2CAR

Crystal Structure Of Human Inosine Triphosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.153 
  • R-Value Observed: 0.095 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of Human Inosine Triphosphatase. Substrate Binding and Implication of the Inosine Triphosphatase Deficiency Mutation P32T.

Stenmark, P.Kursula, P.Flodin, S.Graslund, S.Landry, R.Nordlund, P.Schuler, H.

(2007) J Biol Chem 282: 3182

  • DOI: 10.1074/jbc.M609838200
  • Primary Citation of Related Structures:  
    2CAR, 2J4E

  • PubMed Abstract: 
  • Inosine triphosphatase (ITPA) is a ubiquitous key regulator of cellular non-canonical nucleotide levels. It breaks down inosine and xanthine nucleotides generated by deamination of purine bases. Its enzymatic action prevents accumulation of ITP and r ...

    Inosine triphosphatase (ITPA) is a ubiquitous key regulator of cellular non-canonical nucleotide levels. It breaks down inosine and xanthine nucleotides generated by deamination of purine bases. Its enzymatic action prevents accumulation of ITP and reduces the risk of incorporation of potentially mutagenic inosine nucleotides into nucleic acids. Here we describe the crystal structure of human ITPA in complex with its prime substrate ITP, as well as the apoenzyme at 2.8 and 1.1A, respectively. These structures show for the first time the site of substrate and Mg2+ coordination as well as the conformational changes accompanying substrate binding in this class of enzymes. Enzyme substrate interactions induce an extensive closure of the nucleotide binding grove, resulting in tight interactions with the base that explain the high substrate specificity of ITPA for inosine and xanthine over the canonical nucleotides. One of the dimer contact sites is made up by a loop that is involved in coordinating the metal ion in the active site. We predict that the ITPA deficiency mutation P32T leads to a shift of this loop that results in a disturbed affinity for nucleotides and/or a reduced catalytic activity in both monomers of the physiological dimer.


    Organizational Affiliation

    Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INOSINE TRIPHOSPHATE PYROPHOSPHATASEAB196Homo sapiensMutation(s): 0 
Gene Names: ITPAC20orf37My049OK/SW-cl.9
EC: 3.6.1.19 (PDB Primary Data), 3.6.1.9 (UniProt)
Find proteins for Q9BY32 (Homo sapiens)
Explore Q9BY32 
Go to UniProtKB:  Q9BY32
NIH Common Fund Data Resources
PHAROS  Q9BY32
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.153 
  • R-Value Observed: 0.095 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.23α = 90
b = 105β = 90.01
c = 50.14γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MOLREPphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2006-01-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Data collection, Other, Refinement description