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UniProtKB - P0A8D6 (YMDB_ECOLI)

Entry version 116 (23 Feb 2022)
Sequence version 1 (07 Jun 2005)
Previous versions | rss
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Protein

O-acetyl-ADP-ribose deacetylase

Gene

ymdB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 0.48 sec(-1) (PubMed:21257746). kcat is 1.31 sec(-1) (PubMed:26481419).2 Publications
  1. KM=270 µM for O-acetyl-ADP-ribose1 Publication
  2. KM=430 µM for O-acetyl-ADP-ribose1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei25SubstrateUniRule annotation1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei35Proton acceptorUniRule annotation1 Publication1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionHydrolase
Biological processStress response

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:G6550-MONOMER

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		3.1.1.106, 2026

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:ymdBUniRule annotation
Ordered Locus Names:b1045, JW1032
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi25N → A: 5-fold decrease in catalytic efficiency. Loss of activity; when associated with A-35. 1 Publication1
Mutagenesisi35D → A: 41-fold decrease in catalytic efficiency. Loss of activity; when associated with A-25. 1 Publication1
Mutagenesisi40R → A: Causes a 17-fold increase in the dissociation constant of the YmdB-RNase III interaction. 1 Publication1
Mutagenesisi124G → E: Abolishes enzyme activity. 1 Publication1
Mutagenesisi126Y → A: Loss of activity. 1 Publication1
Mutagenesisi126Y → F: No change in activity. 1 Publication1

Chemistry databases

Drug and drug target database

More...DrugBanki		DB03814, 2-(N-morpholino)ethanesulfonic acid

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000891911 – 177O-acetyl-ADP-ribose deacetylaseAdd BLAST177

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P0A8D6

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P0A8D6

PRoteomics IDEntifications database

More...PRIDEi		P0A8D6

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Expression is induced by both entry into stationary phase, via RpoS, and cold-shock stress.2 Publications

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer (PubMed:19141481).

Interacts with RNase III (PubMed:19141481, PubMed:25546632). Interaction with the ribonuclease decreases homodimer formation (PubMed:19141481).

2 Publications

GO - Molecular functioni

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4260690, 29 interactors

Database of interacting proteins

More...DIPi		DIP-48222N

Protein interaction database and analysis system

More...IntActi		P0A8D6, 3 interactors

STRING: functional protein association networks

More...STRINGi		511145.b1045

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1177
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P0A8D6

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P0A8D6

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini1 – 175MacroUniRule annotationAdd BLAST175

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni11 – 12Substrate bindingUniRule annotation1 Publication2
Regioni33 – 35Substrate bindingUniRule annotation1 Publication3
Regioni122 – 126Substrate bindingUniRule annotation1 Publication5

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the YmdB family.UniRule annotationCurated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG2110, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_046550_5_1_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P0A8D6

Database for complete collections of gene phylogenies

More...PhylomeDBi		P0A8D6

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.40.220.10, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_01205, YmdB, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR002589, Macro_dom
IPR043472, Macro_dom-like
IPR024900, O-Ac-ADP-ribose_deAcase

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01661, Macro, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00506, A1pp, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF52949, SSF52949, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS51154, MACRO, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P0A8D6-1 [UniParc]FASTAAdd to basket
« Hide
        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
Length:177
Mass (Da):18,880
Last modified:June 7, 2005 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i6F4E12D5C181CAAF
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC74129.1
AP009048 Genomic DNA Translation: BAA35835.1

Protein sequence database of the Protein Information Resource

More...PIRi		B64847

NCBI Reference Sequences

More...RefSeqi		NP_415563.1, NC_000913.3
WP_000857405.1, NZ_SSZK01000058.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC74129; AAC74129; b1045
BAA35835; BAA35835; BAA35835

Database of genes from NCBI RefSeq genomes

More...GeneIDi		58463456
946987

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW1032
eco:b1045

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.1224

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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
PIRiB64847
RefSeqiNP_415563.1, NC_000913.3
WP_000857405.1, NZ_SSZK01000058.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SPVX-ray2.00A1-176[»]
5CB3X-ray1.80A1-177[»]
5CB5X-ray2.80A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R1-177[»]
5CMSX-ray2.98A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R1-177[»]
SMRiP0A8D6
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4260690, 29 interactors
DIPiDIP-48222N
IntActiP0A8D6, 3 interactors
STRINGi511145.b1045

Chemistry databases

DrugBankiDB03814, 2-(N-morpholino)ethanesulfonic acid

Proteomic databases

jPOSTiP0A8D6
PaxDbiP0A8D6
PRIDEiP0A8D6

Genome annotation databases

EnsemblBacteriaiAAC74129; AAC74129; b1045
BAA35835; BAA35835; BAA35835
GeneIDi58463456
946987
KEGGiecj:JW1032
eco:b1045
PATRICifig|1411691.4.peg.1224

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB3633

Phylogenomic databases

eggNOGiCOG2110, Bacteria
HOGENOMiCLU_046550_5_1_6
InParanoidiP0A8D6
PhylomeDBiP0A8D6

Enzyme and pathway databases

BioCyciEcoCyc:G6550-MONOMER
BRENDAi3.1.1.106, 2026

Miscellaneous databases

EvolutionaryTraceiP0A8D6

Protein Ontology

More...PROi		PR:P0A8D6

Family and domain databases

Gene3Di3.40.220.10, 1 hit
HAMAPiMF_01205, YmdB, 1 hit
InterProiView protein in InterPro
IPR002589, Macro_dom
IPR043472, Macro_dom-like
IPR024900, O-Ac-ADP-ribose_deAcase
PfamiView protein in Pfam
PF01661, Macro, 1 hit
SMARTiView protein in SMART
SM00506, A1pp, 1 hit
SUPFAMiSSF52949, SSF52949, 1 hit
PROSITEiView protein in PROSITE
PS51154, MACRO, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiYMDB_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P0A8D6
Secondary accession number(s): P75918
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: February 23, 2022
This is version 116 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
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