This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5m31

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Macrodomain of Thermus aquaticus DarG

Structural highlights

5m31 is a 1 chain structure with sequence from Thermus aquaticus Y51MC23. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.67Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DARG_THEA5 Antitoxin component of a hybrid type II/IV toxin-antitoxin (TA) system. De-ADP-ribosylates DNA modified on thymidine by its cognate toxin DarT, which neutralizes the activity of cognate toxin DarT. Upon expression in E.coli neutralizes the effect of cognate toxin DarT (PubMed:27939941). Upon expression in M.tuberculosis neutralizes the toxic effects of endogenous DarT (PubMed:32634279).^[1] ^[2]

Publication Abstract from PubMed

The discovery and study of toxin-antitoxin (TA) systems helps us advance our understanding of the strategies prokaryotes employ to regulate cellular processes related to the general stress response, such as defense against phages, growth control, biofilm formation, persistence, and programmed cell death. Here we identify and characterize a TA system found in various bacteria, including the global pathogen Mycobacterium tuberculosis. The toxin of the system (DarT) is a domain of unknown function (DUF) 4433, and the antitoxin (DarG) a macrodomain protein. We demonstrate that DarT is an enzyme that specifically modifies thymidines on single-stranded DNA in a sequence-specific manner by a nucleotide-type modification called ADP-ribosylation. We also show that this modification can be removed by DarG. Our results provide an example of reversible DNA ADP-ribosylation, and we anticipate potential therapeutic benefits by targeting this enzyme-enzyme TA system in bacterial pathogens such as M. tuberculosis.

The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA.,Jankevicius G, Ariza A, Ahel M, Ahel I Mol Cell. 2016 Dec 15;64(6):1109-1116. doi: 10.1016/j.molcel.2016.11.014. Epub, 2016 Dec 8. PMID:27939941^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Jankevicius G, Ariza A, Ahel M, Ahel I. The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA. Mol Cell. 2016 Dec 15;64(6):1109-1116. doi: 10.1016/j.molcel.2016.11.014. Epub, 2016 Dec 8. PMID:27939941 doi:http://dx.doi.org/10.1016/j.molcel.2016.11.014
↑ Zaveri A, Wang R, Botella L, Sharma R, Zhu L, Wallach JB, Song N, Jansen RS, Rhee KY, Ehrt S, Schnappinger D. Depletion of the DarG antitoxin in Mycobacterium tuberculosis triggers the DNA-damage response and leads to cell death. Mol Microbiol. 2020 Oct;114(4):641-652. PMID:32634279 doi:10.1111/mmi.14571
↑ Jankevicius G, Ariza A, Ahel M, Ahel I. The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA. Mol Cell. 2016 Dec 15;64(6):1109-1116. doi: 10.1016/j.molcel.2016.11.014. Epub, 2016 Dec 8. PMID:27939941 doi:http://dx.doi.org/10.1016/j.molcel.2016.11.014

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5m31"

Categories: Large Structures | Thermus aquaticus Y51MC23 | Ariza A

@@ Line 1: / Line 1: @@
 ==Macrodomain of Thermus aquaticus DarG==
-<StructureSection load='5m31' size='340' side='right' caption='[[5m31]], [[Resolution|resolution]] 1.67&Aring;' scene=''>
+<StructureSection load='5m31' size='340' side='right'caption='[[5m31]], [[Resolution|resolution]] 1.67&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5m31]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M31 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M31 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5m31]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus_Y51MC23 Thermus aquaticus Y51MC23]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M31 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M31 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.67&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5m31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m31 OCA], [http://pdbe.org/5m31 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m31 RCSB], [http://www.ebi.ac.uk/pdbsum/5m31 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m31 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5m31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m31 OCA], [https://pdbe.org/5m31 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m31 RCSB], [https://www.ebi.ac.uk/pdbsum/5m31 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m31 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DARG_THEA5 DARG_THEA5] Antitoxin component of a hybrid type II/IV toxin-antitoxin (TA) system. De-ADP-ribosylates DNA modified on thymidine by its cognate toxin DarT, which neutralizes the activity of cognate toxin DarT. Upon expression in E.coli neutralizes the effect of cognate toxin DarT (PubMed:27939941). Upon expression in M.tuberculosis neutralizes the toxic effects of endogenous DarT (PubMed:32634279).<ref>PMID:27939941</ref> <ref>PMID:32634279</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ariza, A]]
+[[Category: Large Structures]]
-[[Category: Adp-ribose]]
+[[Category: Thermus aquaticus Y51MC23]]
-[[Category: Adp-ribosylation]]
+[[Category: Ariza A]]
-[[Category: Antitoxin]]
-[[Category: Macrodomain]]
-[[Category: Toxin-antitoxin]]

5m31

From Proteopedia

Current revision

Macrodomain of Thermus aquaticus DarG

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox