6SLS | pdb_00006sls

Flavin-dependent tryptophan 6-halogenase Thal in complex with FAD

PDB DOI: https://doi.org/10.2210/pdb6SLS/pdb

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

Deposited: 2019-08-20 Released: 2019-10-16
Deposition Author(s): Moritzer, A., Niemann, H.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.225 (Depositor), 0.227 (DCC)
R-Value Work:
0.181 (Depositor), 0.185 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Binding of FAD and tryptophan to the tryptophan 6-halogenase Thal is negatively coupled.

Moritzer, A.C., Niemann, H.H.

(2019) Protein Sci 28: 2112-2118

PubMed: 31589794 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.3739
Primary Citation Related Structures:
6SLS, 6SLT

PubMed Abstract:
Flavin-dependent halogenases require reduced flavin adenine dinucleotide (FADH ₂ ), O ₂ , and halide salts to halogenate their substrates. We describe the crystal structures of the tryptophan 6-halogenase Thal in complex with FAD or with both tryptophan and FAD. If tryptophan and FAD were soaked simultaneously, both ligands showed impaired binding and in some cases only the adenosine monophosphate or the adenosine moiety of FAD was resolved, suggesting that tryptophan binding increases the mobility mainly of the flavin mononucleotide moiety. This confirms a negative cooperativity between the binding of substrate and cofactor that was previously described for other tryptophan halogenases. Binding of substrate to tryptophan halogenases reduces the affinity for the oxidized cofactor FAD presumably to facilitate the regeneration of FADH ₂ by flavin reductases.

Organizational Affiliation

Department of Chemistry, Bielefeld University, Bielefeld, Germany.

Macromolecule Content

Total Structure Weight: 122.92 kDa
Atom Count: 8,624
Modeled Residue Count: 1,041
Deposited Residue Count: 1,068
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1E280
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.225 (Depositor), 0.227 (DCC)
R-Value Work: 0.181 (Depositor), 0.185 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.56	α = 90
b = 138.56	β = 90
c = 142.05	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-10-16

Deposition Author(s):

Moritzer, A.

Niemann, H.H.

Revision History (Full details and data files)

Version 1.0: 2019-10-16
Type: Initial release
Version 1.1: 2019-10-30
Changes: Data collection, Database references
Version 1.2: 2019-11-27
Changes: Database references
Version 1.3: 2024-01-24
Changes: Data collection, Database references, Refinement description