PDBsum entry 4ljp

Ligase

PDB id: 4ljp

Contents

Protein chains

215 a.a.

76 a.a.

Metals

_ZN ×4

Waters ×120

PDB id:

4ljp

Name:

Ligase

Title:

Structure of an active ligase (hoip-h889a)/ubiquitin transfer complex

Structure:

E3 ubiquitin-protein ligase rnf31. Chain: a. Fragment: e3 ligase hoip catalytic core (unp residues 853-1072). Synonym: hoil-1-interacting protein, hoip, ring finger protein 31, zinc in-between-ring-finger ubiquitin-associated domain protein. Engineered: yes. Mutation: yes. Polyubiquitin-c. Chain: b.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rnf31, zibra. Expressed in: escherichia coli. Expression_system_taxid: 511693. Bos taurus. Bovine,cow,domestic cattle,domestic cow. Organism_taxid: 9913

Resolution:

2.15Å R-factor: 0.178 R-free: 0.216

Authors:

R.R.Rana,B.Stieglitz,M.G.Koliopoulos,A.C.Morris-Davies, E.Christodoulou,S.Howell,N.R.Brown,K.Rittinger

Key ref:

B.Stieglitz et al. (2013). Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP. Nature, 503, 422-426. PubMed id: 24141947 DOI: 10.1038/nature12638

Date:

05-Jul-13 Release date: 16-Oct-13

Protein chain

Q96EP0  (RNF31_HUMAN) -  E3 ubiquitin-protein ligase RNF31 from Homo sapiens

Seq: 1072 a.a.

Struc: 215 a.a.*

Protein chain

P63048  (RL40_BOVIN) -  Ubiquitin-ribosomal protein eL40 fusion protein from Bos taurus

Seq: 128 a.a.

Struc: 76 a.a.

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

Enzyme reactions

• Enzyme class 2: Chain A: E.C.2.3.2.31 - RBR-type E3 ubiquitin transferase.
• Reaction: [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N₆-ubiquitinyl-L-lysine
• Enzyme class 3: Chain B: E.C.?

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/nature12638

Nature 503:422-426 (2013)

PubMed id: 24141947

Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP.

B.Stieglitz, R.R.Rana, M.G.Koliopoulos, A.C.Morris-Davies, V.Schaeffer, E.Christodoulou, S.Howell, N.R.Brown, I.Dikic, K.Rittinger.

ABSTRACT

Linear ubiquitin chains are important regulators of cellular signalling pathways that control innate immunity and inflammation through nuclear factor (NF)-κB activation and protection against tumour necrosis factor-α-induced apoptosis. They are synthesized by HOIP, which belongs to the RBR (RING-between-RING) family of E3 ligases and is the catalytic component of LUBAC (linear ubiquitin chain assembly complex), a multisubunit E3 ligase. RBR family members act as RING/HECT hybrids, employing RING1 to recognize ubiquitin-loaded E2 while a conserved cysteine in RING2 subsequently forms a thioester intermediate with the transferred or 'donor' ubiquitin. Here we report the crystal structure of the catalytic core of HOIP in its apo form and in complex with ubiquitin. The carboxy-terminal portion of HOIP adopts a novel fold that, together with a zinc-finger, forms a ubiquitin-binding platform that orients the acceptor ubiquitin and positions its α-amino group for nucleophilic attack on the E3∼ubiquitin thioester. The C-terminal tail of a second ubiquitin molecule is located in close proximity to the catalytic cysteine, providing a unique snapshot of the ubiquitin transfer complex containing both donor and acceptor ubiquitin. These interactions are required for activation of the NF-κB pathway in vivo, and they explain the determinants of linear ubiquitin chain specificity by LUBAC.