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UniProtKB - O31775 (YMDB_BACSU)

Entry version 107 (12 Aug 2020)
Sequence version 2 (16 Jun 2009)
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Protein

2',3'-cyclic-nucleotide 2'-phosphodiesterase

Gene

ymdB

Organism
Bacillus subtilis (strain 168)
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

Plays a central, regulatory role in the late adaptive responses and affects the levels of many genes (PubMed:24163345). May act via regulation of cAMP levels (PubMed:26904951). Decreases the expression of motility genes and induces genes involved in biofilm formation, by controlling the expression of SlrR (PubMed:21856853). Required for formation of intercellular nanotubes that bridge neighboring cells to allow molecular exchange (PubMed:26906740). Plays a key role in directing the early stages of colony development (PubMed:26904951). In vitro, has a metal-dependent phosphodiesterase activity against 2',3'-cAMP and 2',3'-cGMP. Has also 3',5'-cyclic-nucleotide phosphodiesterase activity, but cannot use cyclic di-AMP or cyclic di-GMP, and does not have phosphatase activity (PubMed:24163345).1 Publication4 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 provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Protein has several cofactor binding sites:

<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 15.0 min(-1) with 2',3'-cAMP as substrate. kcat is 22.1 min(-1) with 2',3'-cGMP as substrate. kcat is 9.2 min(-1) with 3',5'-cAMP as substrate. kcat is 7.7 min(-1) with 3',5'-cGMP as substrate.1 Publication
  1. KM=0.2 mM for 2',3'-cAMP1 Publication
  2. KM=0.29 mM for 2',3'-cGMP1 Publication
  3. KM=1.3 mM for 3',5'-cAMP1 Publication
  4. KM=0.85 mM for 3',5'-cGMP1 Publication
  5. KM=0.94 mM for bis-pNPP1 Publication
  1. Vmax=0.83 µmol/min/mg enzyme with 2',3'-cAMP as substrate1 Publication
  2. Vmax=1.02 µmol/min/mg enzyme with 2',3'-cGMP as substrate1 Publication
  3. Vmax=0.45 µmol/min/mg enzyme with 3',5'-cAMP as substrate1 Publication
  4. Vmax=0.37 µmol/min/mg enzyme with 3',5'-cGMP as substrate1 Publication
  5. Vmax=105 µmol/min/mg enzyme with bis-pNPP as substrate1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi8Iron 1Combined sources1 Publication1
Metal bindingi39Iron 1Combined sources1 Publication1
Metal bindingi39Iron 2Combined sources1 Publication1
Metal bindingi40Iron 1Combined sources1 Publication1
Metal bindingi67Iron 2Combined sources1 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 sitei68Proton donor1 Publication1
Metal bindingi150Iron 2; via tele nitrogenCombined sources1 Publication1
Metal bindingi175Iron 2; via pros nitrogenCombined sources1 Publication1
Metal bindingi177Iron 1; via tele nitrogenCombined sources1 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 ...

<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
LigandIron, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		BSUB:BSU16970-MONOMER

<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:
2',3'-cyclic-nucleotide 2'-phosphodiesteraseCurated (EC:3.1.4.161 Publication)
Alternative name(s):
Global regulator YmdBCurated
<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:ymdB
Ordered Locus Names:BSU16970
<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>OrganismiBacillus subtilis (strain 168)
<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 identifieri224308 [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 › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus ›
<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
  • UP000001570 <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

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Complete GO annotation on QuickGO ...

Keywords - Cellular componenti

Cytoplasm

<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

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Deletion of the gene affects the levels of over 800 mRNAs (PubMed:24163345). Deletion mutant overexpresses flagellin and other genes of the sigma-D-dependent motility regulon. In contrast, the two major operons for biofilm formation are not expressed and the mutant is unable to form biofilms. All cells are short and motile (PubMed:21856853). Deletion also results in a significant decrease in intercellular molecular exchange (PubMed:26906740). Mutant displays aberrant developmental patterns and forms smaller colonies (PubMed:26904951).4 Publications

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>Mutagenesisi8D → A: Increases cAMP levels. Displays aberrant colony morphologies. 1 Publication1
Mutagenesisi39E → Q: Abolishes phosphodiesterase activity. Overexpresses flagellin and forms smooth colonies. Does not affect stability of the protein. 1 Publication1

<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_00003610921 – 2642',3'-cyclic-nucleotide 2'-phosphodiesteraseAdd BLAST264

Proteomic databases

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

More...PaxDbi		O31775

PRoteomics IDEntifications database

More...PRIDEi		O31775

<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.

1 Publication

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		224308.BSU16970

<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

1264
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		O31775

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

<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

<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-like family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG1692, Bacteria

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		O31775

KEGG Orthology (KO)

More...KOi		K09769

Identification of Orthologs from Complete Genome Data

More...OMAi		NHIWDKK

Database for complete collections of gene phylogenies

More...PhylomeDBi		O31775

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.60.21.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR029052, Metallo-depent_PP-like
IPR005235, YmdB-like

The PANTHER Classification System

More...PANTHERi		PTHR36303, PTHR36303, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF13277, YmdB, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF004789, DR1281, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00282, TIGR00282, 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.

O31775-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRILFIGDVV GSPGRDMVKE YVPKLKTKYK PHFTIINGEN AAHGKGLTEK 
        60         70         80         90        100
IYHSLIQSGA DAITMGNHTW DKKEIFDFID DVPNLVRPAN FPEGTPGKGI 
       110        120        130        140        150
TYVKANGKEL AVINLQGRTF LPPLDDPFLK ADELIAEAAK RTPYIFIDFH 
       160        170        180        190        200
AEATSEKLAL GWYTDGRASA VVGTHTHVQT ADNRILPKGT AYITDVGMTG 
       210        220        230        240        250
PYDGILGMDR ETIIKRFKTN LPVRFTVAEG KTTLSGVVID IDDQTKKAVK 
       260 
IERILINDDH MFFE
Length:264
Mass (Da):29,289
Last modified:June 16, 2009 - v2
<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:iB0A58FF04DC56D3F
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
AL009126 Genomic DNA Translation: CAB13570.2

Protein sequence database of the Protein Information Resource

More...PIRi		G69884

NCBI Reference Sequences

More...RefSeqi		NP_389579.2, NC_000964.3
WP_003245138.1, NZ_JNCM01000035.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CAB13570; CAB13570; BSU16970

Database of genes from NCBI RefSeq genomes

More...GeneIDi		51991307
939441

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		bsu:BSU16970

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|224308.179.peg.1838

<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
AL009126 Genomic DNA Translation: CAB13570.2
PIRiG69884
RefSeqiNP_389579.2, NC_000964.3
WP_003245138.1, NZ_JNCM01000035.1

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
4B2OX-ray1.64A/B/C/D1-264[»]
SMRiO31775
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU16970

Proteomic databases

PaxDbiO31775
PRIDEiO31775

Genome annotation databases

EnsemblBacteriaiCAB13570; CAB13570; BSU16970
GeneIDi51991307
939441
KEGGibsu:BSU16970
PATRICifig|224308.179.peg.1838

Phylogenomic databases

eggNOGiCOG1692, Bacteria
InParanoidiO31775
KOiK09769
OMAiNHIWDKK
PhylomeDBiO31775

Enzyme and pathway databases

BioCyciBSUB:BSU16970-MONOMER

Family and domain databases

Gene3Di3.60.21.10, 1 hit
InterProiView protein in InterPro
IPR029052, Metallo-depent_PP-like
IPR005235, YmdB-like
PANTHERiPTHR36303, PTHR36303, 1 hit
PfamiView protein in Pfam
PF13277, YmdB, 1 hit
PIRSFiPIRSF004789, DR1281, 1 hit
TIGRFAMsiTIGR00282, TIGR00282, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

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_BACSU
<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: O31775
<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: January 20, 2009
Last sequence update: June 16, 2009
Last modified: August 12, 2020
This is version 107 of the entry and version 2 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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