Crystal structure of the human mitochondrial seryl-tRNA synthetase (mt SerRS) bound with a seryl-adenylate analogue

Experimental Data Snapshot

  • Resolution: 2.95 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

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Structural basis for shape-selective recognition and aminoacylation of a D-armless human mitochondrial tRNA.

Kuhle, B.Hirschi, M.Doerfel, L.K.Lander, G.C.Schimmel, P.

(2022) Nat Commun 13: 5100-5100

  • DOI: https://doi.org/10.1038/s41467-022-32544-1
  • Primary Citation of Related Structures:  
    7TZB, 7U2A, 7U2B

  • PubMed Abstract: 

    Human mitochondrial gene expression relies on the specific recognition and aminoacylation of mitochondrial tRNAs (mtRNAs) by nuclear-encoded mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs). Despite their essential role in cellular energy homeostasis, strong mutation pressure and genetic drift have led to an unparalleled sequence erosion of animal mtRNAs. The structural and functional consequences of this erosion are not understood. Here, we present cryo-EM structures of the human mitochondrial seryl-tRNA synthetase (mSerRS) in complex with mtRNA Ser(GCU) . These structures reveal a unique mechanism of substrate recognition and aminoacylation. The mtRNA Ser(GCU) is highly degenerated, having lost the entire D-arm, tertiary core, and stable L-shaped fold that define canonical tRNAs. Instead, mtRNA Ser(GCU) evolved unique structural innovations, including a radically altered T-arm topology that serves as critical identity determinant in an unusual shape-selective readout mechanism by mSerRS. Our results provide a molecular framework to understand the principles of mito-nuclear co-evolution and specialized mechanisms of tRNA recognition in mammalian mitochondrial gene expression.

  • Organizational Affiliation

    Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA. bkuhle@scripps.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine--tRNA ligase, mitochondrial
A, B
484Homo sapiensMutation(s): 0 
Gene Names: SARS2SARSM
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP81 (Homo sapiens)
Explore Q9NP81 
Go to UniProtKB:  Q9NP81
GTEx:  ENSG00000104835 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NP81
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.95 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.59α = 90
b = 150.59β = 90
c = 142.47γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM125908-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description