YMDB_ECOLI
ID YMDB_ECOLI Reviewed; 177 AA.
AC P0A8D6; P75918;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 118.
DE RecName: Full=O-acetyl-ADP-ribose deacetylase {ECO:0000255|HAMAP-Rule:MF_01205, ECO:0000303|PubMed:21257746};
DE EC=3.1.1.106 {ECO:0000255|HAMAP-Rule:MF_01205, ECO:0000269|PubMed:21257746, ECO:0000269|PubMed:26481419};
DE AltName: Full=Regulator of RNase III activity {ECO:0000255|HAMAP-Rule:MF_01205, ECO:0000305};
GN Name=ymdB {ECO:0000255|HAMAP-Rule:MF_01205};
GN OrderedLocusNames=b1045, JW1032;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP FUNCTION, SUBUNIT, INTERACTION WITH RIBONUCLEASE 3, AND INDUCTION.
RX PubMed=19141481; DOI=10.1101/gad.1729508;
RA Kim K.S., Manasherob R., Cohen S.N.;
RT "YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase
RT III activity.";
RL Genes Dev. 22:3497-3508(2008).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF GLY-124.
RX PubMed=21257746; DOI=10.1074/jbc.m110.206771;
RA Chen D., Vollmar M., Rossi M.N., Phillips C., Kraehenbuehl R., Slade D.,
RA Mehrotra P.V., von Delft F., Crosthwaite S.K., Gileadi O., Denu J.M.,
RA Ahel I.;
RT "Identification of macrodomain proteins as novel O-acetyl-ADP-ribose
RT deacetylases.";
RL J. Biol. Chem. 286:13261-13271(2011).
RN [6]
RP FUNCTION.
RX PubMed=24267348; DOI=10.1186/1471-2180-13-266;
RA Kim T., Lee J., Kim K.S.;
RT "Escherichia coli YmdB regulates biofilm formation independently of its
RT role as an RNase III modulator.";
RL BMC Microbiol. 13:266-266(2013).
RN [7]
RP INTERACTION WITH RNASE III, AND MUTAGENESIS OF ARG-40.
RX PubMed=25546632; DOI=10.1002/prot.24751;
RA Paudyal S., Alfonso-Prieto M., Carnevale V., Redhu S.K., Klein M.L.,
RA Nicholson A.W.;
RT "Combined computational and experimental analysis of a complex of
RT ribonuclease III and the regulatory macrodomain protein, YmdB.";
RL Proteins 83:459-472(2015).
RN [8]
RP FUNCTION.
RX PubMed=28034758; DOI=10.1016/j.bbrc.2016.12.157;
RA Kim M., Kim M., Kim K.S.;
RT "YmdB-mediated down-regulation of sucA inhibits biofilm formation and
RT induces apramycin susceptibility in Escherichia coli.";
RL Biochem. Biophys. Res. Commun. 483:252-257(2017).
RN [9]
RP FUNCTION, AND INDUCTION.
RX PubMed=28582517; DOI=10.1093/femsle/fnx114;
RA Kim M., Kim K.S.;
RT "Stress-responsively modulated ymdAB-clsC operon plays a role in biofilm
RT formation and apramycin susceptibility in Escherichia coli.";
RL FEMS Microbiol. Lett. 364:0-0(2017).
RN [10] {ECO:0007744|PDB:1SPV}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 1-176.
RG Northeast structural genomics consortium (NESG);
RT "Crystal structure of the putative phosphatase of Escherichia coli,
RT northeast structural genomics target ER58.";
RL Submitted (JAN-2005) to the PDB data bank.
RN [11] {ECO:0007744|PDB:5CB3, ECO:0007744|PDB:5CB5, ECO:0007744|PDB:5CMS}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF WILD-TYPE AND MUTANTS
RP ALA-25/ALA-35 AND ALA-126 IN COMPLEXES WITH ADP-RIBOSE, FUNCTION, CATALYTIC
RP ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, AND MUTAGENESIS OF
RP ASN-25; ASP-35 AND TYR-126.
RX PubMed=26481419; DOI=10.1016/j.jsb.2015.10.010;
RA Zhang W., Wang C., Song Y., Shao C., Zhang X., Zang J.;
RT "Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-
RT acetyl-ADP-ribose deacetylase.";
RL J. Struct. Biol. 192:478-486(2015).
CC -!- FUNCTION: Deacetylates O-acetyl-ADP ribose to yield ADP-ribose and free
CC acetate (PubMed:21257746, PubMed:26481419). Down-regulates ribonuclease
CC 3 (RNase III) activity. Acts by interacting directly with the region of
CC the ribonuclease that is required for dimerization/activation
CC (PubMed:19141481). Overexpression inhibits biofilm formation via an
CC RNase III-independent pathway. This inhibition is RpoS-dependent
CC (PubMed:24267348, PubMed:28582517). Overexpression also results in
CC increased susceptibility to apramycin (PubMed:28034758,
CC PubMed:28582517). {ECO:0000269|PubMed:19141481,
CC ECO:0000269|PubMed:21257746, ECO:0000269|PubMed:24267348,
CC ECO:0000269|PubMed:26481419, ECO:0000269|PubMed:28034758,
CC ECO:0000269|PubMed:28582517}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3''-O-acetyl-ADP-D-ribose + H2O = acetate + ADP-D-ribose +
CC H(+); Xref=Rhea:RHEA:59244, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30089, ChEBI:CHEBI:57967, ChEBI:CHEBI:142723;
CC EC=3.1.1.106; Evidence={ECO:0000255|HAMAP-Rule:MF_01205,
CC ECO:0000269|PubMed:21257746, ECO:0000269|PubMed:26481419};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2''-O-acetyl-ADP-D-ribose + H2O = acetate + ADP-D-ribose +
CC H(+); Xref=Rhea:RHEA:57060, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30089, ChEBI:CHEBI:57967, ChEBI:CHEBI:83767;
CC EC=3.1.1.106; Evidence={ECO:0000255|HAMAP-Rule:MF_01205,
CC ECO:0000269|PubMed:21257746, ECO:0000269|PubMed:26481419};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=270 uM for O-acetyl-ADP-ribose {ECO:0000269|PubMed:21257746};
CC KM=430 uM for O-acetyl-ADP-ribose {ECO:0000269|PubMed:26481419};
CC Note=kcat is 0.48 sec(-1) (PubMed:21257746). kcat is 1.31 sec(-1)
CC (PubMed:26481419). {ECO:0000269|PubMed:21257746,
CC ECO:0000269|PubMed:26481419};
CC -!- SUBUNIT: Homodimer (PubMed:19141481). Interacts with RNase III
CC (PubMed:19141481, PubMed:25546632). Interaction with the ribonuclease
CC decreases homodimer formation (PubMed:19141481).
CC {ECO:0000269|PubMed:19141481, ECO:0000269|PubMed:25546632}.
CC -!- INDUCTION: Expression is induced by both entry into stationary phase,
CC via RpoS, and cold-shock stress. {ECO:0000269|PubMed:19141481,
CC ECO:0000269|PubMed:28582517}.
CC -!- SIMILARITY: Belongs to the YmdB family. {ECO:0000255|HAMAP-
CC Rule:MF_01205, ECO:0000305}.
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DR EMBL; U00096; AAC74129.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35835.1; -; Genomic_DNA.
DR PIR; B64847; B64847.
DR RefSeq; NP_415563.1; NC_000913.3.
DR RefSeq; WP_000857405.1; NZ_SSZK01000058.1.
DR PDB; 1SPV; X-ray; 2.00 A; A=1-176.
DR PDB; 5CB3; X-ray; 1.80 A; A=1-177.
DR PDB; 5CB5; X-ray; 2.80 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R=1-177.
DR PDB; 5CMS; X-ray; 2.98 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R=1-177.
DR PDBsum; 1SPV; -.
DR PDBsum; 5CB3; -.
DR PDBsum; 5CB5; -.
DR PDBsum; 5CMS; -.
DR AlphaFoldDB; P0A8D6; -.
DR SMR; P0A8D6; -.
DR BioGRID; 4260690; 29.
DR DIP; DIP-48222N; -.
DR IntAct; P0A8D6; 3.
DR STRING; 511145.b1045; -.
DR DrugBank; DB03814; 2-(N-morpholino)ethanesulfonic acid.
DR jPOST; P0A8D6; -.
DR PaxDb; P0A8D6; -.
DR PRIDE; P0A8D6; -.
DR EnsemblBacteria; AAC74129; AAC74129; b1045.
DR EnsemblBacteria; BAA35835; BAA35835; BAA35835.
DR GeneID; 58463456; -.
DR GeneID; 946987; -.
DR KEGG; ecj:JW1032; -.
DR KEGG; eco:b1045; -.
DR PATRIC; fig|1411691.4.peg.1224; -.
DR EchoBASE; EB3633; -.
DR eggNOG; COG2110; Bacteria.
DR HOGENOM; CLU_046550_5_1_6; -.
DR InParanoid; P0A8D6; -.
DR OMA; HYGKGLP; -.
DR PhylomeDB; P0A8D6; -.
DR BioCyc; EcoCyc:G6550-MON; -.
DR BioCyc; MetaCyc:G6550-MON; -.
DR BRENDA; 3.1.1.106; 2026.
DR EvolutionaryTrace; P0A8D6; -.
DR PRO; PR:P0A8D6; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0019213; F:deacetylase activity; IBA:GO_Central.
DR GO; GO:0060698; F:endoribonuclease inhibitor activity; IDA:EcoCyc.
DR GO; GO:0061463; F:O-acetyl-ADP-ribose deacetylase activity; IDA:EcoCyc.
DR GO; GO:0001883; F:purine nucleoside binding; IEA:UniProtKB-UniRule.
DR GO; GO:0060702; P:negative regulation of endoribonuclease activity; IMP:EcoCyc.
DR GO; GO:0042278; P:purine nucleoside metabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:1900231; P:regulation of single-species biofilm formation on inanimate substrate; IMP:EcoCyc.
DR GO; GO:0046677; P:response to antibiotic; IMP:EcoCyc.
DR Gene3D; 3.40.220.10; -; 1.
DR HAMAP; MF_01205; YmdB; 1.
DR InterPro; IPR002589; Macro_dom.
DR InterPro; IPR043472; Macro_dom-like.
DR InterPro; IPR024900; O-Ac-ADP-ribose_deAcase.
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; Stress response.
FT CHAIN 1..177
FT /note="O-acetyl-ADP-ribose deacetylase"
FT /id="PRO_0000089191"
FT DOMAIN 1..175
FT /note="Macro"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01205,
FT ECO:0000255|PROSITE-ProRule:PRU00490"
FT ACT_SITE 35
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01205,
FT ECO:0000305|PubMed:26481419"
FT BINDING 11..12
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01205,
FT ECO:0000269|PubMed:26481419"
FT BINDING 25
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01205,
FT ECO:0000269|PubMed:26481419"
FT BINDING 33..35
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01205,
FT ECO:0000269|PubMed:26481419"
FT BINDING 122..126
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01205,
FT ECO:0000269|PubMed:26481419"
FT MUTAGEN 25
FT /note="N->A: 5-fold decrease in catalytic efficiency. Loss
FT of activity; when associated with A-35."
FT /evidence="ECO:0000269|PubMed:26481419"
FT MUTAGEN 35
FT /note="D->A: 41-fold decrease in catalytic efficiency. Loss
FT of activity; when associated with A-25."
FT /evidence="ECO:0000269|PubMed:26481419"
FT MUTAGEN 40
FT /note="R->A: Causes a 17-fold increase in the dissociation
FT constant of the YmdB-RNase III interaction."
FT /evidence="ECO:0000269|PubMed:25546632"
FT MUTAGEN 124
FT /note="G->E: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:21257746"
FT MUTAGEN 126
FT /note="Y->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:26481419"
FT MUTAGEN 126
FT /note="Y->F: No change in activity."
FT /evidence="ECO:0000269|PubMed:26481419"
FT STRAND 5..10
FT /evidence="ECO:0007829|PDB:5CB3"
FT HELIX 12..14
FT /evidence="ECO:0007829|PDB:5CB3"
FT STRAND 18..23
FT /evidence="ECO:0007829|PDB:5CB3"
FT HELIX 34..42
FT /evidence="ECO:0007829|PDB:5CB3"
FT HELIX 44..57
FT /evidence="ECO:0007829|PDB:5CB3"
FT STRAND 65..69
FT /evidence="ECO:0007829|PDB:5CB3"
FT STRAND 73..81
FT /evidence="ECO:0007829|PDB:5CB3"
FT STRAND 87..92
FT /evidence="ECO:0007829|PDB:5CB3"
FT HELIX 93..110
FT /evidence="ECO:0007829|PDB:5CB3"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:5CB3"
FT HELIX 130..147
FT /evidence="ECO:0007829|PDB:5CB3"
FT STRAND 149..160
FT /evidence="ECO:0007829|PDB:5CB3"
FT HELIX 161..171
FT /evidence="ECO:0007829|PDB:5CB3"
SQ SEQUENCE 177 AA; 18880 MW; 6F4E12D5C181CAAF CRC64;
MKTRIHVVQG DITKLAVDVI VNAANPSLMG GGGVDGAIHR AAGPALLDAC LKVRQQQGDC
PTGHAVITLA GDLPAKAVVH TVGPVWRGGE QNEDQLLQDA YLNSLRLVAA NSYTSVAFPA
ISTGVYGYPR AAAAEIAVKT VSEFITRHAL PEQVYFVCYD EENAHLYERL LTQQGDE
