8AD8 | pdb_00008ad8

Flavin-dependent tryptophan 6-halogenase Thal in complex with a D-Trp-Ser dipeptide

• PDB DOI: https://doi.org/10.2210/pdb8AD8/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Streptomyces albogriseolus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-07-08 Released: 2022-10-12 
• Deposition Author(s): Gafe, S., Moritzer, A.C., Montua, N., Sewald, N., Niemann, H.H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.250 (Depositor) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Enzymatic Late-Stage Halogenation of Peptides.

Schnepel, C., Moritzer, A.C., Gafe, S., Montua, N., Minges, H., Niess, A., Niemann, H.H., Sewald, N.

(2023) Chembiochem 24: e202200569-e202200569

• PubMed: 36259362 
• DOI: https://doi.org/10.1002/cbic.202200569
• Primary Citation Related Structures: 
  8AD7, 8AD8


• PubMed Abstract: 
  

  The late-stage site-selective derivatisation of peptides has many potential applications in structure-activity relationship studies and postsynthetic modification or conjugation of bioactive compounds. The development of orthogonal methods for C-H functionalisation is crucial for such peptide derivatisation. Among them, biocatalytic methods are increasingly attracting attention. Tryptophan halogenases emerged as valuable catalysts to functionalise tryptophan (Trp), while direct enzyme-catalysed halogenation of synthetic peptides is yet unprecedented. Here, it is reported that the Trp 6-halogenase Thal accepts a wide range of amides and peptides containing a Trp moiety. Increasing the sequence length and reaction optimisation made bromination of pentapeptides feasible with good turnovers and a broad sequence scope, while regioselectivity turned out to be sequence dependent. Comparison of X-ray single crystal structures of Thal in complex with d-Trp and a dipeptide revealed a significantly altered binding mode for the peptide. The viability of this bioorthogonal approach was exemplified by halogenation of a cyclic RGD peptide.

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Organizational Affiliation: 
• Organische und Bioorganische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany.
Present address: Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
Strukturbiochemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 121.12 kDa 
• Atom Count: 8,347 
• Modeled Residue Count: 1,039 
• Deposited Residue Count: 1,068 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan 6-halogenase	A, B	534	Streptomyces albogriseolus	Mutation(s): 0  Gene Names: thal, thdH EC: 1.14.19.59
UniProt
Find proteins for A1E280 (Streptomyces albogriseolus) Explore A1E280  Go to UniProtKB:  A1E280

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LT0 (Subject of Investigation/LOI)	D [auth A]	D-tryptophyl-L-serine C14 H17 N3 O4 MYVYPSWUSKCCHG-PWSUYJOCSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.195 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/952

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.2	α = 90
b = 137.2	β = 90
c = 143.8	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Gafe, S., Moritzer, A.C., Montua, N., Sewald, N., Niemann, H.H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2022-11-02
  Changes: Database references
• Version 1.2: 2022-12-07
  Changes: Database references
• Version 1.3: 2023-01-11
  Changes: Database references
• Version 1.4: 2023-06-14
  Changes: Structure summary
• Version 1.5: 2024-02-07
  Changes: Data collection, Refinement description