1WLE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1038/sj.emboj.7600811
  • Primary Citation of Related Structures:  
    1WLE

  • 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 ...

    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.


    Related Citations: 
    • Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase
      Yokogawa, T., Shimada, N., Takeuchi, N., Benkowski, L., Suzuki, T., Omori, A., Ueda, T., Nishikawa, K., Spremulli, L.L., Watanabe, K.
      (2000) J Biol Chem 275: 19913
    • Dual mode recognition of two isoacceptor tRNAs by mammalian mitochondrial seryl-tRNA synthetase
      Shimada, N., Suzuki, T., Watanabe, K.
      (2001) J Biol Chem 276: 46770
    • Crystallization and preliminary X-ray diffraction study of mammalian mitochondrial seryl-tRNA synthetase
      Chimnaronk, S., Jeppesen, M.G., Shimada, N., Suzuki, T., Nyborg, J., Watanabe, K.
      (2004) Acta Crystallogr D Biol Crystallogr 60: 1319

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Seryl-tRNA synthetaseAB501Bos taurusMutation(s): 0 
Gene Names: SerRSmtSARS2SARSM
EC: 6.1.1.11
Find proteins for Q9N0F3 (Bos taurus)
Explore Q9N0F3 
Go to UniProtKB:  Q9N0F3
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRP
Query on SRP

Download CCD File 
A, B
SERYL ADENYLATE
C13 H19 N6 O9 P
UVSYURUCZPPUQD-MACXSXHHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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