PDBsum entry 4ic3

Ligase

PDB id: 4ic3

Contents

Protein chains

63 a.a.

Metals

_NI ×2

_ZN ×4

Waters ×94

PDB id:

4ic3

Name:

Ligase

Title:

Crystal structure of the f495l mutant xiap ring domain

Structure:

E3 ubiquitin-protein ligase xiap. Chain: a, b. Fragment: ring domain, unp residues 429-497. Synonym: baculoviral iap repeat-containing protein 4, iap-like protein, ilp, hilp, inhibitor of apoptosis protein 3, iap-3, hiap-3, hiap3, x-linked inhibitor of apoptosis protein, x-linked iap. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: api3, bir4, iap3, xiap. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.78Å R-factor: 0.178 R-free: 0.222

Authors:

Y.Nakatani,C.L.Day

Key ref:

Y.Nakatani et al. (2013). Regulation of ubiquitin transfer by XIAP, a dimeric RING E3 ligase. Biochem J, 450, 629-638. PubMed id: 23259674 DOI: 10.1042/BJ20121702

Date:

09-Dec-12 Release date: 19-Dec-12

Protein chains

P98170  (XIAP_HUMAN) -  E3 ubiquitin-protein ligase XIAP from Homo sapiens

Seq: 497 a.a.

Struc: 63 a.a.*

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

Enzyme reactions

• Enzyme class: 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

DOI no: 10.1042/BJ20121702

Biochem J 450:629-638 (2013)

PubMed id: 23259674

Regulation of ubiquitin transfer by XIAP, a dimeric RING E3 ligase.

Y.Nakatani, T.Kleffmann, K.Linke, S.M.Condon, M.G.Hinds, C.L.Day.

ABSTRACT

RING domains of E3 ligases promote transfer of Ub (ubiquitin) from the E2~Ub conjugate to target proteins. In many cases interaction of the E2~Ub conjugate with the RING domain requires its prior dimerization. Using cross-linking experiments we show that E2 conjugated ubiquitin contacts the RING homodimer interface of the IAP (inhibitor of apoptosis) proteins, XIAP (X-linked IAP) and cIAP (cellular IAP) 2. Structural and biochemical analysis of the XIAP RING dimer shows that an aromatic residue at the dimer interface is required for E2~Ub binding and Ub transfer. Mutation of the aromatic residue abolishes Ub transfer, but not interaction with Ub. This indicates that nuleophilic attack on the thioester bond depends on precise contacts between Ub and the RING domain. RING dimerization is a critical activating step for the cIAP proteins; however, our analysis shows that the RING domain of XIAP forms a stable dimer and its E3 ligase activity does not require an activation step.