1MHT

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

Summary for 1MHT

• Entry DOI: 10.2210/pdb1mht/pdb
• Descriptor: DNA (5'-D(P*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3'), DNA (5'-D(*TP*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3'), PROTEIN (HHAI METHYLTRANSFERASE), ... (4 entities in total)
• Functional Keywords: protein-dna complex, double helix, overhanging base, flipped-out base, modified, transferase-dna complex, transferase/dna
• Biological source: Haemophilus haemolyticus
• Total number of polymer chains: 3
• Total formula weight: 45155.68

Authors

Cheng, X. (deposition date: 1994-12-08, release date: 1995-06-03, Last modification date: 2018-04-18)

Primary citation

Klimasauskas, S.,Kumar, S.,Roberts, R.J.,Cheng, X.
HhaI methyltransferase flips its target base out of the DNA helix.
Cell(Cambridge,Mass.), 76:357-369, 1994

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 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.

PubMed: 8293469
DOI: 10.1016/0092-8674(94)90342-5

Experimental method

X-RAY DIFFRACTION (2.6 Å)