4DKJ

CpG specific methyltransferase in complex with target DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.

Wojciechowski, M.Czapinska, H.Bochtler, M.

(2013) Proc.Natl.Acad.Sci.USA 110: 105-110

  • DOI: 10.1073/pnas.1207986110

  • PubMed Abstract: 
  • Cytosine methylation promotes deamination. In eukaryotes, CpG methylation is thought to account for CpG underrepresentation. Whether scarcity of CpGs in prokaryotic genomes is diagnostic for methylation is not clear. Here, we report that Mycoplasms t ...

    Cytosine methylation promotes deamination. In eukaryotes, CpG methylation is thought to account for CpG underrepresentation. Whether scarcity of CpGs in prokaryotic genomes is diagnostic for methylation is not clear. Here, we report that Mycoplasms tend to be CpG depleted and to harbor a family of constitutively expressed or phase variable CpG-specific DNA methyltransferases. The very CpG poor Mycoplasma penetrans and its constitutively active CpG-specific methyltransferase M.MpeI were chosen for further characterization. Genome-wide sequencing of bisulfite-converted DNA indicated that M.MpeI methylated CpG target sites both in vivo and in vitro in a locus-nonselective manner. A crystal structure of M.MpeI with DNA at 2.15-Å resolution showed that the substrate base was flipped and that its place in the DNA stack was taken by a glutamine residue. A phenylalanine residue was intercalated into the "weak" CpG step of the nonsubstrate strand, indicating mechanistic similarities in the recognition of the short CpG target sequence by prokaryotic and eukaryotic DNA methyltransferases.


    Organizational Affiliation

    Laboratory of Structural Biology, International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytosine-specific methyltransferase
A
403Mycoplasma penetrans (strain HF-2)EC: 2.1.1.37
Find proteins for Q8EVR5 (Mycoplasma penetrans (strain HF-2))
Go to UniProtKB:  Q8EVR5
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(C37)P*GP*CP*TP*GP*AP*A)-3')B14N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)-3')C14N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
C
DNA LINKINGC10 H16 N3 O7 PDC
C37
Query on C37
B
DNA LINKINGC9 H13 F N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.950α = 90.00
b = 83.950β = 90.00
c = 173.840γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
CHAINSAWphasing
CHAINSAWmodel building
MOSFLMdata reduction
ARP/wARPmodel building
REFMACphasing
ADSCdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2012-12-19
    Type: Database references
  • Version 1.2: 2013-01-02
    Type: Database references
  • Version 1.3: 2013-01-16
    Type: Database references