3G3Q

Crystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate polymer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar transporter chaperone 4
A, B
295Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: J1345, PHM3, VTC4, YJL012C
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
GA [auth B],
HA [auth B],
Q [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
D [auth A]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.26α = 90
b = 87.26β = 90
c = 128.53γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description