Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.59 kDa 
• Atom Count: 2556 
• Modelled Residue Count: 293 
• Deposited Residue Count: 306 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2F5Q

Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC2

• PDB DOI: 10.2210/pdb2F5Q/pdb
• NDB: PD0752

• Classification: hydrolase/DNA
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-11-26 Released: 2006-03-07 
• Deposition Author(s): Banerjee, A., Santos, W.L., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.249 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 

Literature

Structure of a DNA glycosylase searching for lesions.

Banerjee, A., Santos, W.L., Verdine, G.L.

(2006) Science 311: 1153-1157

• PubMed: 16497933 
• DOI: 10.1126/science.1120288
• Primary Citation of Related Structures:  
  2F5N, 2F5O, 2F5P, 2F5Q, 2F5S


• PubMed Abstract: 
  

DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) technology to obtain structures of a bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0 angstrom resolution, reveal the nature of the search process: The protein inserts a probe residue into the helical stack and severely buckles the target base pair, which remains intrahelical. MutM therefore actively interrogates the intact DNA helix while searching for damage.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
formamidopyrimidine-DNA glycosidase	C [auth A]	274	Geobacillus stearothermophilus	Mutation(s): 2  Gene Names: mutM, fpg EC: 3.2.2.23 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt
Find proteins for P84131 (Geobacillus stearothermophilus) Explore P84131  Go to UniProtKB:  P84131

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*GP*G*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'	A [auth B]	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*CP*G*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'	B [auth C]	16	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.249 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.413	α = 90
b = 92	β = 90
c = 103.05	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-11-26 
• Released Date: 2006-03-07 
Deposition Author(s): Banerjee, A., Santos, W.L., Verdine, G.L.

Revision History  

• Version 1.0: 2006-03-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations