DARG_MYCTU
ID DARG_MYCTU Reviewed; 352 AA.
AC O53605; F2GPR3; I6XUB1; Q7DAJ0;
DT 03-AUG-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=DNA ADP-ribosyl glycohydrolase {ECO:0000303|PubMed:27939941};
DE Short=DarG {ECO:0000303|PubMed:27939941};
DE EC=3.2.2.- {ECO:0000269|PubMed:27939941};
DE AltName: Full=Antitoxin DarG {ECO:0000303|PubMed:27939941};
GN Name=darG {ECO:0000303|PubMed:9634230};
GN OrderedLocusNames=Rv0060 {ECO:0000312|EMBL:CCP42782.1};
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1] {ECO:0000312|EMBL:CCP42782.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=12657046; DOI=10.1046/j.1365-2958.2003.03425.x;
RA Sassetti C.M., Boyd D.H., Rubin E.J.;
RT "Genes required for mycobacterial growth defined by high density
RT mutagenesis.";
RL Mol. Microbiol. 48:77-84(2003).
RN [3] {ECO:0007744|PubMed:21969609}
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [4]
RP FUNCTION AS AN ANTITOXIN, SUBUNIT, DISRUPTION PHENOTYPE, AND BIOTECHNOLOGY.
RC STRAIN=H37Rv;
RX PubMed=32634279; DOI=10.1111/mmi.14571;
RA Zaveri A., Wang R., Botella L., Sharma R., Zhu L., Wallach J.B., Song N.,
RA Jansen R.S., Rhee K.Y., Ehrt S., Schnappinger D.;
RT "Depletion of the DarG antitoxin in Mycobacterium tuberculosis triggers the
RT DNA-damage response and leads to cell death.";
RL Mol. Microbiol. 114:641-652(2020).
RN [5]
RP FUNCTION AS AN ANTITOXIN, FUNCTION AS AN ADP-RIBOSYL GLYCOHYDROLASE, OPERON
RP STRUCTURE, AND DOMAIN.
RC STRAIN=H37Rv;
RX PubMed=34408320; DOI=10.1038/s41586-021-03825-4;
RA Schuller M., Butler R.E., Ariza A., Tromans-Coia C., Jankevicius G.,
RA Claridge T.D.W., Kendall S.L., Goh S., Stewart G.R., Ahel I.;
RT "Molecular basis for DarT ADP-ribosylation of a DNA base.";
RL Nature 596:597-602(2021).
RN [6] {ECO:0007744|PDB:5M3I}
RP X-RAY CRYSTALLOGRAPHY (2.17 ANGSTROMS) OF 1-155, FUNCTION AS AN ANTITOXIN,
RP AND FUNCTION AS AN ADP-RIBOSYL GLYCOHYDROLASE.
RC STRAIN=H37Rv;
RX PubMed=27939941; DOI=10.1016/j.molcel.2016.11.014;
RA Jankevicius G., Ariza A., Ahel M., Ahel I.;
RT "The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of
RT DNA.";
RL Mol. Cell 64:1109-1116(2016).
CC -!- FUNCTION: Antitoxin component of a hybrid type II/IV toxin-antitoxin
CC (TA) system. De-ADP-ribosylates DNA (probably) modified on thymidine by
CC its cognate toxin DarT, which neutralizes the activity of DarT
CC (PubMed:27939941). Experiments in which DarG levels are depleted lead
CC to cell death; expression of wild-type DarG protein from M.tuberculosis
CC or T.aquaticus restores growth. Cells depleted of DarG are more
CC sensitive to bedaquilline (targets respiration), DNA-damaging drugs
CC (mitomycin C, netropsin) and transcription-targeted drugs (rifabutin
CC and rifampicin). When depleted, a DNA-damage response is induced and
CC mutability is increased (PubMed:32634279). In E.coli the macrodomain
CC alone neutralizes DarT toxin from non-cognate T.aquaticus. The same
CC domain de-ADP-ribosylates genomic DNA (PubMed:34408320).
CC {ECO:0000269|PubMed:27939941, ECO:0000269|PubMed:32634279,
CC ECO:0000269|PubMed:34408320}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an N-(ADP-alpha-D-ribosyl)-thymidine in DNA + H2O = a
CC thymidine in DNA + ADP-D-ribose; Xref=Rhea:RHEA:71655, Rhea:RHEA-
CC COMP:13556, Rhea:RHEA-COMP:18051, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:57967, ChEBI:CHEBI:137386, ChEBI:CHEBI:191199;
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:71656;
CC Evidence={ECO:0000269|PubMed:27939941, ECO:0000269|PubMed:34408320};
CC -!- SUBUNIT: Forms a complex with cognate toxin DarT; this complex
CC neutralizes the toxic effect of DarT (PubMed:32634279). Co-
CC immunoprecipitates with a number proteins known to be involved in DNA
CC metabolism, in the presence and absence of darT; includes alkA, dnaB,
CC dnaE1, dnaG, dus, embR, mtrA, nrdE, nrdR, polA, recA, recB, recF, xerD,
CC Rv2258c (PubMed:32634279). {ECO:0000269|PubMed:32634279}.
CC -!- INDUCTION: Part of the dnaB-darT-darG operon.
CC {ECO:0000269|PubMed:34408320}.
CC -!- DOMAIN: The macro domain alone is sufficient to neutralize DarT from
CC non-cognate T.aquaticus in E.coli, DarT in M.bovis, and to de-ADP-
CC ribosylate DNA in vitro. {ECO:0000269|PubMed:34408320}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene display impaired growth
CC (PubMed:12657046). A double darT-darG deletion shows no change in
CC growth in culture, upon infection of mice, or upon exposure to a
CC variety of stresses (PubMed:32634279). Another group finds the double
CC knockout gives a competitive advantage over wild-type cells in liquid
CC culture growth experiments. Knock-down of darG expression leads to
CC increased RecA expression, ADP-ribosylation of OriC and growth arrest
CC (PubMed:34408320). {ECO:0000269|PubMed:12657046,
CC ECO:0000269|PubMed:32634279, ECO:0000269|PubMed:34408320}.
CC -!- BIOTECHNOLOGY: As expression of DarT is bactericidal (rather than
CC bacteriostatic as are most TA systems in this bacteria), inactivation
CC of DarG may be an attractive drug target.
CC {ECO:0000305|PubMed:32634279}.
CC -!- SIMILARITY: Belongs to the DarG ADP-ribosyl glycohydrolase family.
CC {ECO:0000305}.
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DR EMBL; AL123456; CCP42782.1; -; Genomic_DNA.
DR RefSeq; NP_214574.1; NC_000962.3.
DR RefSeq; WP_003400551.1; NZ_NVQJ01000005.1.
DR PDB; 5M3I; X-ray; 2.17 A; A/B/C/D=1-155.
DR PDBsum; 5M3I; -.
DR SMR; O53605; -.
DR STRING; 83332.Rv0060; -.
DR PaxDb; O53605; -.
DR PRIDE; O53605; -.
DR DNASU; 887004; -.
DR GeneID; 45424019; -.
DR GeneID; 887004; -.
DR KEGG; mtu:Rv0060; -.
DR PATRIC; fig|83332.111.peg.67; -.
DR TubercuList; Rv0060; -.
DR eggNOG; COG2110; Bacteria.
DR OMA; WIVNFPT; -.
DR PhylomeDB; O53605; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; HDA:MTBBASE.
DR GO; GO:0140291; P:peptidyl-glutamate ADP-deribosylation; IBA:GO_Central.
DR Gene3D; 3.40.220.10; -; 1.
DR InterPro; IPR002589; Macro_dom.
DR InterPro; IPR043472; Macro_dom-like.
DR Pfam; PF01661; Macro; 1.
DR SMART; SM00506; A1pp; 1.
DR SUPFAM; SSF52949; SSF52949; 1.
DR PROSITE; PS51154; MACRO; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Reference proteome; Toxin-antitoxin system.
FT CHAIN 1..352
FT /note="DNA ADP-ribosyl glycohydrolase"
FT /id="PRO_0000456046"
FT DOMAIN 1..155
FT /note="Macro"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00490"
FT ACT_SITE 80
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P0DV57"
FT BINDING 8..9
FT /ligand="ADP-D-ribose"
FT /ligand_id="ChEBI:CHEBI:57967"
FT /evidence="ECO:0000250|UniProtKB:P0DV57"
FT BINDING 20..22
FT /ligand="ADP-D-ribose"
FT /ligand_id="ChEBI:CHEBI:57967"
FT /evidence="ECO:0000250|UniProtKB:P0DV57"
FT BINDING 31..34
FT /ligand="ADP-D-ribose"
FT /ligand_id="ChEBI:CHEBI:57967"
FT /evidence="ECO:0000250|UniProtKB:P0DV57"
FT BINDING 79
FT /ligand="ADP-D-ribose"
FT /ligand_id="ChEBI:CHEBI:57967"
FT /evidence="ECO:0000250|UniProtKB:P0DV57"
FT BINDING 117..121
FT /ligand="ADP-D-ribose"
FT /ligand_id="ChEBI:CHEBI:57967"
FT /evidence="ECO:0000250|UniProtKB:P0DV57"
SQ SEQUENCE 352 AA; 38563 MW; CE3CA7024B953593 CRC64;
MITYGSGDLL RADTEALVNT VNCVGVMGKG IALQFKRRYP EMFTAYEKAC KRGEVTIGKM
FVVDTGQLDG PKHIINFPTK KHWRAPSKLA YIDAGLIDLI RVIRELNIAS VAVPPLGVGN
GGLDWEDVEQ RLVSAFQQLP DVDAVIYPPS GGSRAIEGVE GLRMTWGRAV ILEAMRRYLQ
QRRAMEPWED PAGISHLEIQ KLMYFANEAD PDLALDFTPG RYGPYSERVR HLLQGMEGAF
TVGLGDGTAR VLANQPISLT TKGTDAITDY LATDAAADRV SAAVDTVLRV IEGFEGPYGV
ELLASTHWVA TREGAKEPAT AAAAVRKWTK RKGRIYSDDR IGVALDRILM TA
