4L87

Crystal structure of the human seryl-tRNA synthetase in complex with Ser-SA at 2.9 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of Human Seryl-tRNA Synthetase and Ser-SA Complex Reveals a Molecular Lever Specific to Higher Eukaryotes.

Xu, X.Shi, Y.Yang, X.L.

(2013) Structure 21: 2078-2086

  • DOI: https://doi.org/10.1016/j.str.2013.08.021
  • Primary Citation of Related Structures:  
    4L87

  • PubMed Abstract: 

    Seryl-tRNA synthetase (SerRS), an essential enzyme for translation, also regulates vascular development. This "gain-of-function" has been linked to the UNE-S domain added to vertebrate SerRS during evolution. However, the significance of two insertions also specific to higher eukaryotic SerRS remains elusive. Here, we determined the crystal structure of human SerRS in complex with Ser-SA, an aminoacylation reaction intermediate analog, at 2.9 Å resolution. Despite a 70 Å distance, binding of Ser-SA in the catalytic domain dramatically leverages the position of Insertion I in the tRNA binding domain. Importantly, this leverage is specific to higher eukaryotes and not seen in bacterial, archaeal, and lower eukaryotic SerRSs. Deletion of Insertion I does not affect tRNA binding but instead reduce the catalytic efficiency of the synthetase. Thus, a long-range conformational and functional communication specific to higher eukaryotes is found in human SerRS, possibly to coordinate translation with vasculogenesis.


  • Organizational Affiliation

    Departments of Chemical Physiology and Cell and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province 310036, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine--tRNA ligase, cytoplasmic476Homo sapiensMutation(s): 0 
Gene Names: SARSSERS
EC: 6.1.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P49591 (Homo sapiens)
Explore P49591 
Go to UniProtKB:  P49591
PHAROS:  P49591
GTEx:  ENSG00000031698 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49591
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.074α = 90
b = 167.074β = 90
c = 65.156γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Database references
  • Version 1.2: 2013-11-27
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description