6WN2 | pdb_00006wn2

Tyrosyl t-RNA Synthetase Mutant from E.coli Complexed with sulfotyrosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.223 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6WN2

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Functional genetic encoding of sulfotyrosine in mammalian cells.

He, X.Chen, Y.Beltran, D.G.Kelly, M.Ma, B.Lawrie, J.Wang, F.Dodds, E.Zhang, L.Guo, J.Niu, W.

(2020) Nat Commun 11: 4820-4820

  • DOI: https://doi.org/10.1038/s41467-020-18629-9
  • Primary Citation Related Structures: 
    6WN2

  • PubMed Abstract: 

    Protein tyrosine O-sulfation (PTS) plays a crucial role in extracellular biomolecular interactions that dictate various cellular processes. It also involves in the development of many human diseases. Regardless of recent progress, our current understanding of PTS is still in its infancy. To promote and facilitate relevant studies, a generally applicable method is needed to enable efficient expression of sulfoproteins with defined sulfation sites in live mammalian cells. Here we report the engineering, in vitro biochemical characterization, structural study, and in vivo functional verification of a tyrosyl-tRNA synthetase mutant for the genetic encoding of sulfotyrosine in mammalian cells. We further apply this chemical biology tool to cell-based studies on the role of a sulfation site in the activation of chemokine receptor CXCR4 by its ligand. Our work will not only facilitate cellular studies of PTS, but also paves the way for economical production of sulfated proteins as therapeutic agents in mammalian systems.


  • Organizational Affiliation
    • Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA.

Macromolecule Content 

  • Total Structure Weight: 74.18 kDa 
  • Atom Count: 5,538 
  • Modeled Residue Count: 636 
  • Deposited Residue Count: 644 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine--tRNA ligase
A, B
322Escherichia coliMutation(s): 3 
Gene Names: tyrSCR539_12835
EC: 6.1.1.1
UniProt
Find proteins for P0AGJ9 (Escherichia coli (strain K12))
Explore P0AGJ9 
Go to UniProtKB:  P0AGJ9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AGJ9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TYS
(Subject of Investigation/LOI)

Query on TYS



Download:Ideal Coordinates CCD File
C [auth A],
L [auth B]
O-SULFO-L-TYROSINE
C9 H11 N O6 S
CIQHWLTYGMYQQR-QMMMGPOBSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
M [auth B],
N [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
Q [auth B]
R [auth B]
I [auth A],
J [auth A],
K [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA

Query on NA



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
O [auth B],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.223 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.093α = 90
b = 93.904β = 92.63
c = 99.9γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AutoSolphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCLP 1846908

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references