6BZA

Crystal structure of halogenase PltM in complex with phloroglucinol and FAD

• PDB DOI: https://doi.org/10.2210/pdb6BZA/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Pseudomonas protegens Pf-5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-12-22 Released: 2019-03-20 
• Deposition Author(s): Pang, A.H., Garneau-Tsodikova, S., Tsodikov, O.V.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.253 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Literature

Unusual substrate and halide versatility of phenolic halogenase PltM.

Mori, S., Pang, A.H., Thamban Chandrika, N., Garneau-Tsodikova, S., Tsodikov, O.V.

(2019) Nat Commun 10: 1255-1255

• PubMed: 30890712 
• DOI: https://doi.org/10.1038/s41467-019-09215-9
• Primary Citation of Related Structures:  
  6BZA, 6BZI, 6BZN, 6BZQ, 6BZT, 6BZZ


• PubMed Abstract: 
  

  Controlled halogenation of chemically versatile substrates is difficult to achieve. Here we describe a unique flavin-dependent halogenase, PltM, which is capable of utilizing a wide range of halides for installation on a diverse array of phenolic compounds, including FDA-approved drugs and natural products, such as terbutaline, fenoterol, resveratrol, and catechin. Crystal structures of PltM in complex with phloroglucinol and FAD in different states yield insight into substrate recognition and the FAD recycling mechanism of this halogenase.

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Organizational Affiliation: 

Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 235.42 kDa 
• Atom Count: 15,979 
• Modelled Residue Count: 2,001 
• Deposited Residue Count: 2,088 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Halogenase PltM	A, B, C, D	522	Pseudomonas protegens Pf-5	Mutation(s): 0  Gene Names: pltM, PFL_2784 EC: 3.8.1.1
UniProt
Find proteins for Q4KCZ3 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4KCZ3  Go to UniProtKB:  Q4KCZ3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	F [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
13X	E [auth A], H [auth B], I [auth C]	benzene-1,3,5-triol C6 H6 O3 QCDYQQDYXPDABM-UHFFFAOYSA-N
CL	J [auth C], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.253 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.242	α = 90
b = 156.98	β = 90
c = 213.71	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Pang, A.H., Garneau-Tsodikova, S., Tsodikov, O.V.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1149427

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-04-03
  Changes: Data collection, Database references
• Version 1.2: 2019-04-10
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references