Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.87 kDa 
• Atom Count: 1956 
• Modelled Residue Count: 207 
• Deposited Residue Count: 221 
• Unique protein chains: 1

1K7K

crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli

• DOI: 10.2210/pdb1K7K/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-10-19 Released: 2002-08-14 
• Deposition Author(s): Sanishvili, R., Joachimiak, A., Edwards, A., Savchenko, A., Skarina, T., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.238 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

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

• PubMed: 17976651 
• DOI: 10.1016/j.jmb.2007.10.012
• Primary Citation of Related Structures:  
  2Q16, 2PYU, 1K7K


• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yggV	A	221	Escherichia coli	Mutation(s): 2  EC: 3.6.1.66
UniProt
Find proteins for P52061 (Escherichia coli (strain K12)) Explore P52061  Go to UniProtKB:  P52061

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.238 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.18	α = 90
b = 78.18	β = 90
c = 80.4	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
REFMAC	refinement
d*TREK	data reduction
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-10-19 
• Released Date: 2002-08-14 
Deposition Author(s): Sanishvili, R., Joachimiak, A., Edwards, A., Savchenko, A., Skarina, T., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2002-08-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance