7YWK | pdb_00007ywk

Crystal structure of an engineered TycA variant, TycApPLA, in complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 
    0.169 (Depositor), 0.169 (DCC) 
  • R-Value Work: 
    0.119 (Depositor), 0.119 (DCC) 
  • R-Value Observed: 
    0.121 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7YWK

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Reprogramming Nonribosomal Peptide Synthetases for Site-Specific Insertion of alpha-Hydroxy Acids.

Camus, A.Truong, G.Mittl, P.R.E.Markert, G.Hilvert, D.

(2022) J Am Chem Soc 144: 17567-17575

  • DOI: https://doi.org/10.1021/jacs.2c07013
  • Primary Citation Related Structures: 
    7YWJ, 7YWK

  • PubMed Abstract: 

    High-throughput engineering has the potential to revolutionize the customization of biosynthetic assembly lines for the sustainable production of pharmaceutically relevant natural product analogs. Here, we show that the substrate specificity of gatekeeper adenylation domains of nonribosomal peptide synthetases can be switched from an α-amino acid to an α-hydroxy acid in a single round of combinatorial mutagenesis and selection using yeast cell surface display. In addition to shedding light on how such proteins discriminate between amino and hydroxy groups, the remodeled domains function in a pathway context to produce α-hydroxy acid-containing linear peptides and cyclic depsipeptides with high efficiency. Site-specific replacement of backbone amines with oxygens by an engineered synthetase provides the means to probe and tune the activities of diverse peptide metabolites in a simple and predictable fashion.


  • Organizational Affiliation
    • Laboratory of Organic Chemistry, ETH Zürich, 8093 Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 96.5 kDa 
  • Atom Count: 8,117 
  • Modeled Residue Count: 800 
  • Deposited Residue Count: 854 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrocidine synthase 1
A, B
427Brevibacillus 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
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP

Query on AMP



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
BTB

Query on BTB



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free:  0.169 (Depositor), 0.169 (DCC) 
  • R-Value Work:  0.119 (Depositor), 0.119 (DCC) 
  • R-Value Observed: 0.121 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.893α = 90
b = 60.617β = 90
c = 250.537γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-10-12
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description