7WIK | pdb_00007wik

Crystal structure of oligoribonuclease of Mycobacterium smegmatis mc2 155

PDB DOI: https://doi.org/10.2210/pdb7WIK/pdb

Classification: HYDROLASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-03 Released: 2022-12-21
Deposition Author(s): Badhwar, P., Taneja, B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.222 (Depositor), 0.227 (DCC)
R-Value Work:
0.179 (Depositor), 0.188 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Three-dimensional structure of a mycobacterial oligoribonuclease reveals a unique C-terminal tail that stabilizes the homodimer.

Badhwar, P., Khan, S.H., Taneja, B.

(2022) J Biological Chem 298: 102595-102595

PubMed: 36244449 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2022.102595
Primary Citation Related Structures:
7VH4, 7WIK

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.

Organizational Affiliation

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.

Macromolecule Content

Total Structure Weight: 95.46 kDa
Atom Count: 7,150
Modeled Residue Count: 781
Deposited Residue Count: 840
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligoribonuclease	A, B, C, D	210	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: orn EC: 3.1.13.3 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for A0R1E6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R1E6 Go to UniProtKB: A0R1E6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0R1E6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain CA [auth D]	CA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Interactions & Density Focus chain CA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain J [auth B] SDF format, chain IA [auth D] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain BA [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain J [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain BA [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain J [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain BA [auth C]	BA [auth C] GA [auth D] H [auth A] HA [auth D] IA [auth D] BA [auth C], GA [auth D], H [auth A], HA [auth D], IA [auth D], J [auth B], N [auth B], O [auth B], Q [auth B], R [auth C], W [auth C], X [auth C], Y [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth C] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth C] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain P [auth B] SDF format, chain JA [auth D] SDF format, chain I [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain P [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain I [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain P [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain I [auth A]	I [auth A], JA [auth D], P [auth B], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain JA [auth D] Focus chain P [auth B] Focus chain Z [auth C] Interactions & Density Focus chain I [auth A] Focus chain JA [auth D] Focus chain P [auth B] Focus chain Z [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain F [auth A] SDF format, chain EA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D]	EA [auth D] F [auth A] FA [auth D] G [auth A] L [auth B] EA [auth D], F [auth A], FA [auth D], G [auth A], L [auth B], M [auth B], T [auth C], U [auth C], V [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth D] MOL2 format, chain S [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain S [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth D]	DA [auth D], E [auth A], K [auth B], S [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain E [auth A] Focus chain K [auth B] Focus chain S [auth C] Interactions & Density Focus chain DA [auth D] Focus chain E [auth A] Focus chain K [auth B] Focus chain S [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain AA [auth C]	AA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Interactions & Density Focus chain AA [auth C]