5DKT

N-terminal His tagged apPOL exonuclease mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Apicoplast DNA Polymerase from Plasmodium falciparum: The First Look at a Plastidic A-Family DNA Polymerase.

Milton, M.E.Choe, J.Y.Honzatko, R.B.Nelson, S.W.

(2016) J.Mol.Biol. 428: 3920-3934

  • DOI: 10.1016/j.jmb.2016.07.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plasmodium falciparum, the primary cause of malaria, contains a non-photosynthetic plastid called the apicoplast. The apicoplast exists in most members of the phylum Apicomplexa and has its own genome along with organelle-specific enzymes for its rep ...

    Plasmodium falciparum, the primary cause of malaria, contains a non-photosynthetic plastid called the apicoplast. The apicoplast exists in most members of the phylum Apicomplexa and has its own genome along with organelle-specific enzymes for its replication. The only DNA polymerase found in the apicoplast (apPOL) was putatively acquired through horizontal gene transfer from a bacteriophage and is classified as an atypical A-family polymerase. Here, we present its crystal structure at a resolution of 2.9Å. P. falciparum apPOL, the first structural representative of a plastidic A-family polymerase, diverges from typical A-family members in two of three previously identified signature motifs and in a region not implicated by sequence. Moreover, apPOL has an additional N-terminal subdomain, the absence of which severely diminishes its 3' to 5' exonuclease activity. A compound known to be toxic to Plasmodium is a potent inhibitor of apPOL, suggesting that apPOL is a viable drug target. The structure provides new insights into the structural diversity of A-family polymerases and may facilitate structurally guided antimalarial drug design.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of the Plasmodium falciparum apicoplast DNA polymerase.
      Milton, M.E.,Choe, J.Y.,Honzatko, R.B.,Nelson, S.W.
      (2015) Acta Crystallogr.,Sect.F 71: 333


    Organizational Affiliation

    Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prex DNA polymerase
A
648Plasmodium falciparum (isolate 3D7)Mutation(s): 2 
EC: 2.7.7.7
Find proteins for Q8ILY1 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8ILY1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.265 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 141.775α = 90.00
b = 141.775β = 90.00
c = 148.759γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data reduction
MR-Rosettaphasing
PHENIXrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Iowa State University College of Liberal Arts and SciencesUnited States--

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-17
    Type: Database references
  • Version 1.2: 2016-10-19
    Type: Database references