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1mht, resolution 2.60Å ()
Non-Standard Residues:
Activity: Deleted entry, with EC number
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Publication Abstract from PubMed

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.

HhaI methyltransferase flips its target base out of the DNA helix., Klimasauskas S, Kumar S, Roberts RJ, Cheng X, Cell. 1994 Jan 28;76(2):357-69. PMID:8293469

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

1mht is a 3 chain structure with sequence from Haemophilus haemolyticus. The July 2011 RCSB PDB Molecule of the Month feature on DNA Methylases by David Goodsell is 10.2210/rcsb_pdb/mom_2011_7. Full crystallographic information is available from OCA.


  • Klimasauskas S, Kumar S, Roberts RJ, Cheng X. HhaI methyltransferase flips its target base out of the DNA helix. Cell. 1994 Jan 28;76(2):357-69. PMID:8293469

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