2I5D

Crystal Structure of Human Inosine Triphosphate Pyrophosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure of the orthorhombic form of human inosine triphosphate pyrophosphatase.

Porta, J.Kolar, C.Kozmin, S.G.Pavlov, Y.I.Borgstahl, G.E.O.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 1076-1081

  • DOI: https://doi.org/10.1107/S1744309106041790
  • Primary Citation of Related Structures:  
    2I5D

  • PubMed Abstract: 

    The structure of human inosine triphosphate pyrophosphohydrolase (ITPA) has been determined using diffraction data to 1.6 A resolution. ITPA contributes to the accurate replication of DNA by cleansing cellular dNTP pools of mutagenic nucleotide purine analogs such as dITP or dXTP. A similar high-resolution unpublished structure has been deposited in the Protein Data Bank from a monoclinic and pseudo-merohedrally twinned crystal. Here, cocrystallization of ITPA with a molar ratio of XTP appears to have improved the crystals by eliminating twinning and resulted in an orthorhombic space group. However, there was no evidence for bound XTP in the structure. Comparison with substrate-bound NTPase from a thermophilic organism predicts the movement of residues within helix alpha1, the loop before alpha6 and helix alpha7 to cap off the active site when substrate is bound.


  • Organizational Affiliation

    The Eppley Institute for Research in Cancer and Allied Diseases, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
inosine triphosphate pyrophosphohydrolase197Homo sapiensMutation(s): 0 
Gene Names: ITPAC20orf37
EC: 3.6.1.19 (PDB Primary Data), 3.6.1.9 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY32 (Homo sapiens)
Explore Q9BY32 
Go to UniProtKB:  Q9BY32
PHAROS:  Q9BY32
GTEx:  ENSG00000125877 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BY32
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.126α = 90
b = 104.99β = 90
c = 49.888γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Refinement description