6BZI

Crystal structure of halogenase PltM in complex with ethyl mercury and mercury

PDB DOI: https://doi.org/10.2210/pdb6BZI/pdb

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

Deposited: 2017-12-24 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: 2.40 Å
R-Value Free: 0.256
R-Value Work: 0.209
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

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

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: 240.69 kDa
Atom Count: 16,117
Modelled Residue Count: 1,971
Deposited Residue Count: 2,088
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4KCZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EMC Query on EMC Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain N [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	FA [auth C] GA [auth C] HA [auth C] N [auth A] QA [auth D] FA [auth C], GA [auth C], HA [auth C], N [auth A], QA [auth D], RA [auth D], Y [auth B], Z [auth B]	ETHYL MERCURY ION C₂ H₅ Hg MJOUBOKSWBMNGQ-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain N [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain N [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain Y [auth B] Focus chain Z [auth B]
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] F [auth A] BA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], MA [auth D], NA [auth D], OA [auth D], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain PA [auth D] SDF format, chain X [auth B] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain X [auth B] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain X [auth B]	M [auth A], PA [auth D], X [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain PA [auth D] Focus chain X [auth B] Interactions & Density Focus chain M [auth A] Focus chain PA [auth D] Focus chain X [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain E [auth A] SDF format, chain IA [auth D] SDF format, chain O [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain O [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain O [auth B]	AA [auth C], E [auth A], IA [auth D], O [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain IA [auth D] Focus chain O [auth B] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain IA [auth D] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.256
R-Value Work: 0.209
R-Value Observed: 0.212
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.722	α = 90
b = 156.338	β = 90
c = 216.134	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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: 2024-03-13
Changes: Data collection, Database references, Derived calculations