PDBsum entry: 1ur6

Ligase

PDB id: 1ur6

Contents

Protein chains

147 a.a. *

52 a.a. *

Metals

_ZN ×2

* Residue conservation analysis

Theoretical model

PDB id:

1ur6

Name:

Ligase

Title:

Nmr based structural model of the ubch5b-cnot4 complex

Structure:

Ubiquitin-conjugating enzyme e2-17 kda 2. Chain: a. Synonym: ubch5b, ubiquitin carrier protein, e2(17)kb 2. Potential transcriptional repressor not4hp. Chain: b. Fragment: ring finger, residues 12-63. Synonym: cnot4, not4h

Source:

Homo sapiens. Human. Organism_taxid: 9606. Organism_taxid: 9606

NMR struc:

5 models

Authors:

C.Dominguez,A.M.J.J.Bonvin,G.S.Winkler,F.M.A.Van Schaik, H.Th.M.Timmers,R.Boelens

Key ref:

C.Dominguez et al. (2004). Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. Structure, 12, 633-644. PubMed id: 15062086 DOI: 10.1016/j.str.2004.03.004

Date:

27-Oct-03 Release date: 07-May-04

Protein chain

P62837  (UB2D2_HUMAN) -  Ubiquitin-conjugating enzyme E2 D2

Seq: 147 a.a.

Struc: 147 a.a.

Protein chain

O95628  (CNOT4_HUMAN) -  CCR4-NOT transcription complex subunit 4

Seq: 575 a.a.

Struc: 52 a.a.

Enzyme reactions

• Enzyme class: Chain A: E.C.6.3.2.19 - Ubiquitin--protein ligase.
• Reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of protein metabolic process (6 terms)
• Biochemical function: nucleotide binding (7 terms)

reference

DOI no: 10.1016/j.str.2004.03.004

Structure 12:633-644 (2004)

PubMed id: 15062086

Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.

C.Dominguez, A.M.Bonvin, G.S.Winkler, F.M.van Schaik, H.T.Timmers, R.Boelens.

ABSTRACT

The protein CNOT4 possesses an N-terminal RING finger domain that acts as an E3 ubiquitin ligase and specifically interacts with UbcH5B, a ubiquitin-conjugating enzyme. The structure of the CNOT4 RING domain has been solved and the amino acids important for the binding to UbcH5B have been mapped. Here, the residues of UbcH5B important for the binding to CNOT4 RING domain were identified by NMR chemical shift perturbation experiments, and these data were used to generate structural models of the complex with the program HADDOCK. Together with the NMR data, additional biochemical data were included in a second docking, and comparisons of the resulting model with the structure of the c-Cbl/UbcH7 complex reveal some significant differences, notably at specific residues, and give structural insights into the E2/E3 specificity.

Selected figure(s)

Figure 5.
Figure 5. Comparison between the UbcH5B/CNOT4 Docking Model and the c-Cbl/UbcH7 Crystal Structure(A) The orientation of the RING domain compared to the E2 enzyme is similar in both complexes. UbcH5B and UbcH7 are colored blue and purple, CNOT4 and c-Cbl RING domains are colored red and yellow, and the other domains of c-Cbl are colored orange.(B) The helix a1 of UbcH5B makes many contacts with the CNOT4 RING domain, whereas the helix a1 of UbcH7 interact mainly with the linker region of c-Cbl. Residues 1, 4, 5, and 8 of UbcH5B and 5, 9, 12, and 16 of UbcH7 are labeled in blue. Residues 13, 16, 18, and 19 of CNOT4 and 385 of c-Cbl RING are labeled in red. Residues 366, 369, 370, and 373 corresponding to the linker region of c-Cbl are labeled in orange.(C) In the L1 loop of UbcH5B, residue Lys63 interacts with CNOT4 Asp48 and Glu49, whereas the corresponding and conserved residue of UbcH7 (Lys64) is not in contact with c-Cbl. Figures have been generated with the programs Molscript (Kraulis, 1991) and Raster3D (Merrit and Murphy, 1994).

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 633-644) copyright 2004.

Figure was selected by an automated process.