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Insights in Enzyme Research
ISSN: 2573-4466
E u r o S c i C o n C o n g r e s s o n
Enzymology and
Molecular Biology
A u g u s t 1 3 - 1 4 , 2 0 1 8
P a r i s , F r a n c e
Enzymology 2018
The role of Mg2+ions in DNA hydrolysis by homodimeric restriction enzyme
EcoRVwas elucidated based on the three-dimensional reference interaction
site model (3D-RISM-KH) theory and the molecular dynamics (MD) simulation.
From an analysis of the spatial distribution of Mg2+ in an active site using
3D-RISM-KH, we identified a new position for Mg2+in the X-ray EcoRV-DNA
complex structure (1RVB), which turns out to play a crucial role in the reaction.
We refer to the position as site IV†. Site IV† is almost the same position as that
of a Ca2+ ion in the superimposed active-site structure of X-ray PvuII-DNA
complex (1F0O). The 3D-RSIM-KH was also used to locate the position of water
molecules including the water nucleophile at the active site. MD simulations
were carried out with the initial structure having two Mg2 + ions at site IV† and
at site I*, experimentally identified by Horton et al., to find a stable complex
structure in which rearrangement of the DNA fragment occurred to orient the
scissile bond direction toward the water nucleophile. The equilibrium active-
site structure of EcoRV-DNA complex obtained in MD simulation was similar
to the superimposed structure of X-ray Bam HI-DNA complex (2BAM). In the
active-site structure, two metal ions have the same position as that of 2BAM,
and the scissile phosphate is twisted to orient the scissile bond toward the
water nucleophile as is the case in 2BAM. We propose the equilibrium active-
site structure obtained in this study as a precursor of the hydrolysis reaction
of EcoRV.
Biography
Masayuki Irisa has completed a Doctoral program from
Kyoto University without degree and got his PhD by the way
of dissertation from Osaka University. He is an Associate
Professor in Department of Bioscience and Bioinformatics,
Faculty of Computer Science and Systems Engineering, Kyushu
Institute of Technology, which belongs to a national university
corporation, Japan. He has been serving as a Teacher and a
Researcher in the Kyushu Institute of Technology for 20 years.
Role of Mg2+ ions in DNA hydrolysis by EcoRV, studied by 3D-RISM
and MD
M Irisa1, I Onishi1, S Sunaba1, N Yoshida2 and F Hirata3,4
1Kyushu Institute of Technology, Iizuka, Japan
2Kyushu University, Fukuoka, Japan
3Toyota RIKEN (TPCRI), Japan
4Institute for Molecular Science, Okazaki, Japan
M Irisa et al., Insights Enzyme Res 2018, Volume 2
DOI: 10.21767/2573-4466-C1-002