Crystal structure of the ATPase domain from bacterial mismatch repair endonuclease Aquifex aeolicus MutL.

Experimental Data Snapshot

  • Resolution: 3.44 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.260 

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Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus

Fukui, K.Iino, H.Baba, S.Kumasaka, T.Kuramitsu, S.Yano, T.

(2017) Biochim Biophys Acta 1865: 1178-1187

  • DOI: https://doi.org/10.1016/j.bbapap.2017.06.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    DNA mismatch repair (MMR) system corrects mismatched bases that are generated mainly by DNA replication errors. The repair system excises the error-containing single-stranded region and enables the re-synthesis of the strand. In the early reactions of MMR, MutL endonuclease incises the newly-synthesized/error-containing strand of the duplex to initiate the downstream excision reaction. MutL endonuclease consists of the N-terminal ATPase and C-terminal endonuclease domains. In this study, we report the crystal structure of the ATPase domain of MutL endonuclease from Aquifex aeolicus. The overall structure of the domain was similar to those of human MutL homologs and Escherichia coli MutL, although E. coli MutL has no endonuclease activity. The ATPase domain was comprised of two subdomains: the N-terminal ATP-binding subdomain and the C-terminal α-β sandwich subdomain. Site-directed mutagenesis experiment identified DNA-interacting eight basic amino acid residues, which were distributed across both the two subdomains and formed a DNA-binding cleft. Docking simulation between the structures of the ATPase and endonuclease domains generated a reliable model structure for the full-length A. aeolicus MutL, which satisfies our previous result of small-angle X-ray scattering analysis. On the basis of the model structure and further experimental results, we concluded that the two separate DNA-binding sites in the full-length A. aeolicus MutL simultaneously bind a dsDNA molecule.

  • Organizational Affiliation

    Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan. Electronic address: k.fukui@osaka-med.ac.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA mismatch repair protein MutLA [auth C],
B [auth A],
C [auth B]
308Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: mutLaq_1578
Find proteins for O67518 (Aquifex aeolicus (strain VF5))
Explore O67518 
Go to UniProtKB:  O67518
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67518
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 3.44 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.260 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.929α = 90
b = 145.253β = 90
c = 176.769γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan16K18680

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Author supporting evidence
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description