2I5D | pdb_00002i5d

Crystal Structure of Human Inosine Triphosphate Pyrophosphatase

• PDB DOI: https://doi.org/10.2210/pdb2I5D/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-24 Released: 2006-09-05 
• Deposition Author(s): Porta, J.C., Kozmin, S.G., Pavlov, Y.I., Borgstahl, G.E.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.240 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.187 (DCC) 

Starting Model: experimental

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

• PubMed: 17077483 
• DOI: https://doi.org/10.1107/S1744309106041790
• Primary Citation 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 A similar high-resolution unpublished structure has been deposited in the Protein Data Bank from a monoclinic and pseudo-merohedrally twinned crystal.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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.75 kDa 
• Atom Count: 1,888 
• Modeled Residue Count: 195 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
inosine triphosphate pyrophosphohydrolase	A	197	Homo sapiens	Mutation(s): 0  Gene Names: ITPA, C20orf37 EC: 3.6.1.19 (PDB Primary Data), 3.6.1.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY32 (Homo sapiens) Explore Q9BY32  Go to UniProtKB:  Q9BY32
PHAROS:  Q9BY32 GTEx:  ENSG00000125877

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.240 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.187 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.126	α = 90
b = 104.99	β = 90
c = 49.888	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-05 
Deposition Author(s): Porta, J.C., Kozmin, S.G., Pavlov, Y.I., Borgstahl, G.E.O.

Revision History  

• 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