8AQ8

FAD-dependent monooxygenase from Stenotrophomonas maltophilia

PDB DOI: https://doi.org/10.2210/pdb8AQ8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Stenotrophomonas maltophilia
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-08-11 Released: 2023-07-12
Deposition Author(s): Maly, M., Kolenko, P., Duskova, J., Skalova, T., Dohnalek, J.
Funding Organization(s): European Regional Development Fund, Ministry of Education, Youth and Sports of the Czech Republic, Czech Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.241
R-Value Work: 0.200
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia.

Maly, M., Kolenko, P., Stransky, J., Svecova, L., Duskova, J., Koval', T., Skalova, T., Trundova, M., Adamkova, K., Cerny, J., Bozikova, P., Dohnalek, J.

(2023) Acta Crystallogr F Struct Biol Commun 79: 180-192

PubMed: 37405486 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X23005381
Primary Citation of Related Structures:
8AQ8

PubMed Abstract:
The resistance of the emerging human pathogen Stenotrophomonas maltophilia to tetracycline antibiotics mainly depends on multidrug efflux pumps and ribosomal protection enzymes. However, the genomes of several strains of this Gram-negative bacterium code for a FAD-dependent monooxygenase (SmTetX) homologous to tetracycline destructases. This protein was recombinantly produced and its structure and function were investigated. Activity assays using SmTetX showed its ability to modify oxytetracycline with a catalytic rate comparable to those of other destructases. SmTetX shares its fold with the tetracycline destructase TetX from Bacteroides thetaiotaomicron; however, its active site possesses an aromatic region that is unique in this enzyme family. A docking study confirmed tetracycline and its analogues to be the preferred binders amongst various classes of antibiotics.

Organizational Affiliation

Institute of Biotechnology, Czech Academy of Sciences, v.v.i., BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic.

Macromolecule Content

Total Structure Weight: 160.96 kDa
Atom Count: 11,859
Modelled Residue Count: 1,368
Deposited Residue Count: 1,464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monooxygenase	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	366	Stenotrophomonas maltophilia	Mutation(s): 2 Gene Names: B9Y88_09170
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain M [auth BBB] SDF format, chain Q [auth CCC] SDF format, chain V [auth DDD] MOL2 format, chain E [auth AAA] MOL2 format, chain M [auth BBB] MOL2 format, chain Q [auth CCC] MOL2 format, chain V [auth DDD]	E [auth AAA], M [auth BBB], Q [auth CCC], V [auth DDD]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth AAA] Focus chain M [auth BBB] Focus chain Q [auth CCC] Focus chain V [auth DDD] Interactions & Density Focus chain E [auth AAA] Focus chain M [auth BBB] Focus chain Q [auth CCC] Focus chain V [auth DDD]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain K [auth AAA] SDF format, chain X [auth DDD] MOL2 format, chain K [auth AAA] MOL2 format, chain X [auth DDD]	K [auth AAA], X [auth DDD]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth AAA] Focus chain X [auth DDD] Interactions & Density Focus chain K [auth AAA] Focus chain X [auth DDD]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA]	G [auth AAA], H [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth AAA] Focus chain H [auth AAA] Interactions & Density Focus chain G [auth AAA] Focus chain H [auth AAA]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain I [auth AAA] SDF format, chain N [auth BBB] SDF format, chain R [auth CCC] SDF format, chain T [auth CCC] SDF format, chain W [auth DDD] MOL2 format, chain F [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain N [auth BBB] MOL2 format, chain R [auth CCC] MOL2 format, chain T [auth CCC] MOL2 format, chain W [auth DDD]	F [auth AAA] I [auth AAA] N [auth BBB] R [auth CCC] T [auth CCC] F [auth AAA], I [auth AAA], N [auth BBB], R [auth CCC], T [auth CCC], W [auth DDD]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain I [auth AAA] Focus chain N [auth BBB] Focus chain R [auth CCC] Focus chain T [auth CCC] Focus chain W [auth DDD] Interactions & Density Focus chain F [auth AAA] Focus chain I [auth AAA] Focus chain N [auth BBB] Focus chain R [auth CCC] Focus chain T [auth CCC] Focus chain W [auth DDD]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain J [auth AAA] SDF format, chain O [auth BBB] SDF format, chain S [auth CCC] MOL2 format, chain J [auth AAA] MOL2 format, chain O [auth BBB] MOL2 format, chain S [auth CCC]	J [auth AAA], O [auth BBB], S [auth CCC]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain S [auth CCC] Interactions & Density Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain S [auth CCC]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth AAA] SDF format, chain P [auth BBB] SDF format, chain U [auth CCC] SDF format, chain Y [auth DDD] MOL2 format, chain L [auth AAA] MOL2 format, chain P [auth BBB] MOL2 format, chain U [auth CCC] MOL2 format, chain Y [auth DDD]	L [auth AAA], P [auth BBB], U [auth CCC], Y [auth DDD]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth AAA] Focus chain P [auth BBB] Focus chain U [auth CCC] Focus chain Y [auth DDD] Interactions & Density Focus chain L [auth AAA] Focus chain P [auth BBB] Focus chain U [auth CCC] Focus chain Y [auth DDD]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.241
R-Value Work: 0.200
R-Value Observed: 0.202
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.15785/SBGRID/956

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.932	α = 90
b = 160.535	β = 95.914
c = 95.563	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
MoRDa	phasing
PHASER	phasing
Coot	model building
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-12

Deposition Author(s):

Funding Organization	Location	Grant Number
European Regional Development Fund	European Union	No. CZ.02.1.01/0.0/0.0/18_046/0015974
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2018127
European Regional Development Fund	European Union	CZ.02.1.01/0.0/0.0/15_003/0000447
Czech Academy of Sciences	Czech Republic	86652036
European Regional Development Fund	European Union	CZ.02.1.01/0.0/0.0/16_019/0000778

Revision History (Full details and data files)

Version 1.0: 2023-07-12
Type: Initial release
Version 1.1: 2023-07-19
Changes: Database references
Version 1.2: 2024-02-07
Changes: Data collection, Refinement description

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Help and Resources

8AQ8

FAD-dependent monooxygenase from Stenotrophomonas maltophilia

Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia.

Entity ID: 1

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)