1MHT

COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DNA AND S-ADENOSYL-L-HOMOCYSTEINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

HhaI methyltransferase flips its target base out of the DNA helix.

Klimasauskas, S.Kumar, S.Roberts, R.J.Cheng, X.

(1994) Cell 76: 357-369

  • DOI: 10.1016/0092-8674(94)90342-5
  • Primary Citation of Related Structures:  
    1MHT

  • PubMed Abstract: 
  • The crystal structure has been determined at 2.8 A resolution for a chemically-trapped covalent reaction intermediate between the HhaI DNA cytosine-5-methyltransferase, S-adenosyl-L-homocysteine, and a duplex 13-mer DNA oligonucleotide containing met ...

    The crystal structure has been determined at 2.8 A resolution for a chemically-trapped covalent reaction intermediate between the HhaI DNA cytosine-5-methyltransferase, S-adenosyl-L-homocysteine, and a duplex 13-mer DNA oligonucleotide containing methylated 5-fluorocytosine at its target. The DNA is located in a cleft between the two domains of the protein and has the characteristic conformation of B-form DNA, except for a disrupted G-C base pair that contains the target cytosine. The cytosine residue has swung completely out of the DNA helix and is positioned in the active site, which itself has undergone a large conformational change. The DNA is contacted from both the major and the minor grooves, but almost all base-specific interactions between the enzyme and the recognition bases occur in the major groove, through two glycine-rich loops from the small domain. The structure suggests how the active nucleophile reaches its target, directly supports the proposed mechanism for cytosine-5 DNA methylation, and illustrates a novel mode of sequence-specific DNA recognition.


    Related Citations: 
    • 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, New York 11724.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (HHAI METHYLTRANSFERASE)A327Haemophilus haemolyticusMutation(s): 0 
EC: 2.1.1.73 (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(P*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')B12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')C13N/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: 2.60 Å
      • R-Value Work: 0.174 
      • R-Value Observed: 0.174 
      • 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
      MADNESdata reduction

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 1994-12-08 
      • Released Date: 1995-06-03 
      • Deposition Author(s): Cheng, X.

      Revision History 

      • Version 1.0: 1995-06-03
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2018-04-18
        Changes: Data collection