Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.
Recent publication of crystal structures for the putative DNA-binding subunits (HsdS) of the functionally uncharacterized Type I restriction-modification (R-M) enzymes MjaXIP and MgeORF438 have provided a convenient structural template for analysis of the more extensively characterized members of this interesting family of multisubunit molecular motors. Here, we present a structural model of the Type IC M.EcoR124I DNA methyltransferase (MTase), comprising the HsdS subunit, two HsdM subunits, the cofactor AdoMet and the substrate DNA molecule. The structure was obtained by docking models of individual subunits generated by fold-recognition and comparative modelling, followed by optimization of inter-subunit contacts by energy minimization. The model of M.EcoR124I has allowed identification of a number of functionally important residues that appear to be involved in DNA-binding. In addition, we have mapped onto the model the location of several new mutations of the hsdS gene of M.EcoR124I that were produced by misincorporation mutagenesis within the central conserved region of hsdS, we have mapped all previously identified DNA-binding mutants of TRD2 and produced a detailed analysis of the location of surface-modifiable lysines. The model structure, together with location of the mutant residues, provides a better background on which to study protein-protein and protein-DNA interactions in Type I R-M systems.
Obarska
Agnieszka
A
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.
Blundell
Alex
A
Feder
Marcin
M
Vejsadová
Stepánka
S
Sisáková
Eva
E
Weiserová
Marie
M
Bujnicki
Janusz M
JM
Firman
Keith
K
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry; D015280:DNA Restriction-Modification Enzymes / Q000737:chemistry* / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D021122:Protein Subunits / Q000737:chemistry; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000737:chemistry*
D001426:Bacterial Proteins; D015280:DNA Restriction-Modification Enzymes; D004268:DNA-Binding Proteins; C113046:HSDS protein, Bacteria; D021122:Protein Subunits; D004247:DNA; C072994:EcoR124 modification methylase type I; C109829:HsdM protein, Bacteria; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)