6PBD

DNA N6-Adenine Methyltransferase CcrM In Complex with Double-Stranded DNA Oligonucleotide Containing Its Recognition Sequence GAATC

Summary for 6PBD

• Entry DOI: 10.2210/pdb6pbd/pdb
• Descriptor: Modification methylase CcrMI, DNA (5'-D(*CP*GP*AP*TP*TP*CP*AP*AP*TP*GP*AP*AP*TP*CP*CP*CP*AP*AP*G)-3'), DNA (5'-D(*GP*CP*TP*TP*GP*GP*GP*AP*TP*TP*CP*AP*TP*TP*GP*AP*AP*TP*C)-3'), ... (6 entities in total)
• Functional Keywords: dna methylation, gantc recognition, base flipping, transferase-dna complex, transferase/dna
• Biological source: Caulobacter vibrioides; More
• Total number of polymer chains: 4
• Total formula weight: 93944.14

Authors

Horton, J.R.,Cheng, X.,Woodcock, C.B. (deposition date: 2019-06-13, release date: 2019-10-23, Last modification date: 2023-10-11)

Primary citation

Horton, J.R.,Woodcock, C.B.,Opot, S.B.,Reich, N.O.,Zhang, X.,Cheng, X.
The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site.
Nat Commun, 10:4600-4600, 2019

PubMed Abstract: The Caulobacter crescentus cell cycle-regulated DNA methyltransferase (CcrM) methylates the adenine of hemimethylated GANTC after replication. Here we present the structure of CcrM in complex with double-stranded DNA containing the recognition sequence. CcrM contains an N-terminal methyltransferase domain and a C-terminal nonspecific DNA-binding domain. CcrM is a dimer, with each monomer contacting primarily one DNA strand: the methyltransferase domain of one molecule binds the target strand, recognizes the target sequence, and catalyzes methyl transfer, while the C-terminal domain of the second molecule binds the non-target strand. The DNA contacts at the 5-base pair recognition site results in dramatic DNA distortions including bending, unwinding and base flipping. The two DNA strands are pulled apart, creating a bubble comprising four recognized base pairs. The five bases of the target strand are recognized meticulously by stacking contacts, van der Waals interactions and specific Watson-Crick polar hydrogen bonds to ensure high enzymatic specificity.

PubMed: 31601797
DOI: 10.1038/s41467-019-12498-7

Experimental method

X-RAY DIFFRACTION (2.343 Å)