Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 72.01 kDa 
• Atom Count: 4696 
• Modelled Residue Count: 588 
• Deposited Residue Count: 628 
• Unique protein chains: 1

5U36

Crystal Structure Of A Mutant M. Jannashii Tyrosyl-tRNA Synthetase

• PDB DOI: 10.2210/pdb5U36/pdb

• Classification: LIGASE
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-12-01 Released: 2017-06-07 
• Deposition Author(s): Luo, X., Fu, G., Zhu, X., Wilson, I.A., Wang, F.
• 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: 3.03 Å
• R-Value Free: 0.282 
• R-Value Work: 0.201 
• R-Value Observed: 0.205 

Literature

Genetically encoding phosphotyrosine and its nonhydrolyzable analog in bacteria.

Luo, X., Fu, G., Wang, R.E., Zhu, X., Zambaldo, C., Liu, R., Liu, T., Lyu, X., Du, J., Xuan, W., Yao, A., Reed, S.A., Kang, M., Zhang, Y., Guo, H., Huang, C., Yang, P.Y., Wilson, I.A., Schultz, P.G., Wang, F.

(2017) Nat Chem Biol 13: 845-849

• PubMed: 28604693 
• DOI: 10.1038/nchembio.2405
• Primary Citation of Related Structures:  
  5U36


• PubMed Abstract: 
  

Tyrosine phosphorylation is a common protein post-translational modification that plays a critical role in signal transduction and the regulation of many cellular processes. Using a propeptide strategy to increase cellular uptake of O-phosphotyrosine (pTyr) and its nonhydrolyzable analog 4-phosphomethyl-L-phenylalanine (Pmp), we identified an orthogonal aminoacyl-tRNA synthetase-tRNA pair that allows site-specific incorporation of both pTyr and Pmp into recombinant proteins in response to the amber stop codon in Escherichia coli in good yields. The X-ray structure of the synthetase reveals a reconfigured substrate-binding site, formed by nonconservative mutations and substantial local structural perturbations. We demonstrate the utility of this method by introducing Pmp into a putative phosphorylation site and determining the affinities of the individual variants for the substrate 3BP2. In summary, this work provides a useful recombinant tool to dissect the biological functions of tyrosine phosphorylation at specific sites in the proteome.

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Organizational Affiliation: 

California Institute for Biomedical Research (Calibr), La Jolla, California, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine--tRNA ligase	A, B	314	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 6  Gene Names: tyrS, MJ0389 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.03 Å
• R-Value Free: 0.282 
• R-Value Work: 0.201 
• R-Value Observed: 0.205 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.634	α = 90
b = 130.559	β = 117.71
c = 59.956	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-12-01 
• Released Date: 2017-06-07 
Deposition Author(s): Luo, X., Fu, G., Zhu, X., Wilson, I.A., Wang, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM62159-14

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence