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UniProtKB - P46344 (PGPH_BACSU)

Entry version 133 (12 Aug 2020)
Sequence version 2 (01 Oct 1996)
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Protein

Cyclic-di-AMP phosphodiesterase PgpH

Gene

pgpH

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:4 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>-Protein inferred from homologyi <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

Probably has phosphodiesterase (PDE) activity against cyclic-di-AMP (c-di-AMP); may be the major c-di-AMP PDE in the cell (PubMed:26240071). In B.subtilis c-di-AMP is a second messenger that mediates growth, DNA repair and cell wall homeostasis; it is toxic when present in excess (PubMed:26240071).1 Publication

<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

Mn2+By similarity

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 bindingi504Manganese 1; via tele nitrogenBy similarity1
<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 sitei504SubstrateBy similarity1
Metal bindingi533Manganese 1; via tele nitrogenBy similarity1
Metal bindingi534Manganese 1By similarity1
Metal bindingi534Manganese 2By similarity1
Metal bindingi570Manganese 2; via tele nitrogenBy similarity1
Metal bindingi594Manganese 2; via tele nitrogenBy similarity1
Metal bindingi595Manganese 2; via tele nitrogenBy similarity1
Binding sitei621SubstrateBy similarity1
Metal bindingi638Manganese 1By similarity1
Binding sitei638SubstrateBy similarity1

<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
LigandManganese, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		BSUB:BSU25330-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:
Cyclic-di-AMP phosphodiesterase PgpH1 Publication (EC:3.1.4.59By similarity)
Short name:
c-di-AMP phosphodiesterase
<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:pgpH1 Publication
Synonyms:yqfF
Ordered Locus Names:BSU25330
<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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei275 – 295HelicalSequence analysisAdd BLAST21
Transmembranei311 – 331HelicalSequence analysisAdd BLAST21
Transmembranei336 – 356HelicalSequence analysisAdd BLAST21
Transmembranei360 – 380HelicalSequence analysisAdd BLAST21
Transmembranei384 – 404HelicalSequence analysisAdd BLAST21
Transmembranei413 – 433HelicalSequence analysisAdd BLAST21
Transmembranei448 – 468HelicalSequence analysisAdd BLAST21

GO - Cellular componenti

Complete GO annotation on QuickGO ...

Keywords - Cellular componenti

Cell membrane, Membrane

<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

In strain 168 grown in minimal medium and glutamate, 3.5-fold increase in c-di-AMP levels, while a double pgpH-gdpP mutant has 4.2-fold increased levels of in c-di-AMP; double mutants die on solid medium after 2 days (PubMed:26240071).1 Publication

<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_00000497971 – 711Cyclic-di-AMP phosphodiesterase PgpHAdd BLAST711

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P46344

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

More...PaxDbi		P46344

PRoteomics IDEntifications database

More...PRIDEi		P46344

<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

Protein-protein interaction databases

Protein interaction database and analysis system

More...IntActi		P46344, 38 interactors

STRING: functional protein association networks

More...STRINGi		224308.BSU25330

<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

3D structure databases

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

More...SMRi		P46344

Database of comparative protein structure models

More...ModBasei		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

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>Domaini501 – 643HDPROSITE-ProRule annotationAdd BLAST143

<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 PgpH phosphodiesterase family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG1480, Bacteria

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P46344

KEGG Orthology (KO)

More...KOi		K07037

Identification of Orthologs from Complete Genome Data

More...OMAi		DFIRTHH

Database for complete collections of gene phylogenies

More...PhylomeDBi		P46344

Family and domain databases

Conserved Domains Database

More...CDDi		cd00077, HDc, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR003607, HD/PDEase_dom
IPR006674, HD_domain
IPR006675, HDIG_dom
IPR011624, Metal-dep_PHydrolase_7TM_extra
IPR011621, Metal-dep_PHydrolase_7TM_intra

Pfam protein domain database

More...Pfami		View protein in Pfam
PF07698, 7TM-7TMR_HD, 1 hit
PF07697, 7TMR-HDED, 1 hit
PF01966, HD, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00471, HDc, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00277, HDIG, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS51831, HD, 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.

P46344-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLKKKAKTKS SSKKWSSFKN ARSMHVLLYL LLAAIMFALL FVHVKPETLD 
        60         70         80         90        100
LDLFSVSDKT IYAPATVEDQ KATEEKKQAA EDAVEDQYTL KKEYTDNRID 
       110        120        130        140        150
LVSSIFDSIS EVKKSSEEGS KSPSEKSMVK SVKDKLTSDV NDSISEDSIK 
       160        170        180        190        200
TLLKADSEDF SFVRDTVITA VNTVMSSEIP SDKLSDAKDK VEKELKSNSI 
       210        220        230        240        250
PSKYLGAATE IGRFAIIPNY VFDPKATEAK RQEASDNVQQ VQIKQGQVLV 
       260        270        280        290        300
EENDLIDREV YRKLELTGLL NNSNLFKPIS GLLIMIGLFI ATLVYYFEKQ 
       310        320        330        340        350
KQNLKFKNQS ILLFSIITTL LLVIMEVVSL FQKMEYNNIG YLVPIAAGAI 
       360        370        380        390        400
LIKLLMNERI AILGSIILAI CGSMMFNQGV TGTFNYVIGI YYLISGISGV 
       410        420        430        440        450
LFLGKHNARS KILQTGLFVA FINMVVVLSL LLIQNTALSG LEIGTLMLMG 
       460        470        480        490        500
VVSGFASSVL IIGLMPFFET GFGILSTMRL LELSNPNHPL LRKILTETPG 
       510        520        530        540        550
TYHHSVMVAN LSEAACEAVG ANGLLARVGA YYHDLGKTKR PQYFIENQMN 
       560        570        580        590        600
IDNPHDKLSP QLSKNIIISH TTDGANMLRS YKFPKELVDI AEQHHGTSLL 
       610        620        630        640        650
KFFYYKAKEK GDQITEEEFR YPGPKPQSKE AAIISVADSV EAAVRSMHNP 
       660        670        680        690        700
NPERIEKLVR GIISDKLQDG QFSECDLTFK ELDTIAKTLC ATLKGIFHSR 
       710 
IEYPEATKKV K
Length:711
Mass (Da):79,167
Last modified:October 1, 1996 - 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:i1E424AB385D6E3B4
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAA70040 differs from that shown. Reason: Frameshift.Curated
The sequence AAA70041 differs from that shown. Reason: Frameshift.Curated
The sequence AAA70042 differs from that shown. Reason: Frameshift.Curated

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
D84432 Genomic DNA Translation: BAA12478.1
U29177 Genomic DNA Translation: AAA70040.1 Frameshift.
U29177 Genomic DNA Translation: AAA70041.1 Frameshift.
U29177 Genomic DNA Translation: AAA70042.1 Frameshift.
AL009126 Genomic DNA Translation: CAB14462.1

Protein sequence database of the Protein Information Resource

More...PIRi		E69953

NCBI Reference Sequences

More...RefSeqi		NP_390411.1, NC_000964.3
WP_010886570.1, NZ_JNCM01000036.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CAB14462; CAB14462; BSU25330

Database of genes from NCBI RefSeq genomes

More...GeneIDi		937877

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		bsu:BSU25330

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|224308.43.peg.2641

<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
D84432 Genomic DNA Translation: BAA12478.1
U29177 Genomic DNA Translation: AAA70040.1 Frameshift.
U29177 Genomic DNA Translation: AAA70041.1 Frameshift.
U29177 Genomic DNA Translation: AAA70042.1 Frameshift.
AL009126 Genomic DNA Translation: CAB14462.1
PIRiE69953
RefSeqiNP_390411.1, NC_000964.3
WP_010886570.1, NZ_JNCM01000036.1

3D structure databases

SMRiP46344
ModBaseiSearch...

Protein-protein interaction databases

IntActiP46344, 38 interactors
STRINGi224308.BSU25330

Proteomic databases

jPOSTiP46344
PaxDbiP46344
PRIDEiP46344

Genome annotation databases

EnsemblBacteriaiCAB14462; CAB14462; BSU25330
GeneIDi937877
KEGGibsu:BSU25330
PATRICifig|224308.43.peg.2641

Phylogenomic databases

eggNOGiCOG1480, Bacteria
InParanoidiP46344
KOiK07037
OMAiDFIRTHH
PhylomeDBiP46344

Enzyme and pathway databases

BioCyciBSUB:BSU25330-MONOMER

Family and domain databases

CDDicd00077, HDc, 1 hit
InterProiView protein in InterPro
IPR003607, HD/PDEase_dom
IPR006674, HD_domain
IPR006675, HDIG_dom
IPR011624, Metal-dep_PHydrolase_7TM_extra
IPR011621, Metal-dep_PHydrolase_7TM_intra
PfamiView protein in Pfam
PF07698, 7TM-7TMR_HD, 1 hit
PF07697, 7TMR-HDED, 1 hit
PF01966, HD, 1 hit
SMARTiView protein in SMART
SM00471, HDc, 1 hit
TIGRFAMsiTIGR00277, HDIG, 1 hit
PROSITEiView protein in PROSITE
PS51831, HD, 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 nameiPGPH_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: P46344
Secondary accession number(s): P46345, P46346
<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: November 1, 1995
Last sequence update: October 1, 1996
Last modified: August 12, 2020
This is version 133 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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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