1ZH6

Crystal Structure of p-acetylphenylalanine-tRNA synthetase in complex with p-acetylphenylalanine

• PDB DOI: https://doi.org/10.2210/pdb1ZH6/pdb

• Classification: LIGASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-04-22 Released: 2006-04-04 
• Deposition Author(s): Turner, J.M., Graziano, J., Spraggon, G., Schultz, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.278 
• R-Value Work: 0.209 
• R-Value Observed: 0.213 

Literature

Structural characterization of a p-acetylphenylalanyl aminoacyl-tRNA synthetase.

Turner, J.M., Graziano, J., Spraggon, G., Schultz, P.G.

(2005) J Am Chem Soc 127: 14976-14977

• PubMed: 16248607 
• DOI: https://doi.org/10.1021/ja0549042
• Primary Citation of Related Structures:  
  1ZH6


• PubMed Abstract: 
  

  It has been recently shown that orthogonal tRNA/aminoacyl-tRNA synthetase pairs can be evolved to allow genetic incorporation of unnatural amino acids into proteins in both prokaryotes and eukaryotes. Here we describe the crystal structure of an evolved aminoacyl-tRNA synthetase that charges the unnatural amino acid p-acetylphenylalanine. Molecular recognition is due to altered hydrogen bonding and packing interactions with bound substrate that result from changes in both side-chain and backbone conformation.

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Organizational Affiliation: 

Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.46 kDa 
• Atom Count: 2,565 
• Modelled Residue Count: 307 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-tRNA synthetase	A	314	Methanocaldococcus jannaschii	Mutation(s): 4  Gene Names: tyrS EC: 6.1.1.1
UniProt
Find proteins for Q57834 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57834  Go to UniProtKB:  Q57834

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4AF	B [auth A]	4-ACETYL-L-PHENYLALANINE C11 H13 N O3 ZXSBHXZKWRIEIA-JTQLQIEISA-N
BME	C [auth A], D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.278 
• R-Value Work: 0.209 
• R-Value Observed: 0.213 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.362	α = 90
b = 103.362	β = 90
c = 70.837	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-04 
Deposition Author(s): Turner, J.M., Graziano, J., Spraggon, G., Schultz, P.G.

Revision History  

• Version 1.0: 2006-04-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection