7yk3: Difference between revisions
No edit summary |
No edit summary |
||
| (One intermediate revision by the same user not shown) | |||
| Line 4: | Line 4: | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[7yk3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YK3 FirstGlance]. <br> | <table><tr><td colspan='2'>[[7yk3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YK3 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7yk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yk3 OCA], [https://pdbe.org/7yk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yk3 RCSB], [https://www.ebi.ac.uk/pdbsum/7yk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yk3 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7yk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yk3 OCA], [https://pdbe.org/7yk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yk3 RCSB], [https://www.ebi.ac.uk/pdbsum/7yk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yk3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/DART_MYCTU DART_MYCTU] Toxic component of | [https://www.uniprot.org/uniprot/DART_MYCTU DART_MYCTU] Toxic component of the hybrid type II/IV toxin-antitoxin (TA) system DarTG, which plays a crucial role in controlling bacterial growth and bacteriophage infection. Its toxic effect is neutralized by cognate antitoxin DarG (PubMed:27939941). ADP-ribosylates ssDNA, preferentially in the motif TTTW. In case of phage infection, DarT toxin ADP-ribosylates DNA, which inhibits both viral DNA and RNA synthesis and leads to abortive infection (By similarity). Uncontrolled expression of DarT leads to ADP-ribosylation of the origin of chromosomal replication DNA in cells (in vitro the most heavily modified motifs are TTTT/A in the OriC lower strand) and growth arrest (PubMed:34408320). Is very toxic to E.coli, it cannot be expressed in E.coli (PubMed:27939941). Experiments in situ in which antitoxin DarG levels are depleted (similar to overexpression of DarT) lead to cell death; expression of wild-type DarG protein from M.tuberculosis or T.aquaticus restores growth. Cells with decreased levels of DarG are more sensitive to bedaquilline (targets respiration), DNA-damaging drugs (mitomycin C, netropsin) and transcription-targeted drugs (rifabutin and rifampicin). When DarG is depleted, a DNA-damage response is induced and mutability is increased, suggesting ADP-ribosylation of DNA is the toxic effect (PubMed:32634279).[UniProtKB:B7UP20]<ref>PMID:27939941</ref> <ref>PMID:32634279</ref> <ref>PMID:34408320</ref> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
In the DarTG toxin-antitoxin system, the DarT toxin ADP-ribosylates single-stranded DNA (ssDNA), which stalls DNA replication and plays a crucial role in controlling bacterial growth and bacteriophage infection. This toxic activity is reversed by the N-terminal macrodomain of the cognate antitoxin DarG. DarG also binds DarT, but the role of these interactions in DarT neutralization is unknown. Here, we report that the C-terminal domain of DarG (DarG toxin-binding domain [DarG(TBD)]) interacts with DarT to form a 1:1 stoichiometric heterodimeric complex. We determined the 2.2 A resolution crystal structure of the Mycobacterium tuberculosis DarT-DarG(TBD) complex. The comparative structural analysis reveals that DarG(TBD) interacts with DarT at the DarT/ssDNA interaction interface, thus sterically occluding substrate ssDNA binding and consequently inactivating toxin by direct protein-protein interactions. Our data support a unique two-layered DarT toxin neutralization mechanism of DarG, which is important in keeping the toxin molecules in check under normal growth conditions. | In the DarTG toxin-antitoxin system, the DarT toxin ADP-ribosylates single-stranded DNA (ssDNA), which stalls DNA replication and plays a crucial role in controlling bacterial growth and bacteriophage infection. This toxic activity is reversed by the N-terminal macrodomain of the cognate antitoxin DarG. DarG also binds DarT, but the role of these interactions in DarT neutralization is unknown. Here, we report that the C-terminal domain of DarG (DarG toxin-binding domain [DarG(TBD)]) interacts with DarT to form a 1:1 stoichiometric heterodimeric complex. We determined the 2.2 A resolution crystal structure of the Mycobacterium tuberculosis DarT-DarG(TBD) complex. The comparative structural analysis reveals that DarG(TBD) interacts with DarT at the DarT/ssDNA interaction interface, thus sterically occluding substrate ssDNA binding and consequently inactivating toxin by direct protein-protein interactions. Our data support a unique two-layered DarT toxin neutralization mechanism of DarG, which is important in keeping the toxin molecules in check under normal growth conditions. | ||
Structural insights into DarT toxin neutralization by cognate DarG antitoxin: ssDNA mimicry by DarG C-terminal domain keeps the DarT toxin inhibited.,Deep A, Singh L, Kaur J, Velusamy M, Bhardwaj P, Singh R, Thakur KG Structure. 2023 | Structural insights into DarT toxin neutralization by cognate DarG antitoxin: ssDNA mimicry by DarG C-terminal domain keeps the DarT toxin inhibited.,Deep A, Singh L, Kaur J, Velusamy M, Bhardwaj P, Singh R, Thakur KG Structure. 2023 Jul 6;31(7):780-789.e4. doi: 10.1016/j.str.2023.04.008. Epub 2023 , May 10. PMID:37167974<ref>PMID:37167974</ref> | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| Line 24: | Line 25: | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Mycobacterium tuberculosis H37Rv]] | [[Category: Mycobacterium tuberculosis H37Rv]] | ||
[[Category: | [[Category: Deep A]] | ||
[[Category: | [[Category: Kaur J]] | ||
[[Category: | [[Category: Singh L]] | ||
[[Category: Thakur KG]] | |||