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 methylated 5-fluorocytosine at its target ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (HHAI METHYLTRANSFERASE)C [auth A]327Haemophilus haemolyticusMutation(s): 0 
EC: 2.1.1.73 (PDB Primary Data), 2.1.1.37 (UniProt)
UniProt
Find proteins for P05102 (Haemophilus parahaemolyticus)
Explore P05102 
Go to UniProtKB:  P05102
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05102
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')A [auth B]12N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')B [auth C]13N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
D [auth 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

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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