1W2F

Human Inositol (1,4,5)-trisphosphate 3-kinase substituted with selenomethionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a Human Inositol 1,4,5-Trisphosphate 3-Kinase; Substrate Binding Reveals Why It is not a Phosphoinositide 3-Kinase

Gonzalez, B.Schell, M.J.Letcher, A.J.Veprintsev, D.B.Irvine, R.F.Williams, R.L.

(2004) Mol Cell 15: 689

  • DOI: https://doi.org/10.1016/j.molcel.2004.08.004
  • Primary Citation of Related Structures:  
    1W2C, 1W2D, 1W2F

  • PubMed Abstract: 

    Mammalian cells produce a variety of inositol phosphates (InsPs), including Ins(1,4,5)P3 that serves both as a second messenger and as a substrate for inositol polyphosphate kinases (IPKs), which further phosphorylate it. We report the structure of an IPK, the human Ins(1,4,5)P3 3-kinase-A, both free and in complexes with substrates and products. This enzyme catalyzes transfer of a phosphate from ATP to the 3-OH of Ins(1,4,5)P3, and its X-ray crystal structure provides a template for understanding a broad family of InsP kinases. The catalytic domain consists of three lobes. The N and C lobes bind ATP and resemble protein and lipid kinases, despite insignificant sequence similarity. The third lobe binds inositol phosphate and is a unique four-helix insertion in the C lobe. This lobe embraces all of the phosphates of Ins(1,4,5)P3 in a positively charged pocket, explaining the enzyme's substrate specificity and its inability to phosphorylate PtdIns(4,5)P2, the membrane-resident analog of Ins(1,4,5)P3.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INOSITOL-TRISPHOSPHATE 3-KINASE A
A, B
276Homo sapiensMutation(s): 0 
EC: 2.7.1.127
UniProt & NIH Common Fund Data Resources
Find proteins for P23677 (Homo sapiens)
Explore P23677 
Go to UniProtKB:  P23677
PHAROS:  P23677
GTEx:  ENSG00000137825 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23677
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.304α = 90
b = 95.798β = 90
c = 180.352γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary