PDBsum entry 2ydl

Signaling protein

PDB id: 2ydl

Contents

Protein chain

67 a.a.

Waters ×56

PDB id:

2ydl

Name:

Signaling protein

Title:

Crystal structure of sh3c from cin85

Structure:

Sh3 domain-containing kinase-binding protein 1. Chain: a. Fragment: sh3 c, residues 270-328. Synonym: cd2-binding protein 3, cd2bp3, cbl-interacting protein of 85 kda, human src family kinase-binding protein 1, hsb-1, cin85. Engineered: yes. Other_details: third sh3 domain

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.05Å R-factor: 0.207 R-free: 0.252

Authors:

J.Bravo,N.Cardenes

Key ref:

J.L.Ortega Roldan et al. (2013). Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications. Plos One, 8, e73018. PubMed id: 24039852 DOI: 10.1371/journal.pone.0073018

Date:

22-Mar-11 Release date: 28-Mar-12

Protein chain

Q96B97  (SH3K1_HUMAN) -  SH3 domain-containing kinase-binding protein 1 from Homo sapiens

Seq: 665 a.a.

Struc: 67 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1371/journal.pone.0073018

Plos One 8:e73018 (2013)

PubMed id: 24039852

Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications.

J.L.Ortega Roldan, S.Casares, M.Ringkjøbing Jensen, N.Cárdenes, J.Bravo, M.Blackledge, A.I.Azuaga, N.A.van Nuland.

ABSTRACT

SH3 domains constitute a new type of ubiquitin-binding domains. We previously showed that the third SH3 domain (SH3-C) of CD2AP binds ubiquitin in an alternative orientation. We have determined the structure of the complex between first CD2AP SH3 domain and ubiquitin and performed a structural and mutational analysis to decipher the determinants of the SH3-C binding mode to ubiquitin. We found that the Phe-to-Tyr mutation in CD2AP and in the homologous CIN85 SH3-C domain does not abrogate ubiquitin binding, in contrast to previous hypothesis and our findings for the first two CD2AP SH3 domains. The similar alternative binding mode of the SH3-C domains of these related adaptor proteins is characterised by a higher affinity to C-terminal extended ubiquitin molecules. We conclude that CD2AP/CIN85 SH3-C domain interaction with ubiquitin constitutes a new ubiquitin-binding mode involved in a different cellular function and thus changes the previously established mechanism of EGF-dependent CD2AP/CIN85 mono-ubiquitination.