1JKN

Solution Structure of the Nudix Enzyme Diadenosine Tetraphosphate Hydrolase from Lupinus angustifolius Complexed with ATP


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 30 
  • Selection Criteria: structures with favorable non-bond energy, structures with the least restraint violations, target function 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of Ap(4)A hydrolase complexed with ATP-MgF(x) reveals the basis of substrate binding.

Fletcher, J.I.Swarbrick, J.D.Maksel, D.Gayler, K.R.Gooley, P.R.

(2002) Structure 10: 205-213


  • PubMed Abstract: 
  • Ap(4)A hydrolases are Nudix enzymes that regulate intracellular dinucleoside polyphosphate concentrations, implicating them in a range of biological events, including heat shock and metabolic stress. We have demonstrated that ATP x MgF(x) can be used ...

    Ap(4)A hydrolases are Nudix enzymes that regulate intracellular dinucleoside polyphosphate concentrations, implicating them in a range of biological events, including heat shock and metabolic stress. We have demonstrated that ATP x MgF(x) can be used to mimic substrates in the binding site of Ap(4)A hydrolase from Lupinus angustifolius and that, unlike previous substrate analogs, it is in slow exchange with the enzyme. The three-dimensional structure of the enzyme complexed with ATP x MgF(x) was solved and shows significant conformational changes. The substrate binding site of L. angustifolius Ap(4)A hydrolase differs markedly from the two previously published Nudix enzymes, ADP-ribose pyrophosphatase and MutT, despite their common fold and the conservation of active site residues. The majority of residues involved in substrate binding are conserved in asymmetrical Ap(4)A hydrolases from pathogenic bacteria, but are absent in their human counterparts, suggesting that it might be possible to generate compounds that target bacterial, but not human, Ap(4)A hydrolases.


    Related Citations: 
    • The Three-dimensional Structure of the Nudix Enzyme Diadenosine Tetraphosphate Hydrolase from Lupinus angustifolius L
      Swarbrick, J.D.,Bashtannyk, T.,Maksel, D.,Zhang, X.-R.,Blackburn, G.M.,Gayler, K.R.,Gooley, P.R.
      (2000) J.Mol.Biol. 302: 1165


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Melbourne, Victoria 3010, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
diadenosine 5',5'''-P1,P4-tetraphosphate hydrolase
A
165Lupinus angustifoliusMutation(s): 0 
EC: 3.6.1.17
Find proteins for O04841 (Lupinus angustifolius)
Go to UniProtKB:  O04841
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 30 
  • Selection Criteria: structures with favorable non-bond energy, structures with the least restraint violations, target function 
  • Olderado: 1JKN Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance