5MHT

TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH HEMIMETHYLATED DNA AND ADOHCY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase.

O'Gara, M.Roberts, R.J.Cheng, X.

(1996) J Mol Biol 263: 597-606

  • DOI: 10.1006/jmbi.1996.0601
  • Primary Citation of Related Structures:  
    5MHT

  • PubMed Abstract: 
  • The crystal structure of HhaI methyltransferase complexed with non-palindromic duplex DNA, containing a hemimethylated recognition sequence, and with the cofactor analog S-adenosyl-L-homocysteine (AdoHcy), has been determined. The structure provides ...

    The crystal structure of HhaI methyltransferase complexed with non-palindromic duplex DNA, containing a hemimethylated recognition sequence, and with the cofactor analog S-adenosyl-L-homocysteine (AdoHcy), has been determined. The structure provides an explanation for the stronger affinities of DNA methyltransferases for hemimethylated DNA than for unmethylated or fully methylated DNA in the presence of AdoHcy. The unmethylated target 2'-deoxycytidine flips out of the DNA helix and the CH group at position 5 makes van der Waals' contacts with the sulfur atom of AdoHcy. Selectivity/preference for hemimethylated over fully methylated DNA may thus reflect interactions among the chemical substituent (H or CH3) at the C5 position of the flipped cytosine, protein and the bound AdoHcy. The 5-methyl-2'-deoxycytidine on the complementary strand remains in the DNA helix, with the methyl group almost perpendicular to the carboxylate group of Glu239, which is part of the sequence recognition loop. Thus, selectivity/preference for hemimethylated over unmethylated DNA appears to result largely from van der Waals' contacts between the planar Glu239 carboxylate and the methyl group of the 5-methyl-2'-deoxycytidine. Furthermore, the positive electrostatic potential originating from the bound AdoHcy extends to the DNA phosphate groups flanking the flipped cytosine. The increased binding to DNA by long-range electrostatic interactions should also occur with the methyl donor S-adenosyl-L-methionine.


    Related Citations: 
    • Enzymatic C5-Cytosine Methylation of DNA: Mechanistic Implications of New Crystal Structures for HhaI Methyltransferase-DNA-Adohcy Complexes
      O'Gara, M., Klimasauskas, S., Roberts, R.J., Cheng, X.
      (1996) J Mol Biol 261: 634
    • HhaI Methyltransferase Flips its Target Base Out of the DNA Helix
      Klimasauskas, S., Kumar, S., Roberts, R.J., Cheng, X.
      (1994) Cell 76: 357
    • Crystal Structure of the HhaI DNA Methyltransferase Complexed with S-Adenosyl- L-Methionine
      Cheng, X., Kumar, S., Posfai, J., Pflugrath, J.W., Roberts, R.J.
      (1993) Cell 74: 299

    Organizational Affiliation

    W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (HHAI METHYLTRANSFERASE)A327Haemophilus haemolyticusMutation(s): 0 
EC: 2.1.1.7 (PDB Primary Data), 2.1.1.37 (UniProt)
Find proteins for P05102 (Haemophilus parahaemolyticus)
Explore P05102 
Go to UniProtKB:  P05102
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3')C12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3')D12N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SAH
      Query on SAH

      Download CCD File 
      A
      S-ADENOSYL-L-HOMOCYSTEINE
      C14 H20 N6 O5 S
      ZJUKTBDSGOFHSH-WFMPWKQPSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.70 Å
      • R-Value Work: 0.188 
      • R-Value Observed: 0.188 
      • Space Group: H 3 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 99.86α = 90
      b = 99.86β = 90
      c = 325.2γ = 120
      Software Package:
      Software NamePurpose
      X-PLORrefinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 1996-10-22 
      • Released Date: 1997-07-23 
      • Deposition Author(s): Cheng, X.

      Revision History 

      • Version 1.0: 1997-07-23
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance