2ARD | pdb_00002ard

The structure of tryptophan 7-halogenase (PrnA) suggests a mechanism for regioselective chlorination

• PDB DOI: https://doi.org/10.2210/pdb2ARD/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Pseudomonas fluorescens
• Expression System: Pseudomonas fluorescens
• Mutation(s): No 


• Deposited: 2005-08-19 Released: 2005-10-04 
• Deposition Author(s): Dong, C., Flecks, S., Unversucht, S., Haupt, C., Van Pee, K.H., Naismith, J.H., Scottish Structural Proteomics Facility (SSPF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination.

Dong, C., Flecks, S., Unversucht, S., Haupt, C., van Pee, K.H., Naismith, J.H.

(2005) Science 309: 2216-2219

• PubMed: 16195462 
• DOI: https://doi.org/10.1126/science.1116510
• Primary Citation Related Structures: 
  2APG, 2AQJ, 2AR8, 2ARD


• PubMed Abstract: 
  

  Chlorinated natural products include vancomycin and cryptophycin A. Their biosynthesis involves regioselective chlorination by flavin-dependent halogenases. We report the structural characterization of tryptophan 7-halogenase (PrnA), which regioselectively chlorinates tryptophan. Tryptophan and flavin adenine dinucleotide (FAD) are separated by a 10 angstrom-long tunnel and bound by distinct enzyme modules. The FAD module is conserved in halogenases and is related to flavin-dependent monooxygenases. On the basis of biochemical studies, crystal structures, and by analogy with monooxygenases, we predict that FADH2 reacts with O2 to make peroxyflavin, which is decomposed by Cl-. The resulting HOCl is guided through the tunnel to tryptophan, where it is activated to participate in electrophilic aromatic substitution.

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Organizational Affiliation: 
• Centre for Biomolecular Sciences, EaStchem, University of St. Andrews, St. Andrews KY16 9ST, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.93 kDa 
• Atom Count: 4,154 
• Modeled Residue Count: 503 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tryptophan halogenase PrnA	A	538	Pseudomonas fluorescens	Mutation(s): 0  Gene Names: prnA EC: 1.14.19.9
UniProt
Find proteins for P95480 (Pseudomonas fluorescens) Explore P95480  Go to UniProtKB:  P95480

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDA	B [auth A]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C27 H35 N9 O15 P2 YPZRHBJKEMOYQH-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.3	α = 90
b = 68.3	β = 90
c = 274.9	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-04 
Deposition Author(s): Dong, C., Flecks, S., Unversucht, S., Haupt, C., Van Pee, K.H., Naismith, J.H., Scottish Structural Proteomics Facility (SSPF)

Revision History  

• Version 1.0: 2005-10-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2015-12-09
  Changes: Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description