5ZYV

Crystal structure of human MGME1 with single strand DNA2 and Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1093/nar/gky855
  • Primary Citation of Related Structures:  
    5ZYT, 5ZYU, 5ZYV, 5ZYW

  • 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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial genome maintenance exonuclease 1254Homo sapiensMutation(s): 1 
Gene Names: MGME1C20orf72DDK1
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQP7 (Homo sapiens)
Explore Q9BQP7 
Go to UniProtKB:  Q9BQP7
PHAROS:  Q9BQP7
GTEx:  ENSG00000125871 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BQP7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*AP*AP*CP*AP*AP*T)-3')B [auth E]15unidentified
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.282α = 90
b = 106.151β = 90
c = 33.391γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

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
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description