PDBsum entry: 1kmd

Endocytosis/exocytosis

PDB id: 1kmd

Contents

Protein chain

117 a.a. *

* Residue conservation analysis

PDB id:

1kmd

Name:

Endocytosis/exocytosis

Title:

Solution structure of the vam7p px domain

Structure:

Vacuolar morphogenesis protein vam7. Chain: a. Fragment: px domain, residues 8-124. Synonym: vam7p. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

NMR struc:

20 models

Authors:

J.Lu,J.Garcia,I.Dulubova,T.C.Sudhof,J.Rizo

Key ref:

J.Lu et al. (2002). Solution structure of the Vam7p PX domain. Biochemistry, 41, 5956-5962. PubMed id: 11993989 DOI: 10.1021/bi020050b

Date:

14-Dec-01 Release date: 12-Jun-02

Protein chain

P32912  (VAM7_YEAST) -  Vacuolar morphogenesis protein 7

Seq: 316 a.a.

Struc: 117 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: cell communication (1 term)
• Biochemical function: protein binding (2 terms)

DOI no: 10.1021/bi020050b

Biochemistry 41:5956-5962 (2002)

PubMed id: 11993989

Solution structure of the Vam7p PX domain.

J.Lu, J.Garcia, I.Dulubova, T.C.Südhof, J.Rizo.

ABSTRACT

PX domains have been recently found to act as phosphoinositide binding modules. In the yeast SNARE protein Vam7p, the PX domain binds to PtdIns(3)P and is required for vacuolar targeting. To gain insight into how PX domains function, the solution structure of the ligand-free Vam7p PX domain has been determined by NMR spectroscopy. The Vam7p PX domain has the same overall alpha/beta fold observed in the structures of the ligand-free p47(phox) PX domain and the PtdIns(3)P-bound p40(phox) PX domain, exhibiting several similarities and differences with these two PX domains. Most striking is the similarity between the Vam7p and p40(phox) PX domains in a subset of secondary structure elements despite the low level of sequence identity between them, suggesting that these elements form a conserved core in the PX domain fold. These similarities and the observation that a putative PtdIns(3)P binding site is already formed in the apo Vam7p PX domains suggest that ligand binding does not induce major conformational changes, contrary to what was previously thought. The proposed ligand binding site of the Vam7p PX domain includes basic side chains from the conserved structural core that also participate in PtdIns(3)P binding to the p40(phox) PX domain, and basic side chains from a variable loop that probably inserts into the membrane. These results indicate that PX domains contain a combination of conserved and variable features that allow them to have a common function and at the same time exhibit distinct specificities, mechanisms of regulation, or modes of interaction with effector molecules.