Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.09 kDa 
• Atom Count: 2,908 
• Modelled Residue Count: 297 
• Deposited Residue Count: 298 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 1R2Z

MutM (Fpg) bound to 5,6-dihydrouracil (DHU) containing DNA

• PDB DOI: 10.2210/pdb1R2Z/pdb
• NDB: PD0474

• Classification: HYDROLASE/DNA
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-30 Released: 2003-10-14 
• Deposition Author(s): Fromme, J.C., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.233 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

DNA Lesion Recognition by the Bacterial Repair Enzyme MutM.

Fromme, J.C., Verdine, G.L.

(2003) J Biol Chem 278: 51543-51548

• PubMed: 14525999 
• DOI: 10.1074/jbc.M307768200
• Primary Citation of Related Structures:  
  1R2Y, 1R2Z


• PubMed Abstract: 
  

MutM is a bacterial DNA glycosylase that removes the mutagenic lesion 8-oxoguanine (oxoG) from duplex DNA. The means of oxoG recognition by MutM (also known as Fpg) is of fundamental interest, in light of the vast excess of normal guanine bases present in genomic DNA. The crystal structure of a recognition-competent but catalytically inactive version of MutM in complex with oxoG-containing DNA reveals the structural basis for recognition. MutM binds the oxoG nucleoside in the syn glycosidic configuration and distinguishes oxoG from guanine by reading out the protonation state of the N7 atom. The segment of MutM principally responsible for oxoG recognition is a flexible loop, suggesting that conformational mobility influences lesion recognition and catalysis. Furthermore, the structure of MutM in complex with DNA containing an alternative substrate, dihydrouracil, demonstrates how MutM is able to recognize lesions other than oxoG.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MutM	C [auth A]	274	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: mutM, fpg EC: 3.2.2.23 (UniProt), 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*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'	A [auth B]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*CP*GP*TP*CP*CP*AP*(DHU)P*GP*TP*CP*TP*AP*CP*C)-3'	B [auth C]	12	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: 1.63 Å
• R-Value Free: 0.233 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.591	α = 90
b = 94.226	β = 90
c = 102.18	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-14 
Deposition Author(s): Fromme, J.C., Verdine, G.L.

Revision History  

• Version 1.0: 2003-10-14
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance