3IGM

A 2.2A crystal structure of the AP2 domain of PF14_0633 from P. falciparum, bound as a domain-swapped dimer to its cognate DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Determinants of DNA Binding by a P. falciparum ApiAP2 Transcriptional Regulator.

Lindner, S.E.De Silva, E.K.Keck, J.L.Llinas, M.

(2010) J.Mol.Biol. 395: 558-567

  • DOI: 10.1016/j.jmb.2009.11.004

  • PubMed Abstract: 
  • Putative transcription factors have only recently been identified in the Plasmodium spp., with the major family of regulators comprising the Apicomplexan Apetala2 (AP2) proteins. To better understand the DNA-binding mechanisms of these transcriptiona ...

    Putative transcription factors have only recently been identified in the Plasmodium spp., with the major family of regulators comprising the Apicomplexan Apetala2 (AP2) proteins. To better understand the DNA-binding mechanisms of these transcriptional regulators, we characterized the structure and in vitro function of an AP2 DNA-binding domain from a prototypical Apicomplexan AP2 protein, PF14_0633 from Plasmodium falciparum. The X-ray crystal structure of the PF14_0633 AP2 domain bound to DNA reveals a beta-sheet fold that binds the DNA major groove through base-specific and backbone contacts; a prominent alpha-helix supports the beta-sheet structure. Substitution of predicted DNA-binding residues with alanine weakened or eliminated DNA binding in solution. In contrast to plant AP2 domains, the PF14_0633 AP2 domain dimerizes upon binding to DNA through a domain-swapping mechanism in which the alpha-helices of the AP2 domains pack against the beta-sheets of the dimer mates. DNA-induced dimerization of PF14_0633 may be important for tethering two distal DNA loci together in the nucleus and/or for inducing functional rearrangements of its domains to facilitate transcriptional regulation. Consistent with a multisite binding mode, at least two copies of the consensus sequence recognized by PF14_0633 are present upstream of a previously identified group of sporozoite-stage genes. Taken together, these findings illustrate how Plasmodium has adapted the AP2 DNA-binding domain for genome-wide transcriptional regulation.


    Organizational Affiliation

    Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, 550 Medical Sciences Center, 1300 University Avenue, Madison, WI 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PF14_0633 protein
B, A
77Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
Find proteins for Q8IKH2 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IKH2
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*GP*CP*AP*TP*GP*CP*A)-3'W,X,C,D8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 43.810α = 90.00
b = 58.821β = 90.00
c = 177.296γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description