem 290:30225-30239 (2015)

PubMed id: 26475854

Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B.

S.Li, Y.H.Liang, J.Mariano, M.B.Metzger, D.K.Stringer, V.A.Hristova, J.Li, P.A.Randazzo, Y.C.Tsai, X.Ji, A.M.Weissman.

ABSTRACT

RING proteins constitute the largest class of E3 ubiquitin ligases. Unlike most RINGs, AO7 (RNF25) binds the E2 ubiquitin-conjugating enzyme, UbcH5B (UBE2D2), with strikingly high affinity. We have defined, by co-crystallization, the distinctive means by which AO7 binds UbcH5B. AO7 contains a structurally unique UbcH5B binding region (U5BR) that is connected by an 11-amino acid linker to its RING domain, forming a clamp surrounding the E2. The U5BR interacts extensively with a region of UbcH5B that is distinct from both the active site and the RING-interacting region, referred to as the backside of the E2. An apparent paradox is that the high-affinity binding of the AO7 clamp to UbcH5B, which is dependent on the U5BR, decreases the rate of ubiquitination. We establish that this is a consequence of blocking the stimulatory, non-covalent, binding of ubiquitin to the backside of UbcH5B. Interestingly, when non-covalent backside ubiquitin binding cannot occur, the AO7 clamp now enhances the rate of ubiquitination. The high-affinity binding of the AO7 clamp to UbcH5B has also allowed for the co-crystallization of previously described and functionally important RING mutants at the RING-E2 interface. We show that mutations having marked effects on function only minimally affect the intermolecular interactions between the AO7 RING and UbcH5B, establishing a high degree of complexity in activation through the RING-E2 interface.