Structural and Biochemical Insight into the Mechanism of Rv2837c from Mycobacterium tuberculosis as a c-di-NMP Phosphodiesterase

Qing He; Feng Wang; Shiheng Liu; Deyu Zhu; Hengjiang Cong; Fei Gao; Bingqing Li; Hongwei Wang; Zong Lin; Jun Liao; Lichuan Gu

doi:10.1074/jbc.M115.699801

Structural and Biochemical Insight into the Mechanism of Rv2837c from Mycobacterium tuberculosis as a c-di-NMP Phosphodiesterase

J Biol Chem. 2016 Feb 12;291(7):3668-81. doi: 10.1074/jbc.M115.699801. Epub 2015 Dec 14.

Authors

Qing He¹, Feng Wang¹, Shiheng Liu¹, Deyu Zhu¹, Hengjiang Cong¹, Fei Gao¹, Bingqing Li¹, Hongwei Wang¹, Zong Lin², Jun Liao³, Lichuan Gu⁴

Affiliations

¹ From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China.
² the Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang 314006, China, and.
³ the School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China.
⁴ From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China, lcgu@sdu.edu.cn.

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.

Keywords: Mycobacterium tuberculosis; cyclic diadenosine monophosphate (c-di-AMP); enzyme degradation; phosphodiesterases; structure-function.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

3',5'-Cyclic-AMP Phosphodiesterases / chemistry
3',5'-Cyclic-AMP Phosphodiesterases / genetics
3',5'-Cyclic-AMP Phosphodiesterases / metabolism*
3',5'-Cyclic-GMP Phosphodiesterases / chemistry
3',5'-Cyclic-GMP Phosphodiesterases / genetics
3',5'-Cyclic-GMP Phosphodiesterases / metabolism*
Amino Acid Sequence
Bacterial Proteins / chemistry
Bacterial Proteins / genetics
Bacterial Proteins / metabolism*
Biocatalysis
Catalytic Domain
Conserved Sequence
Cyclic AMP / analogs & derivatives
Cyclic AMP / chemistry
Cyclic AMP / metabolism
Cyclic GMP / analogs & derivatives
Cyclic GMP / chemistry
Cyclic GMP / metabolism
Dinucleoside Phosphates / chemistry
Dinucleoside Phosphates / metabolism
Exoribonucleases / chemistry
Exoribonucleases / genetics
Exoribonucleases / metabolism*
Models, Molecular*
Molecular Sequence Data
Mutation
Mycobacterium tuberculosis / enzymology*
Peptide Fragments / chemistry
Peptide Fragments / genetics
Peptide Fragments / metabolism
Protein Conformation
Recombinant Fusion Proteins / chemistry
Recombinant Fusion Proteins / metabolism
Recombinant Proteins / chemistry
Recombinant Proteins / metabolism
Sequence Alignment
Substrate Specificity

Substances

Bacterial Proteins
Dinucleoside Phosphates
Peptide Fragments
Recombinant Fusion Proteins
Recombinant Proteins
cyclic diadenosine phosphate
bis(3',5')-cyclic diguanylic acid
Cyclic AMP
Exoribonucleases
oligoribonuclease
3',5'-Cyclic-AMP Phosphodiesterases
3',5'-Cyclic-GMP Phosphodiesterases
Cyclic GMP

Associated data

PDB/3DEV
PDB/3W5W
PDB/4LS9