3G3R

Crystal structure of a eukaryotic polyphosphate polymerase in complex with AppNHp-Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Catalytic core of a membrane-associated eukaryotic polyphosphate polymerase.

Hothorn, M.Neumann, H.Lenherr, E.D.Wehner, M.Rybin, V.Hassa, P.O.Uttenweiler, A.Reinhardt, M.Schmidt, A.Seiler, J.Ladurner, A.G.Herrmann, C.Scheffzek, K.Mayer, A.

(2009) Science 324: 513-516

  • DOI: 10.1126/science.1168120
  • Primary Citation of Related Structures:  
    3G3O, 3G3Q, 3G3R, 3G3T, 3G3U

  • PubMed Abstract: 
  • Polyphosphate (polyP) occurs ubiquitously in cells, but its functions are poorly understood and its synthesis has only been characterized in bacteria. Using x-ray crystallography, we identified a eukaryotic polyphosphate polymerase within the membrane-integral vacuolar transporter chaperone (VTC) complex ...

    Polyphosphate (polyP) occurs ubiquitously in cells, but its functions are poorly understood and its synthesis has only been characterized in bacteria. Using x-ray crystallography, we identified a eukaryotic polyphosphate polymerase within the membrane-integral vacuolar transporter chaperone (VTC) complex. A 2.6 angstrom crystal structure of the catalytic domain grown in the presence of adenosine triphosphate (ATP) reveals polyP winding through a tunnel-shaped pocket. Nucleotide- and phosphate-bound structures suggest that the enzyme functions by metal-assisted cleavage of the ATP gamma-phosphate, which is then in-line transferred to an acceptor phosphate to form polyP chains. Mutational analysis of the transmembrane domain indicates that VTC may integrate cytoplasmic polymer synthesis with polyP membrane translocation. Identification of the polyP-synthesizing enzyme opens the way to determine the functions of polyP in lower eukaryotes.


    Organizational Affiliation

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar transporter chaperone 4A, B295Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: J1345PHM3VTC4YJL012C
UniProt
Find proteins for P47075 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47075 
Go to UniProtKB:  P47075
Protein Feature View
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ANPKd:  330   nM  Binding MOAD
ANPKd :  330   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.26α = 90
b = 100.97β = 90
c = 102.37γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-02-02 
  • Released Date: 2009-05-05 
  • Deposition Author(s): Hothorn, M.

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance