6PBD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.343 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site.

Horton, J.R.Woodcock, C.B.Opot, S.B.Reich, N.O.Zhang, X.Cheng, X.

(2019) Nat Commun 10: 4600-4600

  • DOI: 10.1038/s41467-019-12498-7

  • 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 sequen ...

    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.


    Organizational Affiliation

    Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. xcheng5@mdanderson.org.,Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. xzhang21@mdnderson.org.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Modification methylase CcrMI
A, B
366Caulobacter vibrioides (strain ATCC 19089 / CB15)Mutation(s): 0 
Gene Names: ccrMIM (ccrM)
EC: 2.1.1.72
Find proteins for P0CAW2 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Go to UniProtKB:  P0CAW2
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*AP*TP*TP*CP*AP*AP*TP*GP*AP*AP*TP*CP*CP*CP*AP*AP*G)-3')X19synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*TP*GP*GP*GP*AP*TP*TP*CP*AP*TP*TP*GP*AP*AP*TP*C)-3')Y19synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SFG
Query on SFG

Download SDF File 
Download CCD File 
A, B
SINEFUNGIN
ADENOSYL-ORNITHINE
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.343 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.683α = 90.00
b = 117.939β = 90.00
c = 119.598γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM049245-23

Revision History 

  • Version 1.0: 2019-10-23
    Type: Initial release