5ZYT

Crystal structure of human MGME1 with 3' overhang double strand DNA3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into DNA degradation by human mitochondrial nuclease MGME1

Yang, C.Wu, R.Liu, H.Chen, Y.Gao, Y.Chen, X.Li, Y.Ma, J.Li, J.Gan, J.

(2018) Nucleic Acids Res 46: 11075-11088

  • DOI: 10.1093/nar/gky855
  • Primary Citation of Related Structures:  
    5ZYU, 5ZYT, 5ZYW, 5ZYV

  • PubMed Abstract: 
  • Mitochondrial nucleases play important roles in accurate maintenance and correct metabolism of mtDNA, the own genetic materials of mitochondria that are passed exclusively from mother to child. MGME1 is a highly conserved DNase that was discovered recently ...

    Mitochondrial nucleases play important roles in accurate maintenance and correct metabolism of mtDNA, the own genetic materials of mitochondria that are passed exclusively from mother to child. MGME1 is a highly conserved DNase that was discovered recently. Mutations in MGME1-coding gene lead to severe mitochondrial syndromes characterized by external ophthalmoplegia, emaciation, and respiratory failure in humans. Unlike many other nucleases that are distributed in multiple cellular organelles, human MGME1 is a mitochondria-specific nuclease; therefore, it can serve as an ideal target for treating related syndromes. Here, we report one HsMGME1-Mn2+ complex and three different HsMGME1-DNA complex structures. In combination with in vitro cleavage assays, our structures reveal the detailed molecular basis for substrate DNA binding and/or unwinding by HsMGME1. Besides the conserved two-cation-assisted catalytic mechanism, structural analysis of HsMGME1 and comparison with homologous proteins also clarified substrate binding and cleavage directionalities of the DNA double-strand break repair complexes RecBCD and AddAB.


    Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial genome maintenance exonuclease 1A, B, C, D324Homo sapiensMutation(s): 0 
Gene Names: MGME1C20orf72DDK1
EC: 3.1
Find proteins for Q9BQP7 (Homo sapiens)
Explore Q9BQP7 
Go to UniProtKB:  Q9BQP7
NIH Common Fund Data Resources
PHAROS:  Q9BQP7
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*TP*TP*CP*TP*TP*CP*C)-3')E, F, G, H18unidentified
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free: 0.296 
    • R-Value Work: 0.249 
    • R-Value Observed: 0.252 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 146.497α = 90
    b = 77.489β = 112.4
    c = 164.714γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-3000data reduction
    HKL-3000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2018-05-28 
    • Released Date: 2018-09-19 
    • Deposition Author(s): Yang, C., Gan, J.

    Revision History  (Full details and data files)

    • Version 1.0: 2018-09-19
      Type: Initial release
    • Version 1.1: 2018-10-31
      Changes: Data collection, Database references
    • Version 1.2: 2018-11-28
      Changes: Data collection, Database references