Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Combined Automated Annotation using Multiple IEA Methods
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
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Complete genome sequence of M. tuberculosis H37Rv, identifying Rv2460c (clpP2).
"The genome comprises 4,411,529 base pairs, contains around 4,000 genes"
Comprehensive proteomic profiling of the membrane constituents of a Mycobacterium tuberculosis strain.
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Large-scale membrane proteomics; identified ClpP2 in membrane fraction (likely contaminant).
"739 proteins have been identified by two or more distinct peptide sequences...approximately 450 proteins represent novel identifications, 79 of which are membrane proteins and more than 100 of which are membrane-associated proteins"
Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association.
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Developed M-PFC interaction system; identified ClpC1 interactions in Mtb.
"Rv3596c (ClpC1), an AAA-ATPase chaperone involved in protein translocation and quality control"
RseA, the SigE specific anti-sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis.
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ClpC1P2 degrades anti-sigma-E factor RseA upon PknB-dependent phosphorylation at T39, activating the SigE regulon under envelope stress.
"PknB-dependent phosphorylation of RseA on T39 is required for its cleavage by ClpC1P2 thereby activating the SigE regulon"
Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry.
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ClpP2 identified by mass spectrometry, confirming protein expression at the protein level.
"we identified 3176 proteins from Mycobacterium tuberculosis representing ~80% of its total predicted gene count"
Validation of the essential ClpP protease in Mycobacterium tuberculosis as a novel drug target.
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Both clpP1 and clpP2 are essential for viability. clpP2 overexpression is toxic. ADEPs are active against Mtb.
"clpP2 overexpression was toxic, suggesting different roles for the two homologs"
The active ClpP protease from M. tuberculosis is a complex composed of a heptameric ClpP1 and a ClpP2 ring.
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Active protease requires both ClpP1 and ClpP2 mixed together; neither homomeric form is active alone. Requires dipeptide activator for in vitro activity.
"We could, however, reconstitute an active, mixed ClpP1P2 complex after identifying N-blocked dipeptides that stimulate dramatically (>1000-fold) ClpP1P2 activity"
Mycobacterium tuberculosis RsdA provides a conformational rationale for selective regulation of σ-factor activity by proteolysis.
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ClpP1P2-ClpX complex degrades anti-sigma-D factor RsdA, providing selective regulation of sigma factor activity.
"the M. tuberculosis ClpX-ClpP1-ClpP2 proteolytic complex could specifically degrade the ASD of RsdA"
Substrate delivery by the AAA+ ClpX and ClpC1 unfoldases activates the mycobacterial ClpP1P2 peptidase.
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AAA+ unfoldases ClpX and ClpC1 deliver substrates to ClpP1P2 for degradation. Substrate delivery itself activates the peptidase.
"Substrate delivery by the AAA+ ClpX and ClpC1 unfoldases activates the mycobacterial ClpP1P2 peptidase"
Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery.
Cleavage Specificity of Mycobacterium tuberculosis ClpP1P2 Protease and Identification of Novel Peptide Substrates and Boronate Inhibitors with Anti-bacterial Activity.
The Mycobacterium tuberculosis ClpP1P2 Protease Interacts Asymmetrically with Its ATPase Partners ClpX and ClpC1.
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ClpX binds specifically to the ClpP2 ring, while ClpC1 can associate with either ring.
"both Mycobacterium tuberculosis Clp chaperones require the intact interaction face of ClpP2 to support degradation"
Acyldepsipeptide antibiotics kill mycobacteria by preventing the physiological functions of the ClpP1P2 protease.
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ADEPs dysregulate the ClpP1P2 protease, providing chemical validation as a drug target.
"mycobacteria are killed by ADEP through inhibition of ClpP function"
An allosteric switch regulates Mycobacterium tuberculosis ClpP1P2 protease function as established by cryo-EM and methyl-TROSY NMR.
The essential M. tuberculosis Clp protease is functionally asymmetric in vivo.