9SVN | pdb_00009svn

Structure of dihydrofolate reductase from Burkholderia thailandensis (I99L variant) complexed with trimethoprim and dihydrofolate

PDB DOI: https://doi.org/10.2210/pdb9SVN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia thailandensis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-10-03 Released: 2026-08-26
Deposition Author(s): Mechulam, Y., Schmitt, E., Lazennec-Schurdevin, C.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.247 (Depositor), 0.242 (DCC)
R-Value Work:
0.217 (Depositor), 0.211 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Evolutionary Convergence on a Dihydrofolate Reductase Mutation Drives Trimethoprim-Sulfamethoxazole Resistance in Burkholderia thailandensis.

Guillier, S., Lazennec-Schurdevin, C., Mondange, L., Sarilar, V., Marchandeau, M., Lemoigne, C., Lamer, O., Lescat, M., Schmitt, E., Mechulam, Y., Garrec, J., Biot, F.

(2026) ACS Infect Dis 12: 2627-2641

PubMed: 42599400 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsinfecdis.5c01132
Primary Citation Related Structures:
9SVM, 9SVN

PubMed Abstract:
Trimethoprim-sulfamethoxazole (SXT) remains central to melioidosis eradication therapy, yet the genetic basis of resistance evolution in Burkholderia pseudomallei is not fully defined. Using Burkholderia thailandensis as a biosafe surrogate, we subjected populations to stepwise in vitro evolution under increasing SXT concentrations. Whole-genome sequencing revealed rapid population diversification followed by selective sweeps leading to fixation of fitter resistant variants. Early adaptation involved mutations in regulators of RND efflux systems and folate-associated genes, consistent with multifactorial resistance. Despite this heterogeneity, all evolutionary trajectories converged on a single nonsynonymous substitution, I99L, in dihydrofolate reductase (DHFR/FolA), which rose to fixation at high SXT concentrations. This substitution mirrors changes reported in SXT-resistant B. pseudomallei isolates from chronic infections. Allelic reconstruction demonstrated that Bt-DHFR(I99L) is sufficient to confer a 4- to 16-fold increase in trimethoprim MIC. Biochemical and structural analyses showed preserved catalytic activity but reduced trimethoprim binding, consistent with an allosteric resistance mechanism. Together, these findings establish DHFR as a dominant evolutionary target under SXT pressure and support B. thailandensis as a robust model for dissecting resistance evolution in B. pseudomallei.

Organizational Affiliation

Unité Bactériologie, Département Microbiologie et Maladies Infectieuses, CNR-LE Charbon, UMR-MD1-Inserm 1261, Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-Sur-Orge91220, France.

Macromolecule Content

Total Structure Weight: 98.69 kDa
Atom Count: 7,104
Modeled Residue Count: 829
Deposited Residue Count: 845
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B, C, D, E	169	Burkholderia thailandensis	Mutation(s): 1 Gene Names: C7S16_1590 EC: 1.5.1.3
UniProt
Find proteins for A0AAW9D207 (Burkholderia thailandensis) Explore A0AAW9D207 Go to UniProtKB: A0AAW9D207
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAW9D207
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download:Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], N [auth C], T [auth D], W [auth E]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D] Focus chain W [auth E] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D] Focus chain W [auth E]
TOP (Subject of Investigation/LOI) Query on TOP Download:Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain S [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain V [auth E] MOL2 format, chain S [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain V [auth E] mmCIF format, chain S [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], M [auth C], S [auth D], V [auth E]	TRIMETHOPRIM C₁₄ H₁₈ N₄ O₃ IEDVJHCEMCRBQM-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain S [auth D] Focus chain V [auth E] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain S [auth D] Focus chain V [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] L [auth B] O [auth C] P [auth C] H [auth A], I [auth A], L [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], U [auth D], X [auth E], Y [auth E], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]