9R97

DhhP of Borrelia burgdorferi in complex with AMP (SAD/Mn)

Summary for 9R97

• Entry DOI: 10.2210/pdb9r97/pdb
• Related: 9R7O
• Descriptor: DHH family, MANGANESE (II) ION, FE (III) ION, ... (5 entities in total)
• Functional Keywords: phosphodiesterase, c-di-amp, cyclic di-amp, heterobimetallic, hydrolase
• Biological source: Borreliella burgdorferi (Lyme disease spirochete)
• Total number of polymer chains: 8
• Total formula weight: 295547.90

Authors

Klima, M.,Boura, E. (deposition date: 2025-05-19, release date: 2026-01-21, Last modification date: 2026-03-11)

Primary citation

Klima, M.,Dejmek, M.,Palusova, A.,Chalupska, D.,Pachl, P.,Huskova, A.,Hranicek, J.,Chalupsky, K.,Moos, M.,Nencka, R.,Perner, J.,Boura, E.
Structural mechanism and inhibitor discovery for DhhP, a Borrelia burgdorferi cyclic di-AMP phosphodiesterase with an Fe/Mn bimetallic center.
Structure, 2026

PubMed Abstract: Second messenger signaling through cyclic dinucleotides regulates critical processes in pathogenic bacteria. DhhP is a phosphodiesterase that regulates levels of cyclic di-AMP (c-di-AMP), an essential second messenger, in Borrelia. Genetic inhibition of DhhP is lethal to Borrelia both in vitro and within a mammalian host. Here, we present the crystal structure of DhhP, revealing a heterobimetallic active site containing precisely positioned manganese and iron ions. We demonstrate specific binding sites for each metal, challenging the prevailing paradigm of homobimetallic active centers in bacterial c-di-AMP phosphodiesterases. The enzyme forms asymmetric dimers with coordinated open and closed conformations, suggesting an alternating mechanism for substrate processing. Additionally, we identified and characterized a series of small-molecule inhibitors of DhhP and demonstrated their ability to inhibit the growth of B. burgdorferi and disrupt spirochete morphology. These compounds establish proof of concept for specific targeting of bacterial c-di-AMP phosphodiesterases and further research of c-di-AMP roles in bacterial cells.

PubMed: 41742401
DOI: 10.1016/j.str.2026.01.016

Experimental method

X-RAY DIFFRACTION (3.3 Å)