6BZZ

Crystal structure of halogenase PltM in complex with partially bound FAD

PDB DOI: https://doi.org/10.2210/pdb6BZZ/pdb

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

Deposited: 2017-12-26 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.245
R-Value Work: 0.219
R-Value Observed: 0.220

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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

PubMed: 30890712 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 236.79 kDa
Atom Count: 16,332
Modelled Residue Count: 1,999
Deposited Residue Count: 2,088
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Halogenase PltM	A, B	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4KCZ3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Halogenase PltM	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4KCZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain L [auth D] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C]	F [auth A], H [auth B], J [auth C], L [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS Query on OCS	C, D	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.245
R-Value Work: 0.219
R-Value Observed: 0.220
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.815	α = 90
b = 157.234	β = 90
c = 214.008	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Pang, A.H.

Garneau-Tsodikova, S.

Tsodikov, O.V.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-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
Version 1.5: 2023-11-15
Changes: Data collection