Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.80 kDa 
• Atom Count: 4502 
• Residue Count: 532 
• Unique protein chains: 1

1EE8

CRYSTAL STRUCTURE OF MUTM (FPG) PROTEIN FROM THERMUS THERMOPHILUS HB8

• DOI: 10.2210/pdb1EE8/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2000-01-31 Released: 2001-01-31 
• Deposition Author(s): Sugahara, M., Mikawa, T., Kumasaka, T., Yamamoto, M., Kato, R., Fukuyama, K., Inoue, Y., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.258 
• R-Value Work: 0.214 

Literature

Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8.

Sugahara, M., Mikawa, T., Kumasaka, T., Yamamoto, M., Kato, R., Fukuyama, K., Inoue, Y., Kuramitsu, S.

(2000) EMBO J 19: 3857-3869

• PubMed: 10921868 
• DOI: 10.1093/emboj/19.15.3857
• Primary Citation of Related Structures:  
  1EE8


• PubMed Abstract: 
  

The MutM [formamidopyrimidine DNA glycosylase (Fpg)] protein is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidatively damaged bases (N-glycosylase activity) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity). The crystal structure of MutM from an extreme thermophile, Thermus thermophilus HB8, was determined at 1.9 A resolution with multiwavelength anomalous diffraction phasing using the intrinsic Zn(2+) ion of the zinc finger. MutM is composed of two distinct and novel domains connected by a flexible hinge. There is a large, electrostatically positive cleft lined by highly conserved residues between the domains. On the basis of the three-dimensional structure and taking account of previous biochemical experiments, we propose a DNA-binding mode and reaction mechanism for MutM. The locations of the putative catalytic residues and the two DNA-binding motifs (the zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes.

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Related Citations: 

• Termostable Repair Enzyme for Oxidative DNA Damage from Extremely Thermophilic Bacterium, Thermus Thermophilus HB8
  Mikawa, T., Kato, R., Sugahara, M., Kuramitsu, S.
  (1998) Nucleic Acids Res 26: 903

• Crystallization and Preliminary X-ray Crystallographic Studies of Thermus Thermophilus HB8 MutM Protein Involved in Repairs Oxidative DNA Damage
  Sugahara, M., Mikawa, T., Kato, R., Kumasaka, T., Yamamoto, M., Fukuyama, K., Inoue, Y., kuramitsu, S.
  (2000) J Biochem 127: 9

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Organizational Affiliation: 

Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MUTM (FPG) PROTEIN	A, B	266	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: mutM, fpg, TTHA1806 EC: 3.2.2.23 (UniProt), 4.2.99.18 (UniProt)
Find proteins for O50606 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Explore O50606  Go to UniProtKB:  O50606

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.258 
• R-Value Work: 0.214 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.421	α = 90
b = 61.289	β = 91.71
c = 98.342	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-01-31 
• Released Date: 2001-01-31 
Deposition Author(s): Sugahara, M., Mikawa, T., Kumasaka, T., Yamamoto, M., Kato, R., Fukuyama, K., Inoue, Y., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• Version 1.0: 2001-01-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance