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: 2.897 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.str.2013.08.021

  • 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 insertio ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine--tRNA ligase, cytoplasmic
A
476Homo sapiensGene Names: SARS (SERS)
EC: 6.1.1.11
Find proteins for P49591 (Homo sapiens)
Go to Gene View: SARS
Go to UniProtKB:  P49591
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SSA
Query on SSA

Download SDF File 
Download CCD File 
A
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.897 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.255 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 167.074α = 90.00
b = 167.074β = 90.00
c = 65.156γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-16 
  • Released Date: 2013-10-02 
  • Deposition Author(s): Xu, X., Yang, X.-L.

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-11-06
    Type: Database references
  • Version 1.2: 2013-11-27
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description