1KT9

Crystal Structure of C. elegans Ap4A Hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms

Bailey, S.Sedelnikova, S.E.Blackburn, G.M.Abdelghany, H.M.Baker, P.J.McLennan, A.G.Rafferty, J.B.

(2002) Structure 10: 589-600

  • DOI: 10.1016/s0969-2126(02)00746-3
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of C. elegans Ap(4)A hydrolase has been determined for the free enzyme and a binary complex at 2.0 A and 1.8 A, respectively. Ap(4)A hydrolase has a key role in regulating the intracellular Ap(4)A levels and hence potentially th ...

    The crystal structure of C. elegans Ap(4)A hydrolase has been determined for the free enzyme and a binary complex at 2.0 A and 1.8 A, respectively. Ap(4)A hydrolase has a key role in regulating the intracellular Ap(4)A levels and hence potentially the cellular response to metabolic stress and/or differentiation and apoptosis via the Ap(3)A/Ap(4)A ratio. The structures reveal that the enzyme has the mixed alpha/beta fold of the Nudix family and also show how the enzyme binds and locates its substrate with respect to the catalytic machinery of the Nudix motif. These results suggest how the enzyme can catalyze the hydrolysis of a range of related dinucleoside tetraphosphate, but not triphosphate, compounds through precise orientation of key elements of the substrate.


    Related Citations: 
    • Cloning, characterisation and crystallisation of a diadenosine 5',5"'-P(1),P(4)-tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans.
      Abdelghany, H.M., Gasmi, L., Cartwright, J.L., Bailey, S., Rafferty, J.B., McLennan, A.G.
      (2001) Biochim Biophys Acta 1550: 27

    Organizational Affiliation

    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diadenosine Tetraphosphate HydrolaseA138Caenorhabditis elegansMutation(s): 0 
Gene Names: Y37H9A.6ndx-4
EC: 3.6.1.17 (PDB Primary Data), 3.6.1 (UniProt)
Find proteins for Q9U2M7 (Caenorhabditis elegans)
Explore Q9U2M7 
Go to UniProtKB:  Q9U2M7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.794α = 90
b = 72.934β = 90
c = 61.046γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance