3UBT

Crystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransferase M.HaeIII Bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb3UBT/pdb
• NAKB: 3UBT

• Classification: TRANSFERASE/DNA
• Organism(s): Haemophilus aegyptius
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-10-24 Released: 2012-10-03 
• Deposition Author(s): Verdine, G.L., Didovyk, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.221 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Structural origins of DNA target selection and nucleobase extrusion by a DNA Cytosine methyltransferase.

Didovyk, A., Verdine, G.L.

(2012) J Biol Chem 287: 40099-40105

• PubMed: 23012373 
• DOI: https://doi.org/10.1074/jbc.M112.413054
• Primary Citation of Related Structures:  
  3UBT


• PubMed Abstract: 
  

  How DNA 5-cytosine methyltransferases (DCMTases) select their substrate nucleobase for extrusion from DNA duplex is poorly understood.

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Organizational Affiliation: 

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 127.24 kDa 
• Atom Count: 9,258 
• Modelled Residue Count: 1,020 
• Deposited Residue Count: 1,029 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Modification methylase HaeIII	A [auth Y], B [auth A], C [auth B]	331	Haemophilus aegyptius	Mutation(s): 1  Gene Names: haeIIIM EC: 2.1.1.37
UniProt
Find proteins for P20589 (Haemophilus aegyptius) Explore P20589  Go to UniProtKB:  P20589

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*GP*CP*CP*A)-3'	D, E, F, G, H, I [auth C]	6	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	K [auth Y], L [auth Y], O [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
2PE	M [auth Y], P [auth A], R [auth B]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
CL	J [auth Y], N [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.221 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.564	α = 90
b = 129.588	β = 90
c = 132.381	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Verdine, G.L., Didovyk, A.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2012-12-19
  Changes: Database references
• Version 1.2: 2014-10-08
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations