1L1Z

MutM (Fpg) Covalent-DNA Intermediate

• PDB DOI: https://doi.org/10.2210/pdb1L1Z/pdb
• NAKB: 1L1Z

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


• Deposited: 2002-02-20 Released: 2002-06-14 
• Deposition Author(s): Fromme, J.C., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.246 
• R-Value Work: 0.221 

Literature

Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM.

Fromme, J.C., Verdine, G.L.

(2002) Nat Struct Biol 9: 544-552

• PubMed: 12055620 
• DOI: https://doi.org/10.1038/nsb809
• Primary Citation of Related Structures:  
  1L1T, 1L1Z, 1L2B, 1L2C, 1L2D


• PubMed Abstract: 
  

  MutM is a bacterial 8-oxoguanine glycosylase responsible for initiating base-excision repair of oxidized guanine residues in DNA. Here we report five different crystal structures of MutM-DNA complexes that represent different steps of the repair reaction cascade catalyzed by the protein and also differ in the identity of the base opposite the lesion (the 'estranged' base). These structures reveal that the MutM active site performs the multiple steps of base-excision and 3' and 5' nicking with minimal rearrangement of the DNA backbone.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.46 kDa 
• Atom Count: 2,696 
• Modelled Residue Count: 287 
• Deposited Residue Count: 306 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MutM	C [auth A]	274	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: mutM
UniProt
Find proteins for P84131 (Geobacillus stearothermophilus) Explore P84131  Go to UniProtKB:  P84131

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*G*GP*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*C*GP*TP*CP*CP*AP*(PED)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: 1.70 Å
• R-Value Free: 0.246 
• R-Value Work: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.022	α = 90
b = 96.047	β = 90
c = 103.889	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-14 
Deposition Author(s): Fromme, J.C., Verdine, G.L.

Revision History  

• Version 1.0: 2002-06-14
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description