7WIK

Crystal structure of oligoribonuclease of Mycobacterium smegmatis mc2 155

Summary for 7WIK

• Entry DOI: 10.2210/pdb7wik/pdb
• Descriptor: Oligoribonuclease, POTASSIUM ION, ACETATE ION, ... (8 entities in total)
• Functional Keywords: oligoribonuclease, orn, rnase h-like fold, dnaq like exoribonuclease, hydrolase
• Biological source: Mycolicibacterium smegmatis MC2 155
• Total number of polymer chains: 4
• Total formula weight: 95464.56

Authors

Badhwar, P.,Taneja, B. (deposition date: 2022-01-03, release date: 2022-12-21, Last modification date: 2023-11-29)

Primary citation

Badhwar, P.,Khan, S.H.,Taneja, B.
Three-dimensional structure of a mycobacterial oligoribonuclease reveals a unique C-terminal tail that stabilizes the homodimer.
J.Biol.Chem., 298:102595-102595, 2022

PubMed Abstract: Oligoribonucleases (Orns) are highly conserved DnaQ-fold 3'-5' exoribonucleases that have been found to carry out the last step of cyclic-di-GMP (c-di-GMP) degradation, that is, pGpG to GMP in several bacteria. Removal of pGpG is critical for c-di-GMP homeostasis, as excess uncleaved pGpG can have feedback inhibition on phosphodiesterases, thereby perturbing cellular signaling pathways regulated by c-di-GMP. Perturbation of c-di-GMP levels not only affects survival under hypoxic, reductive stress, or nutrient-limiting conditions but also affects pathogenicity in infection models as well as antibiotic response in mycobacteria. Here, we have determined the crystal structure of MSMEG_4724, the Orn of Mycobacterium smegmatis (Ms_orn) to 1.87 Å resolution to investigate the function of its extended C-terminal tail that is unique among bacterial Orns. Ms_orn is a homodimer with the canonical RNase-H fold of exoribonucleases and conserved catalytic residues in the active site. Further examination of the substrate-binding site with a modeled pGpG emphasized the role of a phosphate cap and "3'OH cap" in constricting a 2-mer substrate in the active site. The unique C-terminal tail of Ms_orn aids dimerization by forming a handshake-like flap over the second protomer of the dimer. Our thermal and denaturant-induced unfolding experiments suggest that it helps in higher stability of Ms_orn as compared with Escherichia coli Orn or a C-terminal deletion mutant. We also show that the C-terminal tail is required for modulating response to stress agents in vivo. These results will help in further evaluating the role of signaling and regulation by c-di-GMP in mycobacteria.

PubMed: 36244449
DOI: 10.1016/j.jbc.2022.102595

Experimental method

X-RAY DIFFRACTION (1.87 Å)