1MHT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 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


  • 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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HHAI METHYLTRANSFERASE)
A
327Haemophilus parahaemolyticusGene Names: hhaIM
EC: 2.1.1.37
Find proteins for P05102 (Haemophilus parahaemolyticus)
Go to UniProtKB:  P05102
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')B12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
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 SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
C36
Query on C36
B, C
DNA LINKINGC10 H17 F N3 O8 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.174 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 99.860α = 90.00
b = 99.860β = 90.00
c = 325.200γ = 120.00
Software Package:
Software NamePurpose
MADNESdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance