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 
  • R-Value Observed: 0.167 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1074/jbc.M513161200
  • Primary Citation of Related Structures:  
    2HAW, 2IW4

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Manganese-dependent inorganic pyrophosphatase
A, B
309Bacillus subtilisMutation(s): 0 
EC: 3.6.1.1
UniProt
Find proteins for P37487 (Bacillus subtilis (strain 168))
Explore P37487 
Go to UniProtKB:  P37487
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37487
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
T [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

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K [auth A],
U [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
2PN
Query on 2PN

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L [auth A],
V [auth B]
IMIDODIPHOSPHORIC ACID
H5 N O6 P2
GNGSOPFGGKKDQP-UHFFFAOYSA-N
SO4
Query on SO4

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H [auth A],
I [auth A],
R [auth B],
S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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W [auth B],
X [auth B],
Y [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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C [auth A]
D [auth A]
E [auth A]
F [auth A]
M [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
F
Query on F

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G [auth A],
Q [auth B]
FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
MG PDBBind:  2HAW Kd: 1.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.011α = 90
b = 115.867β = 90
c = 147.874γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2007-10-19
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description