4rtp

From Proteopedia

Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoMet and with DNA Containing Proximal Pap Regulon Sequence

PDB ID 4rtp

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Structural highlights

4rtp is a 3 chain structure with sequence from Escherichia coli str. K-12 substr. MDS42 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.39Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DMA_ECOLI Methylates DNA within the sequence GATC and protects the DNA from cleavage by the restriction endonuclease MboI. Although it shares sequence specificity with a number of type II restriction endonucleases and methylases, it is thought to act in postreplication mismatch repair rather than as a part of a restriction modification system. May also play a role in DNA replication.

Publication Abstract from PubMed

DNA adenine methyltransferase (Dam) is widespread and conserved among the gamma-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.

Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression.,Horton JR, Zhang X, Blumenthal RM, Cheng X Nucleic Acids Res. 2015 Apr 6. pii: gkv251. PMID:25845600^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Horton JR, Zhang X, Blumenthal RM, Cheng X. 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. 2015 Apr 6. pii: gkv251. PMID:25845600 doi:http://dx.doi.org/10.1093/nar/gkv251