6GCD | pdb_00006gcd

DNA binding domain of restriction endonuclease McrBC in complex with 5-hydroxymethylcytosine DNA

• PDB DOI: https://doi.org/10.2210/pdb6GCD/pdb
• NAKB: 6GCD

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli str. K-12 substr. DH10B
• Mutation(s): No 


• Deposited: 2018-04-17 Released: 2018-09-19 
• Deposition Author(s): Sasnauskas, G., Manakova, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.214 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.166 (Depositor) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC.

Zagorskaite, E., Manakova, E., Sasnauskas, G.

(2018) FEBS Lett 592: 3335-3345

• PubMed: 30194838 
• DOI: https://doi.org/10.1002/1873-3468.13244
• Primary Citation Related Structures: 
  6GCD, 6GCE, 6GCF


• PubMed Abstract: 
  

  Cytosine modifications expand the information content of genomic DNA in both eukaryotes and prokaryotes, providing means for epigenetic regulation and self versus nonself discrimination. For example, the methyl-directed restriction endonuclease, McrBC, recognizes and cuts invading bacteriophage DNA containing 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and N4-methylcytosine (4mC), leaving the unmodified host DNA intact. Here, we present cocrystal structures of McrB-N bound to DNA oligoduplexes containing 5hmC, 5-formylcytosine (5fC), and 4mC, and characterize the relative affinity of McrB-N to various cytosine variants. We find that McrB-N flips out modified bases into a protein pocket and binds cytosine derivatives in the order of descending affinity: 4mC > 5mC > 5hmC ≫ 5fC. We also show that pocket mutations alter the relative preference of McrB-N to 5mC, 5hmC, and 4mC.

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Organizational Affiliation: 
• Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
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: 46.86 kDa 
• Atom Count: 3,803 
• Modeled Residue Count: 336 
• Deposited Residue Count: 364 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-methylcytosine-specific restriction enzyme B	A, B	170	Escherichia coli K-12	Mutation(s): 0  Gene Names: mcrB, rglB, b4346, JW5871 EC: 3.1.21
UniProt
Find proteins for P15005 (Escherichia coli (strain K12)) Explore P15005  Go to UniProtKB:  P15005

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*GP*AP*(5HC)P*CP*GP*GP*TP*AP*GP*C)-3')	C	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*AP*(5HC)P*CP*GP*GP*TP*CP*TP*C)-3')	D	12	synthetic construct

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.214 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.166 (Depositor) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.071	α = 90
b = 68.934	β = 90
c = 143.708	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Sasnauskas, G., Manakova, E.

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Funding Organization	Location	Grant Number
	Lithuania	Research Council of Lithuania, MIP-027/2012

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2018-10-24
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary