8C56

CpG specific M.MpeI methyltransferase crystallized in the presence of 2'-deoxy-5-methylzebularine (5mZ) and 5-methylcytosine containing dsDNA

• PDB DOI: https://doi.org/10.2210/pdb8C56/pdb
• NAKB: 8C56

• Classification: TRANSFERASE
• Organism(s): Malacoplasma penetrans HF-2, synthetic construct
• Expression System: Escherichia coli, synthetic construct
• Mutation(s): No 


• Deposited: 2023-01-06 Released: 2024-01-17 
• Deposition Author(s): Wojciechowski, M., Czapinska, H., Krwawicz, J., Rafalski, D., Bochtler, M.
• Funding Organization(s): Foundation for Polish Science, European Union (EU), Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.216 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

Cytosine analogues as DNA methyltransferase substrates and inhibitors

Wojciechowski, M., Czapinska, H., Krwawicz, J., Rafalski, D., Bochtler, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.31 kDa 
• Atom Count: 4,470 
• Modelled Residue Count: 416 
• Deposited Residue Count: 423 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine-specific methyltransferase	A	395	Malacoplasma penetrans HF-2	Mutation(s): 0  Gene Names: MYPE4940
UniProt
Find proteins for Q8EVR5 (Malacoplasma penetrans (strain HF-2)) Explore Q8EVR5  Go to UniProtKB:  Q8EVR5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(5PY)P*GP*CP*TP*GP*AP*A)-3')	B	14	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)-3')	C	14	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	F [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.216 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.259	α = 90
b = 84.259	β = 90
c = 173.883	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
REFMAC	phasing
ARP/wARP	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Wojciechowski, M., Czapinska, H., Krwawicz, J., Rafalski, D., Bochtler, M.

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Funding Organization	Location	Grant Number
Foundation for Polish Science	Poland	TEAM/2010-6/1
European Union (EU)	European Union	TEAM/2010-6/1
Foundation for Polish Science	Poland	POIR.04.04.00-00-31DF/17-00
European Union (EU)	European Union	POIR.04.04.00-00-31DF/17-00
Polish National Science Centre	Poland	UMO-2014/13/B/NZ1/03991
Polish National Science Centre	Poland	UMO-2014/14/M/NZ5/00558
Polish National Science Centre	Poland	UMO-2018/30/Q/NZ2/00669
European Union (EU)	European Union	POIG.02.02.00-14-024/08-00

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release