1WGJ

STRUCTURE OF INORGANIC PYROPHOSPHATASE

• PDB DOI: https://doi.org/10.2210/pdb1WGJ/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-10-24 Released: 1997-11-19 
• Deposition Author(s): Heikinheimo, P., Lehtonen, J., Goldman, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 

Literature

The structural basis for pyrophosphatase catalysis.

Heikinheimo, P., Lehtonen, J., Baykov, A., Lahti, R., Cooperman, B.S., Goldman, A.

(1996) Structure 4: 1491-1508

• PubMed: 8994974 
• DOI: https://doi.org/10.1016/s0969-2126(96)00155-4
• Primary Citation of Related Structures:  
  1WGI, 1WGJ


• PubMed Abstract: 
  

  Soluble inorganic pyrophosphatase (PPase), an essential enzyme central to phosphorus metabolism, catalyzes the hydrolysis of the phosphoanhydride bond in inorganic pyrophosphate. Catalysis requires divalent metal ions which affect the apparent pKas of the essential general acid and base on the enzyme, and the pKa of the substrate. Three to five metal ions are required for maximal activity, depending on pH and enzyme source. A detailed understanding of catalysis would aid both in understanding the nature of biological mechanisms of phosphoryl transfer, and in understanding the role of divalent cations. Without a high-resolution complex structure such a model has previously been unobtainable.

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Organizational Affiliation: 

Turku Centre for Biotechnology, Finland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.27 kDa 
• Atom Count: 4,829 
• Modelled Residue Count: 564 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INORGANIC PYROPHOSPHATASE	A, B	286	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PPA1 EC: 3.6.1.1
UniProt
Find proteins for P00817 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00817  Go to UniProtKB:  P00817

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth A], M [auth B], N [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.1	α = 90
b = 103.8	β = 90
c = 117.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-11-19 
Deposition Author(s): Heikinheimo, P., Lehtonen, J., Goldman, A.

Revision History  

• Version 1.0: 1997-11-19
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other