1YFL

T4Dam in Complex with Sinefungin and 16-mer Oligonucleotide Showing Semi-specific and Specific Contact and Flipped Base

Summary for 1YFL

• Entry DOI: 10.2210/pdb1yfl/pdb
• Related: 1Q0S 1Q0T 1YF3 1YFJ
• Descriptor: 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3', DNA adenine methylase, SINEFUNGIN, ... (4 entities in total)
• Functional Keywords: t4dam, methyltransferase, dna, protein-dna complex, base-flipping, transferase-dna complex, transferase/dna
• Biological source: Enterobacteria phage T4; More
• Total number of polymer chains: 8
• Total formula weight: 142965.91

Authors

Horton, J.R.,Liebert, K.,Hattman, S.,Jeltsch, A.,Cheng, X. (deposition date: 2005-01-03, release date: 2005-05-17, Last modification date: 2023-08-23)

Primary citation

Horton, J.R.,Liebert, K.,Hattman, S.,Jeltsch, A.,Cheng, X.
Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase.
Cell(Cambridge,Mass.), 121:349-361, 2005

PubMed Abstract: DNA methyltransferases methylate target bases within specific nucleotide sequences. Three structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary complexes with partially and fully specific DNA and a methyl-donor analog. We also report the effects of substitutions in the related Escherichia coli DNA methyltransferase (EcoDam), altering residues corresponding to those involved in specific interaction with the canonical GATC target sequence in T4Dam. We have identified two types of protein-DNA interactions: discriminatory contacts, which stabilize the transition state and accelerate methylation of the cognate site, and antidiscriminatory contacts, which do not significantly affect methylation of the cognate site but disfavor activity at noncognate sites. These structures illustrate the transition in enzyme-DNA interaction from nonspecific to specific interaction, suggesting that there is a temporal order for formation of specific contacts.

PubMed: 15882618
DOI: 10.1016/j.cell.2005.02.021

Experimental method

X-RAY DIFFRACTION (3.09 Å)