2HAW

Crystal structure of family II Inorganic pyrophosphatase in complex with PNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A trimetal site and substrate distortion in a family II inorganic pyrophosphatase

Fabrichniy, I.P.Lehtio, L.Tammenkoski, M.Zyryanov, A.B.Oksanen, E.Baykov, A.A.Lahti, R.Goldman, A.

(2007) J.Biol.Chem. 282: 1422-1431

  • DOI: 10.1074/jbc.M513161200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the first crystal structures of a family II pyrophosphatase complexed with a substrate analogue, imidodiphosphate (PNP). These provide new insights into the catalytic reaction mechanism of this enzyme family. We were able to capture the sub ...

    We report the first crystal structures of a family II pyrophosphatase complexed with a substrate analogue, imidodiphosphate (PNP). These provide new insights into the catalytic reaction mechanism of this enzyme family. We were able to capture the substrate complex both by fluoride inhibition and by site-directed mutagenesis providing complementary snapshots of the Michaelis complex. Structures of both the fluoride-inhibited wild type and the H98Q variant of the PNP-Bacillus subtilis pyrophosphatase complex show a unique trinuclear metal center. Each metal ion coordinates a terminal oxygen on the electrophilic phosphate and a lone pair on the putative nucleophile, thus placing it in line with the scissile bond without any coordination by protein. The nucleophile moves further away from the electrophilic phosphorus site, to the opposite side of the trimetal plane, upon binding of substrate. In comparison with earlier product complexes, the side chain of Lys296 has swung in and so three positively charged side chains, His98, Lys205 and Lys296, now surround the bridging nitrogen in PNP. Finally, one of the active sites in the wild-type structure appears to show evidence of substrate distortion. Binding to the enzyme may thus strain the substrate and thus enhance the catalytic rate.


    Organizational Affiliation

    Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Biocenter 3, P. O. Box 65, FIN-00014 Helsinki, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Manganese-dependent inorganic pyrophosphatase
A, B
309Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: ppaC
EC: 3.6.1.1
Find proteins for P37487 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P37487
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F
Query on F

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A, B
FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
2PN
Query on 2PN

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A, B
IMIDODIPHOSPHORIC ACID
H5 N O6 P2
GNGSOPFGGKKDQP-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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B
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2PNKd: 12000 nM BINDINGMOAD
MGKd: 12000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.011α = 90.00
b = 115.867β = 90.00
c = 147.874γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
XDSdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2007-10-19
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance