General Information

Database Accession: DI1100037

Name: ABL tyrosine kinase SH3 domain with 3BP-1 peptide

PDB ID: 1abo PDB

Experimental method: X-ray (2.00 Å)

Source organism: Mus musculus

Proof of disorder: Inferred from motif

K_d: 3.40×10^-05 M PubMed

Primary publication of the structure:

Musacchio A, Saraste M, Wilmanns M
High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides.
(1994) Nat. Struct. Biol. 1: 546-51

PMID: 7664083 PubMed

Abstract:

Src-homology 3 (SH3) domains bind to proline-rich motifs in target proteins. We have determined high-resolution crystal structures of the complexes between the SH3 domains of Abl and Fyn tyrosine kinases, and two ten-residue proline-rich peptides derived from the SH3-binding proteins 3BP-1 and 3BP-2. The X-ray data show that the basic mode of binding of both proline-rich peptides is the same. Peptides are bound over their entire length and interact with three major sites on the SH3 molecules by both hydrogen-bonding and van der Waals contacts. Residues 4-10 of the peptide adopt the conformation of a left-handed polyproline helix type II. Binding of the proline at position 2 requires a kink at the non-proline position 3.

Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

SH3 domain binding Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins. GeneOntology

Biological process:

signal transduction The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GeneOntology

positive regulation of catalytic activity Any process that activates or increases the activity of an enzyme. GeneOntology

Cellular component:

cytoplasm All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GeneOntology

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 2 distinct polypeptide molecules

Chains: C, A

Notes: Chains B and D were removed as chains A and C highlight the biologically relevant interaction.

Chain C

Name: SH3 domain-binding protein 1 Disordered Inferred from motif

Source organism: Mus musculus

Length: 10 residues

Sequence:Sequence according to PDB SEQRESAPTMPPPLPP

UniProtKB AC: P55194 (positions: 528-537) UniProt Coverage: 1.7%

UniRef90 AC: UniRef90_P55194 (positions: 485-493) UniRef90

Chain A

Name: Tyrosine-protein kinase ABL1 Ordered

Source organism: Mus musculus

Length: 62 residues

Sequence:Sequence according to PDB SEQRESMNDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNS

UniProtKB AC: P00520 (positions: 60-121) UniProt Coverage: 5.5%

UniRef90 AC: UniRef90_P00520 (positions: 61-121) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Chain C: Disordered Inferred from motif

The protein region involved in the interaction contains the known functional SH3 domin binding linear motif (See more).

Chain A: Ordered

The SH3 domain involved in the interaction is known to adopt a stable structure in isolation (see Pfam domain PF00018). A solved monomeric structure of the domain from a homologous protein is represented by PDB ID 2a36.

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

No related structure was found in the Protein Data Bank.

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