Crystal Structure of mammalian mitochondrial seryl-tRNA synthetase complexed with seryl-adenylate

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.210 

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Dual-mode recognition of noncanonical tRNAs(Ser) by seryl-tRNA synthetase in mammalian mitochondria

Chimnaronk, S.Jeppesen, M.G.Suzuki, T.Nyborg, J.Watanabe, K.

(2005) EMBO J 24: 3369-3379

  • DOI: https://doi.org/10.1038/sj.emboj.7600811
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The secondary structures of metazoan mitochondrial (mt) tRNAs(Ser) deviate markedly from the paradigm of the canonical cloverleaf structure; particularly, tRNA(Ser)(GCU) corresponding to the AGY codon (Y=U and C) is highly truncated and intrinsically missing the entire dihydrouridine arm. None of the mt serine isoacceptors possesses the elongated variable arm, which is the universal landmark for recognition by seryl-tRNA synthetase (SerRS). Here, we report the crystal structure of mammalian mt SerRS from Bos taurus in complex with seryl adenylate at an atomic resolution of 1.65 A. Coupling structural information with a tRNA-docking model and the mutagenesis studies, we have unraveled the key elements that establish tRNA binding specificity, differ from all other known bacterial and eukaryotic systems, are the characteristic extensions in both extremities, as well as a few basic residues residing in the amino-terminal helical arm of mt SerRS. Our data further uncover an unprecedented mechanism of a dual-mode recognition employed to discriminate two distinct 'bizarre' mt tRNAs(Ser) by alternative combination of interaction sites.

  • Organizational Affiliation

    Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Seryl-tRNA synthetase
A, B
501Bos taurusMutation(s): 0 
Gene Names: SerRSmt
Find proteins for Q9N0F3 (Bos taurus)
Explore Q9N0F3 
Go to UniProtKB:  Q9N0F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9N0F3
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.864α = 90
b = 230.35β = 90
c = 135.59γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description