7RGK image
Entry Detail
PDB ID:
7RGK
Keywords:
OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Title:
DfrA5 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)
Biological Source:
Source Organism:
Escherichia coli
Host Organism:
Escherichia coli BL21(DE3)
PDB Version:
Deposition Date:
2021-07-15
Release Date:
2022-05-25
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.19 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 43
7RGK validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:Dihydrofolate reductase type 5
Chain IDs:A, B
Chain Length:157
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P11731 Pfam ID:PF00186
Ligand Molecules
560
NAP
SO4
Primary Citation
Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens.
Commun Biol 5 459 459 (2022)
PMID: 35562546 DOI: 10.1038/s42003-022-03384-y

Abstact

Two plasmid-encoded dihydrofolate reductase (DHFR) isoforms, DfrA1 and DfrA5, that give rise to high levels of resistance in Gram-negative bacteria were structurally and biochemically characterized to reveal the mechanism of TMP resistance and to support phylogenic groupings for drug development against antibiotic resistant pathogens. Preliminary screening of novel antifolates revealed related chemotypes that showed high levels of inhibitory potency against Escherichia coli chromosomal DHFR (EcDHFR), DfrA1, and DfrA5. Kinetics and biophysical analysis, coupled with crystal structures of trimethoprim bound to EcDHFR, DfrA1 and DfrA5, and two propargyl-linked antifolates (PLA) complexed with EcDHFR, DfrA1 and DfrA5, were determined to define structural features of the substrate binding pocket and guide synthesis of pan-DHFR inhibitors.

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Primary Citation of related structures
7RGK