Crystal structure of a eukaryotic polyphosphate polymerase in complex with pyrophosphate

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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This is version 1.2 of the entry. See complete history


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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar transporter chaperone 4
A, B
295Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: J1345PHM3VTC4YJL012C
Find proteins for P47075 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47075 
Go to UniProtKB:  P47075
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47075
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on POP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B]
H2 O7 P2
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
N [auth B]1,2-ETHANEDIOL
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.44α = 90
b = 100.73β = 90
c = 102.49γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

  • 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
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description