6MHT

TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND DNA CONTAINING 4'-THIO-2'DEOXYCYTIDINE AT THE TARGET

Summary for 6MHT

• Entry DOI: 10.2210/pdb6mht/pdb
• Descriptor: DNA (5'-D(P*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'), DNA (5'-D(P*GP*TP*CP*AP*GP*(4SC)P*GP*CP*AP*TP*GP*G)-3'), CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI, ... (5 entities in total)
• Functional Keywords: transferase, methyltransferase, restriction system, complex (methyltransferase-dna), transferase-dna complex, transferase/dna
• Biological source: Haemophilus haemolyticus; More
• Total number of polymer chains: 3
• Total formula weight: 44811.55

Authors

Cheng, X. (deposition date: 1998-08-05, release date: 1998-08-12, Last modification date: 2023-08-02)

Primary citation

Kumar, S.,Horton, J.R.,Jones, G.D.,Walker, R.T.,Roberts, R.J.,Cheng, X.
DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase.
Nucleic Acids Res., 25:2773-2783, 1997

PubMed Abstract: 4'-Thio-2'-deoxycytidine was synthesized as a 5'- protected phosphoramidite compatible with solid phase DNA synthesis. When incorporated as the target cytosine (C*) in the GC*GC recognition sequence for the DNA methyltransferase M. HhaI, methyl transfer was strongly inhibited. In contrast, these same oligonucleotides were normal substrates for the cognate restriction endonuclease R. HhaI and its isoschizomer R. Hin P1I. M. HhaI was able to bind both 4'-thio-modified DNA and unmodified DNA to equivalent extents under equilibrium conditions. However, the presence of 4'-thio-2'-deoxycytidine decreased the half-life of the complex by >10-fold. The crystal structure of a ternary complex of M. HhaI, AdoMet and DNA containing 4'-thio-2'-deoxycytidine was solved at 2.05 A resolution with a crystallographic R-factor of 0.186 and R-free of 0.231. The structure is not grossly different from previously solved ternary complexes containing M. HhaI, DNA and AdoHcy. The difference electron density suggests partial methylation at C5 of the flipped target 4'-thio-2'-deoxycytidine. The inhibitory effect of the 4'sulfur atom on enzymatic activity may be traced to perturbation of a step in the methylation reaction after DNA binding but prior to methyl transfer. This inhibitory effect can be partially overcome after a considerably long time in the crystal environment where the packing prevents complex dissociation and the target is accurately positioned within the active site.

PubMed: 9207024
DOI: 10.1093/nar/25.14.2773

Experimental method

X-RAY DIFFRACTION (2.05 Å)