4S1B

Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain in complex with Cyclic-di-AMP

Summary for 4S1B

• Entry DOI: 10.2210/pdb4s1b/pdb
• Related: 4S1C
• Descriptor: Lmo1466 protein, FE (III) ION, (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide, ... (4 entities in total)
• Functional Keywords: c-di-amp, listeria monocytogenes, phosphodiesterase, hd domain, hydrolase
• Biological source: Listeria monocytogenes
• Total number of polymer chains: 2
• Total formula weight: 51785.81

Authors

Luo, S.,Tong, L. (deposition date: 2015-01-12, release date: 2015-02-11, Last modification date: 2024-02-28)

Primary citation

Huynh, T.N.,Luo, S.,Pensinger, D.,Sauer, J.D.,Tong, L.,Woodward, J.J.
An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence.
Proc.Natl.Acad.Sci.USA, 112:E747-E756, 2015

PubMed Abstract: The nucleotide cyclic di-3',5'- adenosine monophosphate (c-di-AMP) was recently identified as an essential and widespread second messenger in bacterial signaling. Among c-di-AMP-producing bacteria, altered nucleotide levels result in several physiological defects and attenuated virulence. Thus, a detailed molecular understanding of c-di-AMP metabolism is of both fundamental and practical interest. Currently, c-di-AMP degradation is recognized solely among DHH-DHHA1 domain-containing phosphodiesterases. Using chemical proteomics, we identified the Listeria monocytogenes protein PgpH as a molecular target of c-di-AMP. Biochemical and structural studies revealed that the PgpH His-Asp (HD) domain bound c-di-AMP with high affinity and specifically hydrolyzed this nucleotide to 5'-pApA. PgpH hydrolysis activity was inhibited by ppGpp, indicating a cross-talk between c-di-AMP signaling and the stringent response. Genetic analyses supported coordinated regulation of c-di-AMP levels in and out of the host. Intriguingly, a L. monocytogenes mutant that lacks c-di-AMP phosphodiesterases exhibited elevated c-di-AMP levels, hyperinduced a host type-I IFN response, and was significantly attenuated for infection. Furthermore, PgpH homologs, which belong to the 7TMR-HD family, are widespread among hundreds of c-di-AMP synthesizing microorganisms. Thus, PgpH represents a broadly conserved class of c-di-AMP phosphodiesterase with possibly other physiological functions in this crucial signaling network.

PubMed: 25583510
DOI: 10.1073/pnas.1416485112

Experimental method

X-RAY DIFFRACTION (2.099 Å)