1Y7Y

High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila.

McGeehan, J.E.Streeter, S.D.Papapanagiotou, I.Fox, G.C.Kneale, G.G.

(2005) J.Mol.Biol. 346: 689-701

  • DOI: 10.1016/j.jmb.2004.12.025

  • PubMed Abstract: 
  • Restriction-modification (R-M) systems serve to protect the host bacterium from invading bacteriophage. The multi-component system includes a methyltransferase, which recognizes and methylates a specific DNA sequence, and an endonuclease which recogn ...

    Restriction-modification (R-M) systems serve to protect the host bacterium from invading bacteriophage. The multi-component system includes a methyltransferase, which recognizes and methylates a specific DNA sequence, and an endonuclease which recognises the same sequence and cleaves within or close to this site. The endonuclease will only cleave DNA that is unmethylated at the specific site, thus host DNA is protected while non-host DNA is cleaved. However, following DNA replication, expression of the endonuclease must be delayed until the host DNA is appropriately methylated. In many R-M systems, this regulation is achieved at the transcriptional level via the controller protein, or C-protein. We have solved the first X-ray structure of an R-M controller protein, C.AhdI, to 1.69 A resolution using selenomethionine MAD. C.AhdI is part of a Type IIH R-M system from the pathogen Aeromonas hydrophila. The structure reveals an all-alpha protein that contains a classical helix-turn-helix (HTH) domain and can be assigned to the Xre family of transcriptional regulators. Unlike its monomeric structural homologues, an extended helix generates an interface that results in dimerisation of the free protein. The dimer is electrostatically polarised and a positively charged surface corresponds to the position of the DNA recognition helices of the HTH domain. Comparison with the structure of the lambda cI ternary complex suggests that C.AhdI activates transcription through direct contact with the sigma70 subunit of RNA polymerase.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of the controller protein C.AhdI from Aeromonas hydrophilia
      McGeehan, J.E.,Streeter, S.,Cooper, J.B.,Mohammed, F.,Fox, G.C.,Kneale, G.G.
      (2004) Acta Crystallogr.,Sect.D 60: 323


    Organizational Affiliation

    Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, PO1 2DT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C.AhdI
A, B
74Aeromonas hydrophilaMutation(s): 0 
Gene Names: ahdIC
Find proteins for Q7X0F0 (Aeromonas hydrophila)
Go to UniProtKB:  Q7X0F0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 24.403α = 90.00
b = 57.246β = 98.89
c = 46.125γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CCP4data scaling
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance