UniProtKB - P0A8D6 (YMDB_ECOLI)
Protein
O-acetyl-ADP-ribose deacetylase
Gene
ymdB
Organism
Escherichia coli (strain K12)
Status
Functioni
Deacetylates O-acetyl-ADP ribose to yield ADP-ribose and free acetate (PubMed:21257746, PubMed:26481419). Down-regulates ribonuclease 3 (RNase III) activity. Acts by interacting directly with the region of the ribonuclease that is required for dimerization/activation (PubMed:19141481). Overexpression inhibits biofilm formation via an RNase III-independent pathway. This inhibition is RpoS-dependent (PubMed:24267348, PubMed:28582517). Overexpression also results in increased susceptibility to apramycin (PubMed:28034758, PubMed:28582517).6 Publications
Catalytic activityi
Kineticsi
kcat is 0.48 sec(-1) (PubMed:21257746). kcat is 1.31 sec(-1) (PubMed:26481419).2 Publications
- KM=270 µM for O-acetyl-ADP-ribose1 Publication
- KM=430 µM for O-acetyl-ADP-ribose1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 25 | SubstrateUniRule annotation1 Publication | 1 | |
Active sitei | 35 | Proton acceptorUniRule annotation1 Publication | 1 |
GO - Molecular functioni
- deacetylase activity Source: GO_Central
- endoribonuclease inhibitor activity Source: EcoCyc
- enzyme binding Source: EcoCyc
- O-acetyl-ADP-ribose deacetylase activity Source: EcoCyc
- purine nucleoside binding Source: UniProtKB-UniRule
GO - Biological processi
- negative regulation of endoribonuclease activity Source: EcoCyc
- purine nucleoside metabolic process Source: UniProtKB-UniRule
- regulation of single-species biofilm formation on inanimate substrate Source: EcoCyc
- response to antibiotic Source: EcoCyc
Keywordsi
Molecular function | Hydrolase |
Biological process | Stress response |
Enzyme and pathway databases
BioCyci | EcoCyc:G6550-MONOMER MetaCyc:G6550-MONOMER |
Names & Taxonomyi
Protein namesi | Recommended name: O-acetyl-ADP-ribose deacetylase1 PublicationUniRule annotation (EC:3.1.1.106UniRule annotation2 Publications)Alternative name(s): Regulator of RNase III activityUniRule annotationCurated |
Gene namesi | Name:ymdBUniRule annotation Ordered Locus Names:b1045, JW1032 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 25 | N → A: 5-fold decrease in catalytic efficiency. Loss of activity; when associated with A-35. 1 Publication | 1 | |
Mutagenesisi | 35 | D → A: 41-fold decrease in catalytic efficiency. Loss of activity; when associated with A-25. 1 Publication | 1 | |
Mutagenesisi | 40 | R → A: Causes a 17-fold increase in the dissociation constant of the YmdB-RNase III interaction. 1 Publication | 1 | |
Mutagenesisi | 124 | G → E: Abolishes enzyme activity. 1 Publication | 1 | |
Mutagenesisi | 126 | Y → A: Loss of activity. 1 Publication | 1 | |
Mutagenesisi | 126 | Y → F: No change in activity. 1 Publication | 1 |
Chemistry databases
DrugBanki | DB03814, 2-(N-morpholino)ethanesulfonic acid |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000089191 | 1 – 177 | O-acetyl-ADP-ribose deacetylaseAdd BLAST | 177 |
Proteomic databases
jPOSTi | P0A8D6 |
PaxDbi | P0A8D6 |
PRIDEi | P0A8D6 |
Expressioni
Inductioni
Expression is induced by both entry into stationary phase, via RpoS, and cold-shock stress.2 Publications
Interactioni
Subunit structurei
GO - Molecular functioni
- enzyme binding Source: EcoCyc
Protein-protein interaction databases
BioGRIDi | 4260690, 29 interactors |
DIPi | DIP-48222N |
IntActi | P0A8D6, 3 interactors |
STRINGi | 511145.b1045 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P0A8D6 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P0A8D6 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 1 – 175 | MacroUniRule annotationAdd BLAST | 175 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 11 – 12 | Substrate bindingUniRule annotation1 Publication | 2 | |
Regioni | 33 – 35 | Substrate bindingUniRule annotation1 Publication | 3 | |
Regioni | 122 – 126 | Substrate bindingUniRule annotation1 Publication | 5 |
Sequence similaritiesi
Phylogenomic databases
eggNOGi | COG2110, Bacteria |
HOGENOMi | CLU_046550_5_1_6 |
InParanoidi | P0A8D6 |
PhylomeDBi | P0A8D6 |
Family and domain databases
Gene3Di | 3.40.220.10, 1 hit |
HAMAPi | MF_01205, YmdB, 1 hit |
InterProi | View protein in InterPro IPR002589, Macro_dom IPR043472, Macro_dom-like IPR024900, O-Ac-ADP-ribose_deAcase |
Pfami | View protein in Pfam PF01661, Macro, 1 hit |
SMARTi | View protein in SMART SM00506, A1pp, 1 hit |
SUPFAMi | SSF52949, SSF52949, 1 hit |
PROSITEi | View protein in PROSITE PS51154, MACRO, 1 hit |
i Sequence
Sequence statusi: Complete.
P0A8D6-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MKTRIHVVQG DITKLAVDVI VNAANPSLMG GGGVDGAIHR AAGPALLDAC
60 70 80 90 100
LKVRQQQGDC PTGHAVITLA GDLPAKAVVH TVGPVWRGGE QNEDQLLQDA
110 120 130 140 150
YLNSLRLVAA NSYTSVAFPA ISTGVYGYPR AAAAEIAVKT VSEFITRHAL
160 170
PEQVYFVCYD EENAHLYERL LTQQGDE
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U00096 Genomic DNA Translation: AAC74129.1 AP009048 Genomic DNA Translation: BAA35835.1 |
PIRi | B64847 |
RefSeqi | NP_415563.1, NC_000913.3 WP_000857405.1, NZ_SSZK01000058.1 |
Genome annotation databases
EnsemblBacteriai | AAC74129; AAC74129; b1045 BAA35835; BAA35835; BAA35835 |
GeneIDi | 58463456 946987 |
KEGGi | ecj:JW1032 eco:b1045 |
PATRICi | fig|1411691.4.peg.1224 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U00096 Genomic DNA Translation: AAC74129.1 AP009048 Genomic DNA Translation: BAA35835.1 |
PIRi | B64847 |
RefSeqi | NP_415563.1, NC_000913.3 WP_000857405.1, NZ_SSZK01000058.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1SPV | X-ray | 2.00 | A | 1-176 | [»] | |
5CB3 | X-ray | 1.80 | A | 1-177 | [»] | |
5CB5 | X-ray | 2.80 | A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R | 1-177 | [»] | |
5CMS | X-ray | 2.98 | A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R | 1-177 | [»] | |
SMRi | P0A8D6 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4260690, 29 interactors |
DIPi | DIP-48222N |
IntActi | P0A8D6, 3 interactors |
STRINGi | 511145.b1045 |
Chemistry databases
DrugBanki | DB03814, 2-(N-morpholino)ethanesulfonic acid |
Proteomic databases
jPOSTi | P0A8D6 |
PaxDbi | P0A8D6 |
PRIDEi | P0A8D6 |
Genome annotation databases
EnsemblBacteriai | AAC74129; AAC74129; b1045 BAA35835; BAA35835; BAA35835 |
GeneIDi | 58463456 946987 |
KEGGi | ecj:JW1032 eco:b1045 |
PATRICi | fig|1411691.4.peg.1224 |
Organism-specific databases
EchoBASEi | EB3633 |
Phylogenomic databases
eggNOGi | COG2110, Bacteria |
HOGENOMi | CLU_046550_5_1_6 |
InParanoidi | P0A8D6 |
PhylomeDBi | P0A8D6 |
Enzyme and pathway databases
BioCyci | EcoCyc:G6550-MONOMER MetaCyc:G6550-MONOMER |
Miscellaneous databases
EvolutionaryTracei | P0A8D6 |
PROi | PR:P0A8D6 |
Family and domain databases
Gene3Di | 3.40.220.10, 1 hit |
HAMAPi | MF_01205, YmdB, 1 hit |
InterProi | View protein in InterPro IPR002589, Macro_dom IPR043472, Macro_dom-like IPR024900, O-Ac-ADP-ribose_deAcase |
Pfami | View protein in Pfam PF01661, Macro, 1 hit |
SMARTi | View protein in SMART SM00506, A1pp, 1 hit |
SUPFAMi | SSF52949, SSF52949, 1 hit |
PROSITEi | View protein in PROSITE PS51154, MACRO, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | YMDB_ECOLI | |
Accessioni | P0A8D6Primary (citable) accession number: P0A8D6 Secondary accession number(s): P75918 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | June 7, 2005 |
Last sequence update: | June 7, 2005 | |
Last modified: | April 7, 2021 | |
This is version 114 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Uncharacterized protein families (UPF)
List of uncharacterized protein family (UPF) entries - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families