PDBsum entry 2k4d

Ligase

PDB id: 2k4d

Contents

Protein chain

83 a.a. *

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

2k4d

Name:

Ligase

Title:

E2-c-cbl recognition is necessary but not sufficient for ubiquitination activity

Structure:

E3 ubiquitin-protein ligase cbl. Chain: a. Fragment: ring domain, residues 358-437. Synonym: signal transduction protein cbl, proto-oncogenE C-cbl, casitas b-lineage lymphoma proto-oncogene, ring finger protein 55. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cbl, cbl2, rnf55. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

A.Huang,R.N.De Jong,H.Wienk,S.G.Winkler,H.T.M.Timmers,R.Boelens

Key ref:

A.Huang et al. (2009). E2-c-Cbl recognition is necessary but not sufficient for ubiquitination activity. J Mol Biol, 385, 507-519. PubMed id: 18996392 DOI: 10.1016/j.jmb.2008.10.044

Date:

06-Jun-08 Release date: 20-Jan-09

Protein chain

P22681  (CBL_HUMAN) -  E3 ubiquitin-protein ligase CBL from Homo sapiens

Seq: 906 a.a.

Struc: 83 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: 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

DOI no: 10.1016/j.jmb.2008.10.044

J Mol Biol 385:507-519 (2009)

PubMed id: 18996392

E2-c-Cbl recognition is necessary but not sufficient for ubiquitination activity.

A.Huang, R.N.de Jong, H.Wienk, G.S.Winkler, H.T.Timmers, R.Boelens.

ABSTRACT

The E2 ubiquitin-conjugating enzymes UbcH7 and UbcH5B both show specific binding to the RING (really interesting new gene) domain of the E3 ubiquitin-protein ligase c-Cbl, but UbcH7 hardly supports ubiquitination of c-Cbl and substrate in a reconstituted system. Here, we found that neither structural changes nor subtle differences in the E2-E3 interaction surface are possible explanations for the functional specificity of UbcH5B and UbcH7 in their interaction with c-Cbl. The quick transfer of ubiquitin from the UbcH5B-Ub thioester to c-Cbl or other ubiquitin acceptors suggests that UbcH5B might functionally be a relatively pliable E2 enzyme. In contrast, the UbcH7-Ub thioester is too stable to transfer ubiquitin under our assay conditions, indicating that UbcH7 might be a more specific E2 enzyme. Our results imply that the interaction specificity between c-Cbl and E2 is required but not sufficient for transfer of ubiquitin to potential targets.

Selected figure(s)

Figure 3.
Fig. 3. NMR solution structure of c-Cbl linker and RING domain (358–437). (a) Free NMR solution structure of c-Cbl linker and RING domain. (b) The solution structure of free c-Cbl RING finger domain (lime) superimposed on the crystal structure of the c-Cbl RING finger domain (gray) complexed to UbcH7 (PDB ID: 1FBV).

Figure 7.
Fig. 7. Comparison of surface properties of UbcH5B and UbcH7. (a) Top: electrostatic surface potential of UbcH5B was calculated using the APBS plugin to PyMOL and indicated as a charge scale from negative (red) to positive (blue). Bottom: surface representation of interaction sites on UbcH5B. The catalytic site (yellow), E2 vert, similar Ub binding interface (cyan), E3 binding interface (orange), and the noncovalent Ub-binding interface on UbcH5B (green) are indicated. (b) UbcH7 electrostatic surface potential (top) and interaction sites (bottom), colored as indicated under (a).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 385, 507-519) copyright 2009.

Figures were selected by an automated process.