2J4E

THE ITP COMPLEX OF HUMAN INOSINE TRIPHOSPHATASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


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: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INOSINE TRIPHOSPHATE PYROPHOSPHATASE
A, B, C, D, E
A, B, C, D, E, F, G, H
196Homo sapiensMutation(s): 0 
EC: 3.6.1.19
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ITT
Query on ITT

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
R [auth E]
T [auth F]
I [auth A],
K [auth B],
M [auth C],
R [auth E],
T [auth F],
V [auth G],
X [auth H]
INOSINE 5'-TRIPHOSPHATE
C10 H15 N4 O14 P3
HAEJPQIATWHALX-KQYNXXCUSA-N
IMP
Query on IMP

Download Ideal Coordinates CCD File 
P [auth D]INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
POP
Query on POP

Download Ideal Coordinates CCD File 
O [auth D]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
Q [auth D]
S [auth E]
J [auth A],
L [auth B],
N [auth C],
Q [auth D],
S [auth E],
U [auth F],
W [auth G],
Y [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.998α = 85.12
b = 75.292β = 77.72
c = 110.793γ = 69.19
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-11-20
    Changes: Derived calculations, Source and taxonomy
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description