2PGF

Crystal structure of adenosine deaminase from Plasmodium vivax in complex with adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity.

Larson, E.T.Deng, W.Krumm, B.E.Napuli, A.Mueller, N.Van Voorhis, W.C.Buckner, F.S.Fan, E.Lauricella, A.DeTitta, G.Luft, J.Zucker, F.Hol, W.G.Verlinde, C.L.Merritt, E.A.

(2008) J.Mol.Biol. 381: 975-988

  • DOI: 10.1016/j.jmb.2008.06.048
  • Primary Citation of Related Structures:  2PGR, 2QVN

  • PubMed Abstract: 
  • Plasmodium and other apicomplexan parasites are deficient in purine biosynthesis, relying instead on the salvage of purines from their host environment. Therefore, interference with the purine salvage pathway is an attractive therapeutic target. The ...

    Plasmodium and other apicomplexan parasites are deficient in purine biosynthesis, relying instead on the salvage of purines from their host environment. Therefore, interference with the purine salvage pathway is an attractive therapeutic target. The plasmodial enzyme adenosine deaminase (ADA) plays a central role in purine salvage and, unlike mammalian ADA homologs, has a further secondary role in methylthiopurine recycling. For this reason, plasmodial ADA accepts a wider range of substrates, as it is responsible for deamination of both adenosine and 5'-methylthioadenosine. The latter substrate is not accepted by mammalian ADA homologs. The structural basis for this natural difference in specificity between plasmodial and mammalian ADA has not been well understood. We now report crystal structures of Plasmodium vivax ADA in complex with adenosine, guanosine, and the picomolar inhibitor 2'-deoxycoformycin. These structures highlight a drastic conformational change in plasmodial ADA upon substrate binding that has not been observed for mammalian ADA enzymes. Further, these complexes illuminate the structural basis for the differential substrate specificity and potential drug selectivity between mammalian and parasite enzymes.


    Organizational Affiliation

    Medical Structural Genomics of Pathogenic Protozoa Consortium, University of Washington, Seattle, WA 98195-7742, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
adenosine deaminase
A
371Plasmodium vivax (strain Salvador I)N/A
Find proteins for A5KE01 (Plasmodium vivax (strain Salvador I))
Go to UniProtKB:  A5KE01
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADN
Query on ADN

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Download CCD File 
A
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
CCN
Query on CCN

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Download CCD File 
A
ACETONITRILE
C2 H3 N
WEVYAHXRMPXWCK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.157 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 143.962α = 90.00
b = 146.608β = 90.00
c = 50.398γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2007-09-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance