Primary Citation PubMed: 8800212
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Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes.
(2005) Nucleic Acids Res 33
PubMed: 16340006 | PubMedCentral: PMC1310896 | DOI: 10.1093/nar/gki995
The structure was solved by molecular replacement using the protein backbone of the previously solved ternary complex (PDB entry 3mht) as the initial model.
Publication Year: 2005
A directed evolution design of a GCG-specific DNA hemimethylase.
(2009) Nucleic Acids Res 37
PubMed: 19783820 | PubMedCentral: PMC2790894 | DOI: 10.1093/nar/gkp772
( B ) and ( C )—stick models depicting interactions of M.HhaI with the fourth and third target G:C base pair, respectively, based on a crystal structure of the M.HhaI-DNA-AdoHcy complex (PDB c... de 3mht).
Publication Year: 2009
Structural insights into the function of aminoglycoside-resistance A1408 16S rRNA methyltransferases from antibiotic-producing and human pathogenic bacteria.
(2010) Nucleic Acids Res 38
PubMed: 20639535 | PubMedCentral: PMC2995053 | DOI: 10.1093/nar/gkq627
The water-mediated interaction of Asp30 has been observed in structures of several methyltransferases that act on mRNA (PDB code 1RI4), tRNA (PDB code 3DXY) and DNA (PDB code 3MHT).
Superposition of KamB onto the methyltransferase Hha I (PDB code 3MHT) ( 33 ) bound to DNA, positions the extended structural motif of Loop β5–β6 (residues 141–156) next to the major groove of the nucleic acid helix.
Publication Year: 2010
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 latter curve was computed by CRYSOL from the crystal structure of the 12-bp DNA duplex (crystallized in complex with M.HhaI, PDB entry: 3MHT)  .
In the second case, the M.SsoII–15met complex structure was reconstructed by homology modeling using the crystallographic data for the M.HhaI complex with the 15-bp DNA duplex containing the methylation site (PDB entry: 3MHT).
For the homology modeling, the structure of M.HhaI in complex with the 15-bp DNA duplex containing its methylation site has been taken as a template (PDB entry: 3MHT)  .
Publication Year: 2014
Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase.
PubMed: 15653631 | PubMedCentral: PMC546160 | DOI: 10.1093/nar/gki175
( 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 ... n light blue; DNA shown as dark red and flipped-out base is red; AdoHcy is orange.
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