PDBsum entry 2rpn

Structural protein

PDB id: 2rpn

Contents

Protein chains

59 a.a. *

18 a.a. *

* Residue conservation analysis

PDB id:

2rpn

Name:

Structural protein

Title:

A crucial role for high intrinsic specificity in the function of yeast sh3 domains

Structure:

Actin-binding protein. Chain: a. Fragment: sh3 domain. Synonym: abp1p. Engineered: yes. Actin-regulating kinase 1. Chain: b. Fragment: unp residues 605-621. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

E.J.Stollar,B.Garcia,A.Chong,J.Forman-Kay,A.Davidson

Key ref:

E.J.Stollar et al. (2009). Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p. J Biol Chem, 284, 26918-26927. PubMed id: 19590096

Date:

12-Jun-08 Release date: 16-Jun-09

Protein chain

P15891  (ABP1_YEAST) -  Actin-binding protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 592 a.a.

Struc: 59 a.a.*

Protein chain

P53974  (ARK1_YEAST) -  Actin-regulating kinase 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 638 a.a.

Struc: 18 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain A: E.C.?
• Enzyme class 3: Chain B: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

J Biol Chem 284:26918-26927 (2009)

PubMed id: 19590096

Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p.

E.J.Stollar, B.Garcia, P.A.Chong, A.Rath, H.Lin, J.D.Forman-Kay, A.R.Davidson.

ABSTRACT

SH3 domains, which are among the most frequently occurring protein interaction modules in nature, bind to peptide targets ranging in length from 7 to more than 25 residues. Although the bulk of studies on the peptide binding properties of SH3 domains have focused on interactions with relatively short peptides (less than 10 residues), a number of domains have been recently shown to require much longer sequences for optimal binding affinity. To gain greater insight into the binding mechanism and biological importance of interactions between an SH3 domain and extended peptide sequences, we have investigated interactions of the yeast Abp1p SH3 domain (AbpSH3) with several physiologically relevant 17-residue target peptide sequences. To obtain a molecular model for AbpSH3 interactions, we solved the structure of the AbpSH3 bound to a target peptide from the yeast actin patch kinase, Ark1p. Peptide target complexes from binding partners Scp1p and Sjl2p were also characterized, revealing that the AbpSH3 uses a common extended interface for interaction with these peptides, despite K(d) values for these peptides ranging from 0.3 to 6 mum. Mutagenesis studies demonstrated that residues across the whole 17-residue binding site are important both for maximal in vitro binding affinity and for in vivo function. Sequence conservation analysis revealed that both the AbpSH3 and its extended target sequences are highly conserved across diverse fungal species as well as higher eukaryotes. Our data imply that the AbpSH3 must bind extended target sites to function efficiently inside the cell.