Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 43.23 kDa 
• Atom Count: 3905 
• Modelled Residue Count: 390 
• Deposited Residue Count: 392 
• Unique protein chains: 1

2CAR

Crystal Structure Of Human Inosine Triphosphatase

• PDB DOI: 10.2210/pdb2CAR/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-12-22 Released: 2006-01-04 
• Deposition Author(s): Stenmark, P., Kursula, P., Arrowsmith, C., Berglund, H., Edwards, A., Ehn, M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Hogbom, M., Holmberg Schiavone, L., Kotenyova, T., Nilsson-Ehle, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Schuler, H., Sundstrom, M., Thorsell, A.G., van den Berg, S., Weigelt, J., Nordlund, P.

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Experimental Data Snapshot

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

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

• PubMed: 17138556 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INOSINE TRIPHOSPHATE PYROPHOSPHATASE	A, B	196	Homo sapiens	Mutation(s): 0  Gene Names: ITPA, C20orf37, My049, OK/SW-cl.9 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

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 = 31.23	α = 90
b = 105	β = 90.01
c = 50.14	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
MOLREP	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-22 
• Released Date: 2006-01-04 
Deposition Author(s): Stenmark, P., Kursula, P., Arrowsmith, C., Berglund, H., Edwards, A., Ehn, M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Hogbom, M., Holmberg Schiavone, L., Kotenyova, T., Nilsson-Ehle, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Schuler, H., Sundstrom, M., Thorsell, A.G., van den Berg, S., Weigelt, J., Nordlund, P.

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