6CUZ

Engineered TrpB from Pyrococcus furiosus, PfTrpB7E6 with (2S,3R)-ethylserine bound as the amino-acrylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Engineered Biosynthesis of beta-Alkyl Tryptophan Analogues.

Boville, C.E.Scheele, R.A.Koch, P.Brinkmann-Chen, S.Buller, A.R.Arnold, F.H.

(2018) Angew Chem Int Ed Engl 57: 14764-14768

  • DOI: 10.1002/anie.201807998
  • Primary Citation of Related Structures:  
    6CUZ, 6CUT, 6CUV

  • PubMed Abstract: 
  • Noncanonical amino acids (ncAAs) with dual stereocenters at the α and β positions are valuable precursors to natural products and therapeutics. Despite the potential applications of such bioactive β-branched ncAAs, their availability is limited due to the inefficiency of the multistep methods used to prepare them ...

    Noncanonical amino acids (ncAAs) with dual stereocenters at the α and β positions are valuable precursors to natural products and therapeutics. Despite the potential applications of such bioactive β-branched ncAAs, their availability is limited due to the inefficiency of the multistep methods used to prepare them. Herein we report a stereoselective biocatalytic synthesis of β-branched tryptophan analogues using an engineered variant of Pyrococcus furiosus tryptophan synthase (PfTrpB), PfTrpB 7E6 . PfTrpB 7E6 is the first biocatalyst to synthesize bulky β-branched tryptophan analogues in a single step, with demonstrated access to 27 ncAAs. The molecular basis for the efficient catalysis and broad substrate tolerance of PfTrpB 7E6 was explored through X-ray crystallography and UV/Vis spectroscopy, which revealed that a combination of active-site and remote mutations increase the abundance and persistence of a key reactive intermediate. PfTrpB 7E6 provides an operationally simple and environmentally benign platform for the preparation of β-branched tryptophan building blocks.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California, 91125, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase beta chain 1A, D388Pyrococcus furiosus DSM 3638Mutation(s): 9 
Gene Names: trpB1PF1706
EC: 4.2.1.20
UniProt
Find proteins for Q8U093 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U093 
Go to UniProtKB:  Q8U093
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase beta chain 1B, C388Pyrococcus furiosus DSM 3638Mutation(s): 9 
Gene Names: trpB1PF1706
EC: 4.2.1.20
UniProt
Find proteins for Q8U093 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U093 
Go to UniProtKB:  Q8U093
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEV (Subject of Investigation/LOI)
Query on FEV

Download Ideal Coordinates CCD File 
G [auth A], M [auth D](2E)-2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-2-enoic acid
C13 H17 N2 O7 P
GKBVRDDWDGNBFQ-VVUJNEFVSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
J [auth C]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], H [auth B], I [auth C], K [auth D], L [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
B, CL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.222α = 90
b = 109.297β = 90
c = 159.928γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-07
    Changes: Data collection, Database references