1F3Y

SOLUTION STRUCTURE OF THE NUDIX ENZYME DIADENOSINE TETRAPHOSPHATE HYDROLASE FROM LUPINUS ANGUSTIFOLIUS L.


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 25 
  • 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 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: 1165-1177

  • DOI: 10.1006/jmbi.2000.4085

  • PubMed Abstract: 
  • The solution structure of diadenosine 5',5'''-P1,P4-tetraphosphate hydrolase from Lupinus angustifolius L., an enzyme of the Nudix family, has been determined by heteronuclear NMR, using a torsion angle dynamics/simulated annealing protocol based on ...

    The solution structure of diadenosine 5',5'''-P1,P4-tetraphosphate hydrolase from Lupinus angustifolius L., an enzyme of the Nudix family, has been determined by heteronuclear NMR, using a torsion angle dynamics/simulated annealing protocol based on approximately 12 interresidue NOEs per residue. The structure represents the first Ap4A hydrolase to be determined, and sequence homology suggests that other members will have the same fold. The family of structures shows a well-defined fold comprised of a central four-stranded mixed beta-sheet, a two-stranded antiparallel beta-sheet and three helices (alphaI, alphaIII, alphaIV). The root-mean-squared deviation for the backbone (C',O,N,Calpha) of the rigid parts (residues 9 to 75, 97 to 115, 125 to 160) of the protein is 0.32 A. Several regions, however, show lower definition, particularly an isolated helix (alphaII) that connects two strands of the central sheet. This poor definition is mainly due to a lack of long-range NOEs between alphaII and other parts of the protein. Mapping conserved residues outside of the Nudix signature and those sensitive to an Ap4A analogue suggests that the adenosine-ribose moiety of the substrate binds into a large cleft above the four-stranded beta-sheet. Four conserved glutamate residues (Glu55, Glu58, Glu59 and Glu125) form a cluster that most likely ligates an essential magnesium ion, however, Gly41 also an expected magnesium ligand, is distant from this cluster.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIADENOSINE 5',5'''-P1,P4-TETRAPHOSPHATE HYDROLASE
A
165Lupinus angustifoliusMutation(s): 4 
EC: 3.6.1.17
Find proteins for O04841 (Lupinus angustifolius)
Go to UniProtKB:  O04841
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 25 
  • Selection Criteria: structures with favorable non-bond energy,structures with the least restraint violations,target function 
  • Olderado: 1F3Y Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance