PDBsum entry 5c7j

Ligase/signaling protein

PDB id: 5c7j

Contents

Protein chains

373 a.a.

85 a.a.

Waters ×4

PDB id:

5c7j

Name:

Ligase/signaling protein

Title:

Crystal structure of nedd4 with a ub variant

Structure:

E3 ubiquitin-protein ligase nedd4. Chain: a, b. Fragment: hect domain (unp residues 520-900). Synonym: cell proliferation-inducing gene 53 protein,neural precursor cell expressed developmentally down-regulated protein 4,nedd-4. Engineered: yes. Polyubiquitin-c. Chain: c, d. Fragment: unp residues 1-74.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: nedd4, kiaa0093, nedd4-1, pig53. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: v2r. Gene: ubc.

Resolution:

3.00Å R-factor: 0.228 R-free: 0.277

Authors:

J.R.Walker,J.Hu,A.Dong,C.Bountra,A.M.Edwards,C.H.Arrowsmith,Y.Tong, Structural Genomics Consortium (Sgc)

Key ref:

W.Zhang et al. (2016). System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes. Mol Cell, 62, 121-136. PubMed id: 26949039 DOI: 10.1016/j.molcel.2016.02.005

Date:

24-Jun-15 Release date: 16-Mar-16

Protein chains

P46934  (NEDD4_HUMAN) -  E3 ubiquitin-protein ligase NEDD4 from Homo sapiens

Seq: 1319 a.a.

Struc: 373 a.a.

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 85 a.a.*

* PDB and UniProt seqs differ at 18 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.2.3.2.26 - HECT-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
• Enzyme class 3: Chains C, D: 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: 10.1016/j.molcel.2016.02.005

Mol Cell 62:121-136 (2016)

PubMed id: 26949039

System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes.

W.Zhang, K.P.Wu, M.A.Sartori, H.B.Kamadurai, A.Ordureau, C.Jiang, P.Y.Mercredi, R.Murchie, J.Hu, A.Persaud, M.Mukherjee, N.Li, A.Doye, J.R.Walker, Y.Sheng, Z.Hao, Y.Li, K.R.Brown, E.Lemichez, J.Chen, Y.Tong, J.W.Harper, J.Moffat, D.Rotin, B.A.Schulman, S.S.Sidhu.

ABSTRACT

No abstract given.