6LY3

PylRS C-terminus domain mutant bound with 3-Benzothienyl-L-alanine and AMPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues.

Jiang, H.K.Wang, Y.H.Weng, J.H.Kurkute, P.Li, C.L.Lee, M.N.Chen, P.J.Tseng, H.W.Tsai, M.D.Wang, Y.S.

(2020) Biochemistry 59: 2205-2209

  • DOI: 10.1021/acs.biochem.0c00307
  • Primary Citation of Related Structures:  
    6LYB, 6LYA, 6LY3, 6LY6, 6LY7

  • PubMed Abstract: 
  • Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA have been evolved to generate genetically encoded noncanonical amino acids (ncAAs). Use of tryptophan (Trp) analogues with pyrrole ring modification for their spatial and polarity tuning in enzyme activity and substrate specificity is still limited ...

    Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA have been evolved to generate genetically encoded noncanonical amino acids (ncAAs). Use of tryptophan (Trp) analogues with pyrrole ring modification for their spatial and polarity tuning in enzyme activity and substrate specificity is still limited. Herein, we report the application of an evolved PylRS, FOWRS2, for efficient incorporation of five Trp analogues into the deubiquitinase USP30 to decipher the role of W475 for diubiquitin selectivity. Structures of the five FOWRS-C/Trp analogue complexes at 1.7-2.5 Å resolution showed multiple ncAA binding modes. The W475 near the USP30 active site was replaced with Trp analogues, and the effect on the activity as well as the selectivity toward diubiquitin linkage types was examined. It was found that the Trp analogue with a formyl group attached to the nitrogen atom of the indole ring led to an improved activity of USP30 likely due to enhanced polar interactions and that another Trp analogue, 3-benzothienyl-l-alanine, induced a unique K6-specificity. Collectively, genetically encoded noncanonical Trp analogues by evolved PylRS· tRNA CUA Pyl pair unravel the spatial role of USP30-W475 in its diubiquitin selectivity.


    Organizational Affiliation

    Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyrrolysine--tRNA ligaseA277Methanosarcina mazeiMutation(s): 3 
Gene Names: pylSDU43_20175DU67_18120
EC: 6.1.1.26
Find proteins for A0A0F8JXW8 (Methanosarcina mazei)
Explore A0A0F8JXW8 
Go to UniProtKB:  A0A0F8JXW8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
4OG
Query on 4OG

Download CCD File 
A
3-(1-benzothiophen-3-yl)-L-alanine
C11 H11 N O2 S
GAUUPDQWKHTCAX-VIFPVBQESA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.252α = 90
b = 105.252β = 90
c = 71.701γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)TaiwanAS-KPQ-109-TPP2
Academia Sinica (Taiwan)TaiwanAS-KPQ-105-TPP
Ministry of Science and Technology (MoST, Taiwan)Taiwan107-2113-M-001-025-MY3

Revision History 

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Derived calculations, Structure summary