6PBD | pdb_00006pbd

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

• PDB DOI: https://doi.org/10.2210/pdb6PBD/pdb
• NAKB: 6PBD

• Classification: TRANSFERASE/DNA
• Organism(s): Caulobacter vibrioides, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-06-13 Released: 2019-10-23 
• Deposition Author(s): Horton, J.R., Cheng, X., Woodcock, C.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

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

• PubMed: 31601797 
• DOI: https://doi.org/10.1038/s41467-019-12498-7
• Primary Citation Related Structures: 
  6PBD


• 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.

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Organizational Affiliation: 
• Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.
Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. [e-mail].
Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 93.94 kDa 
• Atom Count: 6,191 
• Modeled Residue Count: 719 
• Deposited Residue Count: 770 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Modification methylase CcrMI	A, B	366	Caulobacter vibrioides	Mutation(s): 0  Gene Names: ccrMIM, ccrM, CC_0378 EC: 2.1.1.72
UniProt
Find proteins for P0CAW2 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore P0CAW2  Go to UniProtKB:  P0CAW2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*AP*TP*TP*CP*AP*AP*TP*GP*AP*AP*TP*CP*CP*CP*AP*AP*G)-3')	C [auth X]	19	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*TP*GP*GP*GP*AP*TP*TP*CP*AP*TP*TP*GP*AP*AP*TP*C)-3')	D [auth Y]	19	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SFG	E [auth A], F [auth B]	SINEFUNGIN C15 H23 N7 O5 LMXOHSDXUQEUSF-YECHIGJVSA-N
EDO	G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.683	α = 90
b = 117.939	β = 90
c = 119.598	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Horton, J.R., Cheng, X., Woodcock, C.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM049245-23

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description