PDBsum entry 2oo9

Ligase

PDB id: 2oo9

Contents

Protein chains

46 a.a. *

41 a.a. *

Waters ×73

* Residue conservation analysis

PDB id:

2oo9

Name:

Ligase

Title:

Crystal structure of the uba domain from human c-cbl ubiquitin ligase

Structure:

E3 ubiquitin-protein ligase cbl. Chain: a, b, c. Fragment: uba domain. 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 bl21. Expression_system_taxid: 511693.

Resolution:

2.10Å R-factor: 0.218 R-free: 0.260

Authors:

G.Kozlov,K.Gehring

Key ref:

G.Kozlov et al. (2007). Structural basis for UBA-mediated dimerization of c-Cbl ubiquitin ligase. J Biol Chem, 282, 27547-27555. PubMed id: 17635922 DOI: 10.1074/jbc.M703333200

Date:

25-Jan-07 Release date: 06-Feb-07

Protein chains

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

Seq: 906 a.a.

Struc: 46 a.a.*

Protein chain

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

Seq: 906 a.a.

Struc: 41 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C: 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: 10.1074/jbc.M703333200

J Biol Chem 282:27547-27555 (2007)

PubMed id: 17635922

Structural basis for UBA-mediated dimerization of c-Cbl ubiquitin ligase.

G.Kozlov, P.Peschard, B.Zimmerman, T.Lin, T.Moldoveanu, N.Mansur-Azzam, K.Gehring, M.Park.

ABSTRACT

Ligand-induced down-regulation by the ubiquitin-protein ligases, c-Cbl and Cbl-b, controls signaling downstream from many receptor-tyrosine kinases (RTK). Cbl proteins bind to phosphotyrosine residues on activated RTKs to affect ligand-dependent ubiquitylation of these receptors targeting them for degradation in the lysosome. Both c-Cbl and Cbl-b contain a ubiquitin-associated (UBA) domain, which is important for Cbl dimerization and tyrosine phosphorylation; however, the mechanism of UBA-mediated dimerization and its requirement for Cbl biological activity is unclear. Here, we report the crystal structure of the UBA domain of c-Cbl refined to 2.1-A resolution. The structure reveals the protein is a symmetric dimer tightly packed along a large hydrophobic surface formed by helices 2 and 3. NMR chemical shift mapping reveals heterodimerization can occur with the related Cbl-b UBA domain via the same surface employed for homodimerization. Disruption of c-Cbl dimerization by site-directed mutagenesis impairs c-Cbl phosphorylation following activation of the Met/hepatocyte growth factor RTK and c-Cbl-dependent ubiquitination of Met. This provides direct evidence for a role of Cbl dimerization in terminating signaling following activation of RTKs.

Selected figure(s)

Figure 3.
Structure of the UBA domain from c-Cbl.A, ribbon representation of the UBA dimer. One protomer is shown in magenta, another is in yellow. Helices are labeled as α1-α3 in one protomer and α1′-α3′ in another protomer. B, hydrophobic core of the c-Cbl UBA domain. Respective residues are shown as sticks and labeled. C, the enlarged view of the hydrophobic dimer interface. Key residues in the dimer are shown as sticks and labeled. D, intermolecular hydrogen bonds (dotted line) involving Lys^876 and Glu^894 from both c-Cbl UBA protomers.

Figure 6.
Comparison of protomer arrangement in the structures of (A) c-Cbl UBA domain, (B) Cbl-b UBA domain (PDB code 2OOA), and (C) dimerization domain of doublesex protein (PDB code 1ZV1). Color changes from NH[2] terminus (blue) to COOH terminus (red).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 27547-27555) copyright 2007.

Figures were selected by an automated process.