Primary Citation PubMed: 10080885
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Coupling between catalytic loop motions and enzyme global dynamics.
(2012) PLoS Comput Biol 8
PubMed: 23028297 | PubMedCentral: PMC3459879 | DOI: 10.1371/journal.pcbi.1002705
A. Open ( mauve/magenta loop; PDB id 2HMY  ) and closed ( cyan/blue ; PDB id 3HMT  ) forms of M. Hha I are shown with bound DNA ( light brown ).
Publication Year: 2012
Flexibility of the linker between the domains of DNA methyltransferase SsoII revealed by small-angle X-ray scattering: implications for transcription regulation in SsoII restriction-modification system.
(2014) PLoS One 9
PubMed: 24710319 | PubMedCentral: PMC3978073 | DOI: 10.1371/journal.pone.0093453
Object Method of model construction Model title M.NlaX ab initio modeling (DAMMIN) ab initio model of M.NlaX M.NlaX homology modeling: the crystallographic structure of M.HhaI (PDB entry: 2HMY) as a t... mplate, CRYSOL for scattering calculation M.HhaI model M.SsoII ab initio modeling (DAMMIN) ab initio model of M.SsoII M.SsoII homology modeling: the crystallographic structure of M.HhaI (PDB entry: 2HMY)+the N-terminal region made of dummy residues hybrid M.HhaI model M.SsoII homology modeling: the crystallographic structure of M.HhaI (PDB entry: 2HMY)+the crystallographic structure of phage 434 repressor (PDB entry: 1PER)+dummy residues linker in order to connect the two domains hybrid M.HhaI-R434 model M.SsoII–15met ab initio modeling (MONSA) ab initio model of M.SsoII–DNA complex M.SsoII–15met homology modeling: the crystallographic structure of M.HhaI–DNA complex (PDB entry: 3MHT)+the N-terminal region made of dummy residues hybrid M.HhaI–DNA model M.SsoII–15met homology modeling: the crystallographic structure of M.HhaI–DNA complex (PDB entry: 3MHT)+the crystallographic structure of phage 434 repressor (PDB entry: 1PER)+dummy residues linker in order to connect the two domains hybrid M.HhaI-R434–DNA model The model of M.SsoII complex with a 15-bp DNA containing the methylation site (15met) was also constructed by two different methods, ab initio and homology modeling.
The M.HhaI structure from PDB entry 2HMY  has been taken for modeling of M.NlaX and M.SsoII apo-forms.
The MTase domain of M.SsoII was represented by the crystallographic model of M.HhaI, a homologous one-domain MTase (PDB entry: 2HMY)  , referred further as “M.HhaI model” (see Table 1 ).
Publication Year: 2014
Metadynamics simulation study on the conformational transformation of HhaI methyltransferase: an induced-fit base-flipping hypothesis.
(2014) Biomed Res Int 2014
PubMed: 25045662 | PubMedCentral: PMC4090504 | DOI: 10.1155/2014/304563
M.HhaI adopts an open conformation in the solution (PDBID:2HMY) [ 15 ]: the catalytic loop stays away from the TRD and the heteroatom of the polar side chain in the catalytic loop points opposite to t... rget recognition loops.
(I) The structure of the M.HhaI-SAM binary complex (PDBID:2HMY) shows the inactive status of M.HhaI.
Starting Structure for Simulation Crystal structures of the binary complex (PDB ID: 2HMY [ 7 ]) were used to construct the protein model, in which all water molecules were removed.
Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase.
(2005) Nucleic Acids Res 33
PubMed: 15653631 | PubMedCentral: PMC546160 | DOI: 10.1093/nar/gki175
( C ) A stick model of the AdoMet–Trp41 stacking interaction in the binary complex (2hmy); atom coloring: C is in gray, O in red, N in blue and S in yellow.
( A ) The C α trace of the HhaI–DNA–AdoHcy complex (PDB code 3mht); the closed catalytic loop is marked in blue and the open catalytic loop (from HhaI–AdoMet; 2hmy) is in light blue; DNA shown as dark red and flipped-out base is red; AdoHcy is orange.
Publication Year: 2005
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