PDBsum entry 4whv

Ligase/protein binding

PDB id: 4whv

Contents

Protein chains

147 a.a.

136 a.a.

101 a.a.

71 a.a.

Metals

_ZN ×8

PDB id:

4whv

Name:

Ligase/protein binding

Title:

E3 ubiquitin-protein ligase rnf8 in complex with ubiquitin-conjugating enzyme e2 n and polyubiquitin-b

Structure:

Ubiquitin-conjugating enzyme e2 n. Chain: b, e, h, k. Fragment: unp residues 1-152. Synonym: bendless-like ubiquitin-conjugating enzyme,ubc13,ubch13, ubiquitin carrier protein n,ubiquitin-protein ligase n. Engineered: yes. Mutation: yes. E3 ubiquitin-protein ligase rnf8. Chain: c, d, i, j.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ube2n, blu. Expressed in: escherichia coli. Expression_system_taxid: 469008. Gene: rnf8, kiaa0646. Gene: ubb. Expression_system_taxid: 562.

Resolution:

8.30Å R-factor: 0.330 R-free: 0.337

Authors:

C.D.Hodge,R.A.Edwards,J.N.M.Glover

Key ref:

C.D.Hodge et al. (2016). RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment. J Biol Chem, 291, 9396-9410. PubMed id: 26903517 DOI: 10.1074/jbc.M116.715698

Date:

23-Sep-14 Release date: 30-Sep-15

Protein chains

P61088  (UBE2N_HUMAN) -  Ubiquitin-conjugating enzyme E2 N from Homo sapiens

Seq: 152 a.a.

Struc: 147 a.a.*

Protein chains

O76064  (RNF8_HUMAN) -  E3 ubiquitin-protein ligase RNF8 from Homo sapiens

Seq: 485 a.a.

Struc: 136 a.a.

Protein chains

O76064  (RNF8_HUMAN) -  E3 ubiquitin-protein ligase RNF8 from Homo sapiens

Seq: 485 a.a.

Struc: 101 a.a.

Protein chains

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 71 a.a.

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

Enzyme reactions

• Enzyme class 2: Chains A, F, G, L: E.C.?
• Enzyme class 3: Chains B, E, H, K: 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, J: 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.M116.715698

J Biol Chem 291:9396-9410 (2016)

PubMed id: 26903517

RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment.

C.D.Hodge, I.H.Ismail, R.A.Edwards, G.L.Hura, A.T.Xiao, J.A.Tainer, M.J.Hendzel, J.N.Glover.

ABSTRACT

No abstract given.