5N81

Crystal structure of an engineered TycA variant in complex with an O-propargyl-beta-Tyr-AMP analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Nonribosomal biosynthesis of backbone-modified peptides.

Niquille, D.L.Hansen, D.A.Mori, T.Fercher, D.Kries, H.Hilvert, D.

(2018) Nat Chem 10: 282-287

  • DOI: 10.1038/nchem.2891
  • Primary Citation of Related Structures:  
    5N81, 5N82

  • PubMed Abstract: 
  • Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of therapeutics. Using a high-throughput assay for catalytic activity, we show here that an L-Phe-specific module of an archetypal nonribosomal peptide synthetase can be reprogrammed to accept and process the backbone-modified amino acid (S)-β-Phe with near-native specificity and efficiency ...

    Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of therapeutics. Using a high-throughput assay for catalytic activity, we show here that an L-Phe-specific module of an archetypal nonribosomal peptide synthetase can be reprogrammed to accept and process the backbone-modified amino acid (S)-β-Phe with near-native specificity and efficiency. A co-crystal structure with a non-hydrolysable aminoacyl-AMP analogue reveals the origins of the 40,000-fold α/β-specificity switch, illuminating subtle but precise remodelling of the active site. When the engineered catalyst was paired with downstream module(s), (S)-β-Phe-containing peptides were produced at preparative scale in vitro (~1 mmol) and high titres in vivo (~100 mg l -1 ), highlighting the potential of biosynthetic pathway engineering for the construction of novel nonribosomal β-frameworks.


    Organizational Affiliation

    Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrocidine synthase 1A, B427Brevibacillus parabrevisMutation(s): 0 
Gene Names: tycA
EC: 5.1.1.11
UniProt
Find proteins for P09095 (Brevibacillus parabrevis)
Explore P09095 
Go to UniProtKB:  P09095
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09095
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8Q2
Query on 8Q2

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-(4-prop-2-ynoxyphenyl)propanoyl]sulfamate
C22 H25 N7 O8 S
SOQSTTVKSPLYCJ-KSHOWADASA-N
 Ligand Interaction
BTB
Query on BTB

Download Ideal Coordinates CCD File 
F [auth B]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.574α = 90
b = 60.245β = 90
c = 247.804γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references