6BZT

Crystal structure of halogenase PltM L111Y mutant in complex with FAD

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Halogenase PltM
A, B, C, D
522Pseudomonas protegens Pf-5Mutation(s): 1 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4KCZ3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
Q [auth C],
U [auth D]		FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
BR
Query on BR
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
N [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
X [auth D]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
CA
Query on CA
Download Ideal Coordinates CCD File 
K [auth A],
P [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
R [auth C],
V [auth D],
W [auth D]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.974α = 90
b = 157.462β = 90
c = 213.036γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1149427

Revision History  (Full details and data files)

  • 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: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description