7DOJ | pdb_00007doj

Solution structure of TGS domain of the Mycobacterium tuberculosis Rel protein

PDB DOI: https://doi.org/10.2210/pdb7DOJ/pdb
BMRB: 36403

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-12-14 Released: 2021-12-01
Deposition Author(s): Joon, S., Singal, B., Grueber, G.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 19
Selection Criteria: structures with the lowest energy

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Literature

Atomic structure of the regulatory TGS domain of Rel protein from Mycobacterium tuberculosis and its interaction with deacylated tRNA.

Shin, J., Singal, B., Gruber, A., Wong, D.M.K., Ragunathan, P., Gruber, G.

(2021) FEBS Lett 595: 3006-3018

PubMed: 34808002 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.14236
Primary Citation Related Structures:
7DOJ

PubMed Abstract:
The stringent response is critical for the survival of Mycobacterium tuberculosis (Mtb) under nutrient starvation. The mechanism is mediated by a GTP pyrophosphokinase known as Rel, containing N-terminal synthetase and hydrolase domains and C-terminal regulatory domains, which include the TGS domain (ThrRS, GTPase, and SpoT proteins) that has been proposed to activate the synthetase domain via interaction with deacylated tRNA. Here, we present the NMR solution structure of the Mtb Rel TGS domain (MtRel TGS), consisting of five antiparallel β-strands and one helix-loop-helix motif. The interaction of MtRel TGS with deacylated tRNA is shown, indicating the critical amino acids of MtRel TGS in tRNA binding, and presenting the first structural evidence of MtRel TGS binding to deacylated tRNA in solution in the absence of the translational machinery.

Organizational Affiliation

School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore.

Macromolecule Content

Total Structure Weight: 8.61 kDa
Atom Count: 507
Modeled Residue Count: 66
Deposited Residue Count: 77
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP pyrophosphokinase	A	77	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: relA, ERS007661_01112, ERS007688_02630 EC: 2.7.6.5 (PDB Primary Data), 3.1.7.2 (UniProt)
UniProt
Find proteins for P9WHG9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHG9 Go to UniProtKB: P9WHG9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WHG9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 19
Selection Criteria: structures with the lowest energy

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-12-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-12-01
Type: Initial release
Version 1.1: 2022-02-16
Changes: Database references
Version 1.2: 2023-06-14
Changes: Other
Version 1.3: 2024-05-15
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.