5YRP

Crystal structure of the EAL domain of Mycobacterium smegmatis DcpA

Summary for 5YRP

• Entry DOI: 10.2210/pdb5yrp/pdb
• Descriptor: Sensory box/response regulator, MAGNESIUM ION (3 entities in total)
• Functional Keywords: c-di-gmp, diguanylate cyclase, phosphodiesterase, gaf, biosynthetic protein
• Biological source: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
• Total number of polymer chains: 2
• Total formula weight: 53347.15

Authors

Chen, H.J.,li, N.,Luo, Y.,Jiang, Y.L.,Zhou, C.Z.,Chen, Y.,Li, Q. (deposition date: 2017-11-09, release date: 2018-05-09, Last modification date: 2024-11-06)

Primary citation

Chen, H.J.,Li, N.,Luo, Y.,Jiang, Y.L.,Zhou, C.Z.,Chen, Y.,Li, Q.
The GDP-switched GAF domain of DcpA modulates the concerted synthesis/hydrolysis of c-di-GMP inMycobacterium smegmatis.
Biochem. J., 475:1295-1308, 2018

PubMed Abstract: The second messenger c-di-GMP [bis-(3'-5')-cyclic dimeric guanosine monophosphate] plays a key role in bacterial growth, survival and pathogenesis, and thus its intracellular homeostasis should be finely maintained. encodes a GAF (mammalian cMP-regulated phosphodiesterases, denylyl cyclases and transcription activator hlA) domain containing bifunctional enzyme DcpA (iguanylate yclase and hosphodiesterase ) that catalyzes the synthesis and hydrolysis of c-di-GMP Here, we found that DcpA catalyzes the hydrolysis of c-di-GMP at a higher velocity, compared with synthetic activity, resulting in a sum reaction from the ultimate substrate GTP to the final product pGpG [5'-phosphoguanylyl-(3'-5')-guanosine]. Fusion with the N-terminal GAF domain enables the GGDEF (Gly-Gly-Asp-Glu-Phe) domain of DcpA to dimerize and accordingly gain synthetic activity. Screening of putative metabolites revealed that GDP is the ligand of the GAF domain. Binding of GDP to the GAF domain down-regulates synthetic activity, but up-regulates hydrolytic activity, which, in consequence, might enable a timely response to the transient accumulation of c-di-GMP at the stationary phase or under stresses. Combined with the crystal structure of the EAL (Glu-Ala-Leu) domain and the small-angle X-ray scattering data, we propose a putative regulatory model of the GAF domain finely tuned by the intracellular GTP/GDP ratio. These findings help us to better understand the concerted control of the synthesis and hydrolysis of c-di-GMP in in various microenvironments.

PubMed: 29555845
DOI: 10.1042/BCJ20180079

Experimental method

X-RAY DIFFRACTION (2.99 Å)