5V58 | pdb_00005v58

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

• PDB DOI: https://doi.org/10.2210/pdb5V58/pdb

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.272 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

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

• PubMed: 29273753 
• DOI: https://doi.org/10.1038/s41467-017-02201-z
• Primary Citation 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.

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Organizational Affiliation: 
• The Scripps Laboratories for tRNA Synthetase Research and the Department of Molecular Medicine, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA.
Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, China.
Department of Chemistry, New York University, Abu Dhabi, PO Box 129188, United Arab Emirates.
Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, 43220, USA.
Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA.
The Scripps Laboratories for tRNA Synthetase Research and Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
The Scripps Laboratories for tRNA Synthetase Research and the Department of Molecular Medicine, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA. [e-mail].
The Scripps Laboratories for tRNA Synthetase Research and Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.56 kDa 
• Atom Count: 3,805 
• Modeled Residue Count: 476 
• Deposited Residue Count: 519 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional glutamate/proline--tRNA ligase	A	519	Homo sapiens	Mutation(s): 0  Gene Names: EPRS, GLNS, PARS, QARS, QPRS, PIG32 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
PHAROS:  P07814 GTEx:  ENSG00000136628

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8X1	B [auth A]	5'-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine C14 H19 N7 O7 S DQFRXHHGQUUTOL-XLZJSAHRSA-N
ZN	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 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.766	α = 90
b = 86.766	β = 90
c = 108.773	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-10 
Deposition Author(s): Zhou, H., Song, Y., Schimmel, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM23562

Revision History  

• 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
• Version 1.3: 2024-11-20
  Changes: Structure summary