PDBsum entry 5edv

Ligase/transferase

PDB id: 5edv

Contents

Protein chains

286 a.a.

333 a.a.

145 a.a.

76 a.a.

Metals

_ZN ×16

PDB id:

5edv

Name:

Ligase/transferase

Title:

Structure of the hoip-rbr/ubch5b~ubiquitin transfer complex

Structure:

E3 ubiquitin-protein ligase rnf31. Chain: a, b. Fragment: unp residues 696-1072. Synonym: hoil-1-interacting protein,hoip,ring finger protein 31,zinc in-between-ring-finger ubiquitin-associated domain protein. Engineered: yes. Ubiquitin-conjugating enzyme e2 d2. Chain: c, d, i. Synonym: (e3-independent) e2 ubiquitin-conjugating enzyme d2,e2

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rnf31, zibra. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: ube2d2, pubc1, ubc4, ubc5b, ubch4, ubch5b. Gene: ubb. Expression_system_taxid: 562

Resolution:

3.48Å R-factor: 0.251 R-free: 0.303

Authors:

B.C.Lechtenberg,P.D.Mace,R.Sanishvili,S.J.Riedl

Key ref:

B.C.Lechtenberg et al. (2016). Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation. Nature, 529, 546-550. PubMed id: 26789245 DOI: 10.1038/nature16511

Date:

22-Oct-15 Release date: 20-Jan-16

Protein chain

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

Seq: 1072 a.a.

Struc: 286 a.a.

Protein chain

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

Seq: 1072 a.a.

Struc: 333 a.a.

Protein chains

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

Seq: 147 a.a.

Struc: 145 a.a.*

Protein chains

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 76 a.a.

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

Enzyme reactions

• Enzyme class 2: Chains A, B: 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: Chains C, D, I: 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 4: Chains C, D, I: 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/nature16511

Nature 529:546-550 (2016)

PubMed id: 26789245

Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation.

B.C.Lechtenberg, A.Rajput, R.Sanishvili, M.K.Dobaczewska, C.F.Ware, P.D.Mace, S.J.Riedl.

ABSTRACT

Ubiquitination is a central process affecting all facets of cellular signalling and function. A critical step in ubiquitination is the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to a substrate or a growing ubiquitin chain, which is mediated by E3 ubiquitin ligases. RING-type E3 ligases typically facilitate the transfer of ubiquitin from the E2 directly to the substrate. The RING-between-RING (RBR) family of RING-type E3 ligases, however, breaks this paradigm by forming a covalent intermediate with ubiquitin similarly to HECT-type E3 ligases. The RBR family includes Parkin and HOIP, the central catalytic factor of the LUBAC (linear ubiquitin chain assembly complex). While structural insights into the RBR E3 ligases Parkin and HHARI in their overall auto-inhibited forms are available, no structures exist of intact fully active RBR E3 ligases or any of their complexes. Thus, the RBR mechanism of action has remained largely unknown. Here we present the first structure, to our knowledge, of the fully active human HOIP RBR in its transfer complex with an E2~ubiquitin conjugate, which elucidates the intricate nature of RBR E3 ligases. The active HOIP RBR adopts a conformation markedly different from that of auto-inhibited RBRs. HOIP RBR binds the E2~ubiquitin conjugate in an elongated fashion, with the E2 and E3 catalytic centres ideally aligned for ubiquitin transfer, which structurally both requires and enables a HECT-like mechanism. In addition, three distinct helix-IBR-fold motifs inherent to RBRs form ubiquitin-binding regions that engage the activated ubiquitin of the E2~ubiquitin conjugate and, surprisingly, an additional regulatory ubiquitin molecule. The features uncovered reveal critical states of the HOIP RBR E3 ligase cycle, and comparison with Parkin and HHARI suggests a general mechanism for RBR E3 ligases.