2Q16

Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli.

Savchenko, A.Proudfoot, M.Skarina, T.Singer, A.Litvinova, O.Sanishvili, R.Brown, G.Chirgadze, N.Yakunin, A.F.

(2007) J.Mol.Biol. 374: 1091-1103

  • DOI: 10.1016/j.jmb.2007.10.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inosine triphosphate pyrophosphatases, which are ubiquitous house-cleaning enzymes, hydrolyze noncanonical nucleoside triphosphates (inosine triphosphate (ITP) and xanthosine triphosphate (XTP)) and prevent the incorporation of hypoxanthine or xanthi ...

    Inosine triphosphate pyrophosphatases, which are ubiquitous house-cleaning enzymes, hydrolyze noncanonical nucleoside triphosphates (inosine triphosphate (ITP) and xanthosine triphosphate (XTP)) and prevent the incorporation of hypoxanthine or xanthine into nascent DNA or RNA. Here we present the 1.5-A-resolution crystal structure of the inosine triphosphate pyrophosphatase RdgB from Escherichia coli in a free state and in complex with a substrate (ITP+Ca(2+)) or a product (inosine monophosphate (IMP)). ITP binding to RdgB induced a large displacement of the alpha1 helix, closing the enzyme active site. This positions the conserved Lys13 close to the bridging oxygen between the alpha- and beta-phosphates of the substrate, weakening the P(alpha)-O bond. On the other side of the substrate, the conserved Asp69 is proposed to act as a base coordinating the catalytic water molecule. Our data provide insight into the molecular mechanisms of the substrate selectivity and catalysis of RdgB and other ITPases.


    Organizational Affiliation

    Banting and Best Department of Medical Research and Ontario Center for Structural Proteomics, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HAM1 protein homolog
A, B
219Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: rdgB (yggV)
EC: 3.6.1.66
Find proteins for P52061 (Escherichia coli (strain K12))
Go to UniProtKB:  P52061
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ITT
Query on ITT

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A, B
INOSINE 5'-TRIPHOSPHATE
INOSINE TRIPHOSPHATE
C10 H15 N4 O14 P3
HAEJPQIATWHALX-KQYNXXCUSA-N
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 120.646α = 90.00
b = 120.646β = 90.00
c = 66.562γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data collection
HKL-3000data scaling
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance