Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.

Nucleic Acids Research
Agnieszka ObarskaKeith Firman

Abstract

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. ...Continue Reading

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Citations

Nov 19, 2010·Journal of Industrial Microbiology & Biotechnology·Jan Nešvera
Dec 17, 2008·Nucleic Acids Research·Christopher K KennawayDavid T F Dryden
Jan 5, 2012·Genes & Development·Christopher K KennawayDavid T F Dryden
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Jun 7, 2008·Microbiology and Molecular Biology Reviews : MMBR·James Youell, Keith Firman
Feb 27, 2010·Critical Reviews in Biochemistry and Molecular Biology·Urulangodi Kunhiraman Madhusoodanan, Desirazu N Rao
Mar 11, 2016·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Koji YaharaIchizo Kobayashi
Mar 23, 2010·Journal of Molecular Biology·James E TaylorG Geoff Kneale
Jan 1, 2008·Journal of Molecular Biology·Agnieszka Obarska-KosinskaG Geoff Kneale
Oct 5, 2017·Proceedings of the National Academy of Sciences of the United States of America·Yan-Ping LiuXiao-Xue Yan

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Datasets Mentioned

BETA
X13145

Methods Mentioned

BETA
PCR

Software Mentioned

JUFO
FUGUE
GeneSilico
AMBER
T02
GeneSilico metaserver
PROFsec
SABLE
Pcons
PSIPRED

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