4RTQ image
Deposition Date 2014-11-15
Release Date 2015-04-15
Last Version Date 2023-09-20
Entry Detail
PDB ID:
4RTQ
Keywords:
Title:
Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoHcy and a 5-bp non-canonical site (GTTTA )
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.19
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA adenine methylase
Chain IDs:A
Chain Length:298
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*CP*TP*TP*AP*AP*AP*CP*TP*TP*AP*A)-3')
Chain IDs:B (auth: F)
Chain Length:12
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*TP*TP*AP*AP*GP*TP*TP*TP*AP*AP*G)-3')
Chain IDs:C (auth: G)
Chain Length:12
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression.
Nucleic Acids Res. 43 4296 4308 (2015)
PMID: 25845600 DOI: 10.1093/nar/gkv251

Abstact

DNA adenine methyltransferase (Dam) is widespread and conserved among the γ-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. An unexplained and perplexing observation about Escherichia coli Dam (EcoDam) is that there is no obvious relationship between the genes that are transcriptionally responsive to Dam and the promoter-proximal presence of GATC sequences. Here, we demonstrate that EcoDam interacts with a 5-base pair non-cognate sequence distinct from GATC. The crystal structure of a non-cognate complex allowed us to identify a DNA binding element, GTYTA/TARAC (where Y = C/T and R = A/G). This element immediately flanks GATC sites in some Dam-regulated promoters, including the Pap operon which specifies pyelonephritis-associated pili. In addition, Dam interacts with near-cognate GATC sequences (i.e. 3/4-site ATC and GAT). Taken together, these results imply that Dam, in addition to being responsible for GATC methylation, could also function as a methylation-independent transcriptional repressor.

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Primary Citation of related structures