8CIX

DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with Griselimycin.

Summary for 8CIX

• Entry DOI: 10.2210/pdb8cix/pdb
• Related PRD ID: PRD_002311
• Descriptor: Beta sliding clamp, Griselimycin, GLYCEROL, ... (8 entities in total)
• Functional Keywords: dnan, sliding clamp, dna-polymerase beta subunit, antibiotic, natural product, anti-tuberculosis, transferase
• Biological source: Escherichia coli; More
• Total number of polymer chains: 2
• Total formula weight: 42779.19

Authors

Fu, C.,Liu, Y.,Walt, C.,Bader, C.,Rasheed, S.,Lukat, P.,Neuber, M.,Blankenfeldt, W.,Kalinina, O.,Mueller, R. (deposition date: 2023-02-11, release date: 2023-11-29, Last modification date: 2024-02-07)

Primary citation

Fu, C.,Liu, Y.,Walt, C.,Rasheed, S.,Bader, C.D.,Lukat, P.,Neuber, M.,Haeckl, F.P.J.,Blankenfeldt, W.,Kalinina, O.V.,Muller, R.
Elucidation of unusual biosynthesis and DnaN-targeting mode of action of potent anti-tuberculosis antibiotics Mycoplanecins.
Nat Commun, 15:791-791, 2024

PubMed Abstract: DNA polymerase III sliding clamp (DnaN) was recently validated as a new anti-tuberculosis target employing griselimycins. Three (2 S,4 R)-4-methylproline moieties of methylgriselimycin play significant roles in target binding and metabolic stability. Here, we identify the mycoplanecin biosynthetic gene cluster by genome mining using bait genes from the 4-methylproline pathway. We isolate and structurally elucidate four mycoplanecins comprising scarce homo-amino acids and 4-alkylprolines. Evaluating mycoplanecin E against Mycobacterium tuberculosis surprisingly reveals an excitingly low minimum inhibition concentration at 83 ng/mL, thus outcompeting griselimycin by approximately 24-fold. We show that mycoplanecins bind DnaN with nanomolar affinity and provide a co-crystal structure of mycoplanecin A-bound DnaN. Additionally, we reconstitute the biosyntheses of the unusual L-homoleucine, L-homonorleucine, and (2 S,4 R)-4-ethylproline building blocks by characterizing in vitro the full set of eight enzymes involved. The biosynthetic study, bioactivity evaluation, and drug target validation of mycoplanecins pave the way for their further development to tackle multidrug-resistant mycobacterial infections.

PubMed: 38278788
DOI: 10.1038/s41467-024-44953-5

Experimental method

X-RAY DIFFRACTION (1.76 Å)