title: High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila.
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 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.
authors.affiliation: Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, PO1 2DT, UK.
authors.forename: J E
authors.initials: JE
authors.lastname: McGeehan
authors.forename: S D
authors.initials: SD
authors.lastname: Streeter
authors.forename: I
authors.initials: I
authors.lastname: Papapanagiotou
authors.forename: G C
authors.initials: GC
authors.lastname: Fox
authors.forename: G G
authors.initials: GG
authors.lastname: Kneale
mesh_terms: D016980:Aeromonas hydrophila / Q000201:enzymology* / Q000235:genetics; D000595:Amino Acid Sequence; D001483:Base Sequence; D018360:Crystallography, X-Ray; D015280:DNA Restriction-Modification Enzymes / Q000737:chemistry* / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D019281:Dimerization; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D016297:Mutagenesis, Site-Directed; D011487:Protein Conformation; D020836:Protein Structure, Quaternary; D017386:Sequence Homology, Amino Acid; D055672:Static Electricity
chemical_list: D015280:DNA Restriction-Modification Enzymes; D004269:DNA, Bacterial