Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 165.20 kDa 
• Atom Count: 11759 
• Residue Count: 1480 
• Unique protein chains: 1

4A01

Crystal Structure of the H-Translocating Pyrophosphatase

• DOI: 10.2210/pdb4A01/pdb

• Classification: HYDROLASE
• Organism(s): Vigna radiata
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2011-09-07 Released: 2012-03-28 
• Deposition Author(s): Lin, S.-M., Tsai, J.-Y., Hsiao, C.-D., Chiu, C.-L., Pan, R.-L., Sun, Y.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Crystal Structure of a Membrane Embedded H1-Translocating Pyrophosphatase

Lin, S.-M., Tsai, J.-Y., Hsiao, C.-D., Chiu, C.-L., Pan, R.-L., Sun, Y.-J.

(2012) Nature 484: 399

• PubMed: 22456709 
• DOI: 10.1038/nature10963
• Primary Citation of Related Structures:  
  4A01


• PubMed Abstract: 
  

H(+)-translocating pyrophosphatases (H(+)-PPases) are active proton transporters that establish a proton gradient across the endomembrane by means of pyrophosphate (PP(i)) hydrolysis. H(+)-PPases are found primarily as homodimers in the vacuolar membrane of plants and the plasma membrane of several protozoa and prokaryotes. The three-dimensional structure and detailed mechanisms underlying the enzymatic and proton translocation reactions of H(+)-PPases are unclear. Here we report the crystal structure of a Vigna radiata H(+)-PPase (VrH(+)-PPase) in complex with a non-hydrolysable substrate analogue, imidodiphosphate (IDP), at 2.35 Å resolution. Each VrH(+)-PPase subunit consists of an integral membrane domain formed by 16 transmembrane helices. IDP is bound in the cytosolic region of each subunit and trapped by numerous charged residues and five Mg(2+) ions. A previously undescribed proton translocation pathway is formed by six core transmembrane helices. Proton pumping can be initialized by PP(i) hydrolysis, and H(+) is then transported into the vacuolar lumen through a pathway consisting of Arg 242, Asp 294, Lys 742 and Glu 301. We propose a working model of the mechanism for the coupling between proton pumping and PP(i) hydrolysis by H(+)-PPases.

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Organizational Affiliation: 

Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTON PYROPHOSPHATASE	A, B	766	Vigna radiata	Mutation(s): 0  EC: 3.6.1.1 (PDB Primary Data), 7.1.3.1 (UniProt)
Find proteins for P21616 (Vigna radiata var. radiata) Explore P21616  Go to UniProtKB:  P21616

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMU	A, B	DECYL-BETA-D-MALTOPYRANOSIDE C22 H42 O11 WOQQAWHSKSSAGF-WXFJLFHKSA-N
2PN	A, B	IMIDODIPHOSPHORIC ACID H5 N O6 P2 GNGSOPFGGKKDQP-UHFFFAOYSA-N
K	A, B	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.619	α = 90
b = 88.241	β = 125.53
c = 159.105	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-07 
• Released Date: 2012-03-28 
Deposition Author(s): Lin, S.-M., Tsai, J.-Y., Hsiao, C.-D., Chiu, C.-L., Pan, R.-L., Sun, Y.-J.

Revision History 

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Other