Database accession: MF2120024
Name: Antitoxin phd dimer (Mycobacterium tuberculosis)
PDB ID: 3g5o
Experimental method: X-ray (2.00 Å)
Assembly: Homodimer
Source organism: Mycobacterium tuberculosis
Primary publication of the structure:
Miallau L, Jain P, Arbing MA, Cascio D, Phan T, Ahn CJ, Chan S, Chernishof I, Maxson M, Chiang J, Jacobs WR, Eisenberg DS
Comparative proteomics identifies the cell-associated lethality of M. tuberculosis RelBE-like toxin-antitoxin complexes.
(2013) Structure 21: 627-37
PMID: 23523424
Abstract:
The Mycobacterium tuberculosis (Mtb) genome encodes approximately 90 toxin-antitoxin protein complexes, including three RelBE family members, which are believed to play a major role in bacterial fitness and pathogenicity. We have determined the crystal structures of Mtb RelBE-2 and RelBE-3, and the structures reveal homologous heterotetramers. Our structures suggest RelE-2, and by extension the closely related RelE-1, use a different catalytic mechanism than RelE-3, because our analysis of the RelE-2 structure predicts additional amino acid residues that are likely to be functionally significant and are missing from analogous positions in the RelE-3 structure. Toxicity assays corroborate our structural findings; overexpression of RelE-3, whose active site is more similar to Escherichia coli YoeB, has limited consequences on bacterial growth, whereas RelE-1 and RelE-2 overexpression results in acute toxicity. Moreover, RelE-2 overexpression results in an elongated cell phenotype in Mycobacterium smegmatis and protects M. tuberculosis against antibiotics, suggesting a different functional role for RelE-2.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
DNA binding DNA binding
toxin sequestering activity toxin sequestering activity
Biological process:
positive regulation of growth positive regulation of growth
regulation of DNA-templated transcription regulation of DNA-templated transcription
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, D
Notes: According to the most probable oligomerization state stored in PDBe B,C chains were not considered.
Number of unique protein segments: 1
Name: Antitoxin RelF
Source organism: Mycobacterium tuberculosis
Length: 93 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRILPISTIKGKLNEFVDAVSSTQDQITITKNGAPAAVLVGADEWESLQETLYWLAQPGIRESIAEADADIASGRTYGEDEIRAEFGVPRRPH
UniProtKB AC: O33347 (positions: 1-91)
Coverage: 97%
Name: Antitoxin RelF
Source organism: Mycobacterium tuberculosis
Length: 93 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRILPISTIKGKLNEFVDAVSSTQDQITITKNGAPAAVLVGADEWESLQETLYWLAQPGIRESIAEADADIASGRTYGEDEIRAEFGVPRRPH
UniProtKB AC: O33347 (positions: 1-91)
Coverage: 97%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Antitoxin Phd_YefM
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
The dimerization of the prevents host death (phd) antitoxin from Escherichia virus P1 has been shown with differential scanning calorimetry to fit well to a two-state model consisting of a dimer unfolding into monomer species (PMID:20603017).
Chain A:
N/A
Chain D:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
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