ISDA: 1YF3

Deposition Date 2004-12-30

Release Date 2005-05-17

Last Version Date 2023-08-23

Entry Detail

PDB ID:

1YF3

Keywords:

Transferase/DNA

Title:

T4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making Non- and Semi-specific (~1/4) Contact

Biological Source:

Source Organism:

Enterobacteria phage T4 (Taxon ID: 10665)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.29 Å

R-Value Free:

0.27

R-Value Work:

0.21

R-Value Observed:

0.22

Space Group:

P 1 21 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA adenine methylase
Gene (Uniprot):DAM
Chain IDs:C (auth: A), D (auth: B)
Chain Length:259
Number of Molecules:2
Biological Source:Enterobacteria phage T4

UniProt ID:P04392 Pfam ID:PF02086 EC:2.1.1.72

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3'
Chain IDs:A (auth: C)
Chain Length:13
Number of Molecules:1
Biological Source:

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*CP*AP*TP*GP*G)-3'
Chain IDs:B (auth: D)
Chain Length:13
Number of Molecules:1
Biological Source:

Ligand Molecules

GOL

SAH

Primary Citation

Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase.

Horton, J.R, Liebert, K, Hattman, S, Jeltsch, A, Cheng, X, Yang, Z, Horton, J.R, Zhou, L, Zhang, X.J, Dong, A, Zhang, X, Schlagman, S.L, Kossykh, V, Cheng, X.Show

Cell(Cambridge,Mass.) 121 349 361 (2005)

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

Abstact

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.

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