5GKG

Structure of EndoMS-dsDNA1'' complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease

Nakae, S.Hijikata, A.Tsuji, T.Yonezawa, K.Kouyama, K.I.Mayanagi, K.Ishino, S.Ishino, Y.Shirai, T.

(2016) Structure 24: 1960-1971

  • DOI: 10.1016/j.str.2016.09.005
  • Primary Citation of Related Structures:  
    5GKE, 5GKF, 5GKG, 5GKH, 5GKI, 5GKJ

  • PubMed Abstract: 
  • Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases ...

    Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway.


    Organizational Affiliation

    Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga 526-0829, Japan. Electronic address: t_shirai@nagahama-i-bio.ac.jp.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endonuclease EndoMSA, B252Thermococcus kodakarensis KOD1Mutation(s): 1 
Gene Names: TK1898nucS
EC: 3.1
UniProt
Find proteins for Q5JER9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JER9 
Go to UniProtKB:  Q5JER9
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*GP*GP*TP*CP*GP*TP*CP*C)-3')C15synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3')D15synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.60 Å
      • R-Value Free: 0.231 
      • R-Value Work: 0.168 
      • R-Value Observed: 0.171 
      • Space Group: P 61 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 92.42α = 90
      b = 92.42β = 90
      c = 405.08γ = 120
      Software Package:
      Software NamePurpose
      MOSFLMdata reduction
      MOSFLMdata scaling
      PHASERphasing
      PHENIXrefinement

      Structure Validation

      View Full Validation Report




      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Japan Agency for Medical Research and DevelopmentJapanDrug Discovery and Life Science Research(Platform for Drug Discovery, Informatics and Structural Life Science)
      Ministry of Education, Culture, Sports, Science and TechnologyJapan25280109
      Ministry of Education, Culture, Sports, Science and TechnologyJapan26242075

      Revision History  (Full details and data files)

      • Version 1.0: 2016-11-02
        Type: Initial release
      • Version 1.1: 2016-11-16
        Changes: Database references
      • Version 1.2: 2020-02-26
        Changes: Data collection, Database references, Derived calculations