1KMD

SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: STRUCTURES WITH THE MINIMAL NOE ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the Vam7p PX domain.

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

(2002) Biochemistry 41: 5956-5962


  • PubMed 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 str ...

    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.


    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar morphogenesis protein VAM7
A
117Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: VAM7
Find proteins for P32912 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32912
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: STRUCTURES WITH THE MINIMAL NOE ENERGY 
  • Olderado: 1KMD Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance