5XSN

The catalytic domain of GdpP with c-di-AMP

Summary for 5XSN

• Entry DOI: 10.2210/pdb5xsn/pdb
• Descriptor: Phosphodiesterase acting on cyclic dinucleotides, MANGANESE (II) 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: phosphodiesterase, hydrolase
• Biological source: Staphylococcus aureus
• Total number of polymer chains: 2
• Total formula weight: 77798.89

Authors

Wang, F.,Gu, L. (deposition date: 2017-06-14, release date: 2018-01-31, Last modification date: 2023-11-22)

Primary citation

Wang, F.,He, Q.,Su, K.,Wei, T.,Xu, S.,Gu, L.
Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase
Biochem. J., 475:191-205, 2018

PubMed Abstract: The Asp-His-His and Asp-His-His-associated (DHH/DHHA1) domain-containing phosphodiesterases (PDEs) that catalyze degradation of cyclic di-adenosine monophosphate (c-di-AMP) could be subdivided into two subfamilies based on the final product [5'-phosphadenylyl-adenosine (5'-pApA) or AMP]. In a previous study, we revealed that Rv2837c, a stand-alone DHH/DHHA1 PDE, employs a 5'-pApA internal flipping mechanism to produce AMPs. However, why the membrane-bound DHH/DHHA1 PDE can only degrade c-di-AMP to 5'-pApA remains obscure. Here, we report the crystal structure of the DHH/DHHA1 domain of GdpP (GdpP-C), and structures in complex with c-di-AMP, cyclic di-guanosine monophosphate (c-di-GMP), and 5'-pApA. Structural analysis reveals that GdpP-C binds nucleotide substrates quite differently from how Rv2837c does in terms of substrate-binding position. Accordingly, the nucleotide-binding site of the DHH/DHHA1 PDEs is organized into three (C, G, and R) subsites. For GdpP-C, in the C and G sites c-di-AMP binds and degrades into 5'-pApA, and its G site determines nucleotide specificity. To further degrade into AMPs, 5'-pApA must slide into the C and R sites for flipping and hydrolysis as in Rv2837c. Subsequent mutagenesis and enzymatic studies of GdpP-C and Rv2837c uncover the complete flipping process and reveal a unified catalytic mechanism for members of both DHH/DHHA1 PDE subfamilies.

PubMed: 29203646
DOI: 10.1042/BCJ20170739

Experimental method

X-RAY DIFFRACTION (2.501 Å)