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Entry version 139 (25 May 2022)
Sequence version 1 (01 Feb 1997)
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Protein

Probable cyclic di-GMP phosphodiesterase PdeN

Gene

pdeN

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

Annotation score:3 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 transcript 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

Phosphodiesterase (PDE) that catalyzes the hydrolysis of cyclic-di-GMP (c-di-GMP) to 5'-pGpG.

By similarity

Caution

Was originally (Ref. 4) thought to originate from Proteus vulgaris, but was shown to originate from E.coli.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>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

<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
Ligandc-di-GMP

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:G7148-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:
Probable cyclic di-GMP phosphodiesterase PdeNCurated (EC:3.1.4.52By similarity)
<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:pdeN1 Publication
Synonyms:rtn
Ordered Locus Names:b2176, JW2164
<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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<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 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>Transmembranei16 – 36HelicalSequence analysisAdd BLAST21
Transmembranei236 – 256HelicalSequence analysisAdd BLAST21

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

<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_00000975171 – 518Probable cyclic di-GMP phosphodiesterase PdeNAdd BLAST518

Proteomic databases

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

More...
PaxDbi
P76446

PRoteomics IDEntifications database

More...
PRIDEi
P76446

<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

Expressed at both 28 and 37 degrees Celsius during exponential growth. Repressed by RpoS.1 Publication

<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

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4261095, 10 interactors

Database of interacting proteins

More...
DIPi
DIP-10813N

STRING: functional protein association networks

More...
STRINGi
511145.b2176

<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

AlphaFold Protein Structure Database

More...
AlphaFoldDBi
P76446

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

More...
SMRi
P76446

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>Domaini261 – 514EALPROSITE-ProRule annotationAdd BLAST254

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG2200, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_000445_131_2_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P76446

Identification of Orthologs from Complete Genome Data

More...
OMAi
FLQGYWI

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P76446

Family and domain databases

Conserved Domains Database

More...
CDDi
cd01948, EAL, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.20.20.450, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR024744, CSS-motif_dom
IPR001633, EAL_dom
IPR035919, EAL_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF12792, CSS-motif, 1 hit
PF00563, EAL, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00052, EAL, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF141868, SSF141868, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50883, EAL, 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.

P76446-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MFIRAPNFGR KLLLTCIVAG VMIAILVSCL QFLVAWHKHE VKYDTLITDV
60 70 80 90 100
QKYLDTYFAD LKSTTDRLQP LTLDTCQQAN PELTARAAFS MNVRTFVLVK
110 120 130 140 150
DKKTFCSSAT GEMDIPLNEL IPALDINKNV DMAILPGTPM VPNKPAIVIW
160 170 180 190 200
YRNPLLKNSG VFAALNLNLT PSLFYSSRQE DYDGVALIIG NTALSTFSSR
210 220 230 240 250
LMNVNELTDM PVRETKIAGI PLTVRLYADD WTWNDVWYAF LLGGMSGTVV
260 270 280 290 300
GLLCYYLMSV RMRPGREIMT AIKREQFYVA YQPVVDTQAL RVTGLEVLLR
310 320 330 340 350
WRHPVAGEIP PDAFINFAES QKMIVPLTQH LFELIARDAA ELEKVLPVGV
360 370 380 390 400
KFGINIAPDH LHSESFKADI QKLLTSLPAH HFQIVLEITE RDMLKEQEAT
410 420 430 440 450
QLFAWLHSVG VEIAIDDFGT GHSALIYLER FTLDYLKIDR GFINAIGTET
460 470 480 490 500
ITSPVLDAVL TLAKRLNMLT VAEGVETPEQ ARWLSERGVN FMQGYWISRP
510
LPLDDFVRWL KKPYTPQW
Length:518
Mass (Da):58,588
Last modified:February 1, 1997 - 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:iBABA5768CBC47C41
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti482 – 518RWLSE…YTPQW → D no nucleotide entry (Ref. 4) CuratedAdd BLAST37

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: AAC75237.1
AP009048 Genomic DNA Translation: BAA15984.1
U12780 Genomic DNA Translation: AAA50754.1
U83404 Genomic DNA Translation: AAB51508.1

Protein sequence database of the Protein Information Resource

More...
PIRi
G64986

NCBI Reference Sequences

More...
RefSeqi
NP_416681.1, NC_000913.3
WP_000470560.1, NZ_SSZK01000027.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC75237; AAC75237; b2176
BAA15984; BAA15984; BAA15984

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
946695

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW2164
eco:b2176

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.60

<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: AAC75237.1
AP009048 Genomic DNA Translation: BAA15984.1
U12780 Genomic DNA Translation: AAA50754.1
U83404 Genomic DNA Translation: AAB51508.1
PIRiG64986
RefSeqiNP_416681.1, NC_000913.3
WP_000470560.1, NZ_SSZK01000027.1

3D structure databases

AlphaFoldDBiP76446
SMRiP76446
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4261095, 10 interactors
DIPiDIP-10813N
STRINGi511145.b2176

Proteomic databases

PaxDbiP76446
PRIDEiP76446

Genome annotation databases

EnsemblBacteriaiAAC75237; AAC75237; b2176
BAA15984; BAA15984; BAA15984
GeneIDi946695
KEGGiecj:JW2164
eco:b2176
PATRICifig|1411691.4.peg.60

Organism-specific databases

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

More...
EchoBASEi
EB3830

Phylogenomic databases

eggNOGiCOG2200, Bacteria
HOGENOMiCLU_000445_131_2_6
InParanoidiP76446
OMAiFLQGYWI
PhylomeDBiP76446

Enzyme and pathway databases

BioCyciEcoCyc:G7148-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P76446

Family and domain databases

CDDicd01948, EAL, 1 hit
Gene3Di3.20.20.450, 1 hit
InterProiView protein in InterPro
IPR024744, CSS-motif_dom
IPR001633, EAL_dom
IPR035919, EAL_sf
PfamiView protein in Pfam
PF12792, CSS-motif, 1 hit
PF00563, EAL, 1 hit
SMARTiView protein in SMART
SM00052, EAL, 1 hit
SUPFAMiSSF141868, SSF141868, 1 hit
PROSITEiView protein in PROSITE
PS50883, EAL, 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 nameiPDEN_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: P76446
Secondary accession number(s): P77139, Q52613
<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, 1997
Last sequence update: February 1, 1997
Last modified: May 25, 2022
This is version 139 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

Reference proteome
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