Crystal structure of Inositol Phosphate Multikinase Ipk2 in complex with ADP and Mn2+ from S. cerevisiae

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Crystal structure of inositol phosphate multikinase 2 and implications for substrate specificity.

Holmes, W.Jogl, G.

(2006) J Biol Chem 281: 38109-38116

  • DOI: https://doi.org/10.1074/jbc.M606883200
  • Primary Citation of Related Structures:  
    2IEW, 2IF8

  • PubMed Abstract: 

    Inositol polyphosphates perform essential functions as second messengers in eukaryotic cells, and their cellular levels are regulated by inositol phosphate kinases. Most of these enzymes belong to the inositol phosphate kinase superfamily, which consists of three subgroups, inositol 3-kinases, inositol phosphate multikinases, and inositol hexakisphosphate kinases. Family members share several strictly conserved signature motifs and are expected to have the same backbone fold, despite very limited overall amino acid sequence identity. Sequence differences are expected to play important roles in defining the different substrate selectivity of these enzymes. To investigate the structural basis for substrate specificity, we have determined the crystal structure of the yeast inositol phosphate multikinase Ipk2 in the apoform and in a complex with ADP and Mn(2+) at up to 2.0A resolution. The overall structure of Ipk2 is related to inositol trisphosphate 3-kinase. The ATP binding site is similar in both enzymes; however, the inositol binding domain is significantly smaller in Ipk2. Replacement of critical side chains in the inositolbinding site suggests how modification of substrate recognition motifs determines enzymatic substrate preference and catalysis.

  • Organizational Affiliation

    Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol polyphosphate multikinase
A, B
363Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: IPK2
Find proteins for P07250 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07250 
Go to UniProtKB:  P07250
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07250
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.996α = 90
b = 184.996β = 90
c = 49.998γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description