5V58

Crystal structure of human prolyl-tRNA synthetase in complex with Aze-SA

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-03-13 Released: 2018-01-10 
  • Deposition Author(s): Zhou, H., Song, Y., Schimmel, P.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.

Song, Y.Zhou, H.Vo, M.N.Shi, Y.Nawaz, M.H.Vargas-Rodriguez, O.Diedrich, J.K.Yates, J.R.Kishi, S.Musier-Forsyth, K.Schimmel, P.

(2017) Nat Commun 8: 2281-2281

  • DOI: https://doi.org/10.1038/s41467-017-02201-z
  • Primary Citation of Related Structures:  
    5V58, 5V59

  • PubMed Abstract: 

    Hundreds of non-proteinogenic (np) amino acids (AA) are found in plants and can in principle enter human protein synthesis through foods. While aminoacyl-tRNA synthetase (AARS) editing potentially provides a mechanism to reject np AAs, some have pathological associations. Co-crystal structures show that vegetable-sourced azetidine-2-carboxylic acid (Aze), a dual mimic of proline and alanine, is activated by both human prolyl- and alanyl-tRNA synthetases. However, it inserts into proteins as proline, with toxic consequences in vivo. Thus, dual mimicry increases odds for mistranslation through evasion of one but not both tRNA synthetase editing systems.


  • Organizational Affiliation

    The Scripps Laboratories for tRNA Synthetase Research and Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional glutamate/proline--tRNA ligase519Homo sapiensMutation(s): 0 
Gene Names: EPRSGLNSPARSQARSQPRSPIG32
EC: 6.1.1.17 (PDB Primary Data), 6.1.1.15 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P07814 (Homo sapiens)
Explore P07814 
Go to UniProtKB:  P07814
GTEx:  ENSG00000136628 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07814
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8X1
Query on 8X1

Download Ideal Coordinates CCD File 
B [auth A]5'-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine
C14 H19 N7 O7 S
DQFRXHHGQUUTOL-XLZJSAHRSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.766α = 90
b = 86.766β = 90
c = 108.773γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



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 StatesGM23562

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description