title: Structural and Biochemical Insight into the Mechanism of Rv2837c from Mycobacterium tuberculosis as a c-di-NMP Phosphodiesterase.
abstract: The intracellular infections of Mycobacterium tuberculosis, which is the causative agent of tuberculosis, are regulated by many cyclic dinucleotide signaling. Rv2837c from M. tuberculosis is a soluble, stand-alone DHH-DHHA1 domain phosphodiesterase that down-regulates c-di-AMP through catalytic degradation and plays an important role in M. tuberculosis infections. Here, we report the crystal structure of Rv2837c (2.0 Å), and its complex with hydrolysis intermediate 5'-pApA (2.35 Å). Our structures indicate that both DHH and DHHA1 domains are essential for c-di-AMP degradation. Further structural analysis shows that Rv2837c does not distinguish adenine from guanine, which explains why Rv2837c hydrolyzes all linear dinucleotides with almost the same efficiency. We observed that Rv2837c degraded other c-di-NMPs at a lower rate than it did on c-di-AMP. Nevertheless, our data also showed that Rv2837c significantly decreases concentrations of both c-di-AMP and c-di-GMP in vivo. Our results suggest that beside its major role in c-di-AMP degradation Rv2837c could also regulate c-di-GMP signaling pathways in bacterial cell.
authors.affiliation: From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: He
authors.affiliation: From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.affiliation: From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China.
authors.forename: Shiheng
authors.initials: S
authors.lastname: Liu
authors.affiliation: From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China.
authors.forename: Deyu
authors.initials: D
authors.lastname: Zhu
authors.affiliation: From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China.
authors.forename: Hengjiang
authors.initials: H
authors.lastname: Cong
authors.affiliation: From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Gao
authors.affiliation: From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China.
authors.forename: Bingqing
authors.initials: B
authors.lastname: Li
authors.affiliation: From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Wang
authors.affiliation: the Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang 314006, China, and.
authors.forename: Zong
authors.initials: Z
authors.lastname: Lin
authors.affiliation: the School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Liao
authors.affiliation: From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China, lcgu@sdu.edu.cn.
authors.forename: Lichuan
authors.initials: L
authors.lastname: Gu
mesh_terms: D015105:3',5'-Cyclic-AMP Phosphodiesterases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015106:3',5'-Cyclic-GMP Phosphodiesterases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D055162:Biocatalysis; D020134:Catalytic Domain; D017124:Conserved Sequence; D000242:Cyclic AMP / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D006152:Cyclic GMP / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D015226:Dinucleoside Phosphates / Q000737:chemistry / Q000378:metabolism; D005095:Exoribonucleases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000201:enzymology*; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011487:Protein Conformation; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D015226:Dinucleoside Phosphates; D010446:Peptide Fragments; D011993:Recombinant Fusion Proteins; D011994:Recombinant Proteins; C528998:cyclic diadenosine phosphate; C062025:bis(3',5')-cyclic diguanylic acid; D000242:Cyclic AMP; D005095:Exoribonucleases; C094587:oligoribonuclease; D015105:3',5'-Cyclic-AMP Phosphodiesterases; D015106:3',5'-Cyclic-GMP Phosphodiesterases; D006152:Cyclic GMP
keywords: Mycobacterium tuberculosis; cyclic diadenosine monophosphate (c-di-AMP); enzyme degradation; phosphodiesterases; structure-function