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Entry version 144 (07 Oct 2020)
Sequence version 1 (01 Feb 1997)
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Protein

Cyclic di-GMP phosphodiesterase PdeF

Gene

pdeF

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

Phosphodiesterase (PDE) that catalyzes the hydrolysis of cyclic-di-GMP (c-di-GMP) to 5'-pGpG. Truncated proteins consisting of the GGDEF/EAL domains (residues 319-747) or of the EAL domain alone (481-747) have c-di-GMP phosphodiesterase activity. They do not have diguanylate cyclase activity. Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria.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

Mg2+1 Publication, Mn2+1 PublicationNote: Mg2+, and possibly also Mn2+.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Inhibited by pGpG.1 Publication

<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>pH dependencei

Optimum pH is 7.5 for the truncated enzyme.1 Publication

<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

  • cyclic-guanylate-specific phosphodiesterase activity Source: EcoCyc
  • nucleotide binding Source: UniProtKB-KW

GO - Biological processi

  • cellular response to anoxia Source: EcoCyc
  • cellular response to hydrogen peroxide Source: EcoCyc
  • regulation of single-species biofilm formation Source: EcoCyc

<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, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:G7314-MONOMER
MetaCyc:G7314-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-GMP phosphodiesterase PdeFCurated (EC:3.1.4.521 Publication)
<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:pdeF1 Publication
Synonyms:yfgF
Ordered Locus Names:b2503, JW2488
<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 subcellular compartment where each non-membrane region of a membrane-spanning protein is found.<p><a href='/help/topo_dom' target='_top'>More...</a></p>Topological domaini1 – 14PeriplasmicCuratedAdd BLAST14
<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>Transmembranei15 – 36HelicalSequence analysisAdd BLAST22
Topological domaini37 – 42CytoplasmicCurated6
Transmembranei43 – 65HelicalSequence analysisAdd BLAST23
Topological domaini66 – 79PeriplasmicCuratedAdd BLAST14
Transmembranei80 – 102HelicalSequence analysisAdd BLAST23
Topological domaini103 – 128CytoplasmicCuratedAdd BLAST26
Transmembranei129 – 151HelicalSequence analysisAdd BLAST23
Topological domaini152 – 165PeriplasmicCuratedAdd BLAST14
Transmembranei166 – 188HelicalSequence analysisAdd BLAST23
Topological domaini189 – 215CytoplasmicCuratedAdd BLAST27
Transmembranei216 – 235HelicalSequence analysisAdd BLAST20
Topological domaini236 – 239PeriplasmicCurated4
Transmembranei240 – 259HelicalSequence analysisAdd BLAST20
Topological domaini260 – 265CytoplasmicCurated6
Transmembranei266 – 285HelicalSequence analysisAdd BLAST20
Topological domaini286 – 294PeriplasmicCurated9
Transmembranei295 – 317HelicalSequence analysisAdd BLAST23
Topological domaini318 – 747Cytoplasmic1 PublicationAdd BLAST430

GO - Cellular componenti

Keywords - Cellular componenti

Cell inner membrane, 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

Increased biofilm formation but a decreased tendency to sediment and aggregate. Cells are more sensitive to peroxide.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_00001692411 – 747Cyclic di-GMP phosphodiesterase PdeFAdd BLAST747

Proteomic databases

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

More...
PaxDbi
P77172

PRoteomics IDEntifications database

More...
PRIDEi
P77172

<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

Induced by FNR. Expression is highest under anaerobic conditions at 28 degrees Celsius in stationary phase.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
4260585, 25 interactors

Database of interacting proteins

More...
DIPi
DIP-12038N

Protein interaction database and analysis system

More...
IntActi
P77172, 1 interactor

STRING: functional protein association networks

More...
STRINGi
511145.b2503

<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
P77172

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>Domaini493 – 744EALPROSITE-ProRule annotationAdd BLAST252

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_023566_2_0_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P77172

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P77172

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
IPR001633, EAL_dom
IPR035919, EAL_sf
IPR000160, GGDEF_dom
IPR007895, MASE1

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00563, EAL, 1 hit
PF05231, MASE1, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00052, EAL, 1 hit
SM00267, GGDEF, 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.

P77172-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKLNATYIKI RDKWWGLPLF LPSLILPIFA HINTFAHISS GEVFLFYLPL
60 70 80 90 100
ALMISMMMFF SWAALPGIAL GIFVRKYAEL GFYETLSLTA NFIIIIILCW
110 120 130 140 150
GGYRVFTPRR NNVSHGDTRL ISQRIFWQIV FPATLFLILF QFAAFVGLLA
160 170 180 190 200
SRENLVGVMP FNLGTLINYQ ALLVGNLIGV PLCYFIIRVV RNPFYLRSYY
210 220 230 240 250
SQLKQQVDAK VTKKEFALWL LALGALLLLL CMPLNEKSTI FSTNYTLSLL
260 270 280 290 300
LPLMMWGAMR YGYKLISLLW AVVLMISIHS YQNYIPIYPG YTTQLTITSS
310 320 330 340 350
SYLVFSFIVN YMAVLATRQR AVVRRIQRLA YVDPVVHLPN VRALNRALRD
360 370 380 390 400
APWSALCYLR IPGMEMLVKN YGIMLRIQYK QKLSHWLSPL LEPGEDVYQL
410 420 430 440 450
SGNDLALRLN TESHQERITA LDSHLKQFRF FWDGMPMQPQ IGVSYCYVRS
460 470 480 490 500
PVNHIYLLLG ELNTVAELSI VTNAPENMQR RGAMYLQREL KDKVAMMNRL
510 520 530 540 550
QQALEHNHFF LMAQPITGMR GDVYHEILLR MKGENDELIS PDSFLPVAHE
560 570 580 590 600
FGLSSSIDMW VIEHTLQFMA ENRAKMPAHR FAINLSPTSV CQARFPVEVS
610 620 630 640 650
QLLAKYQIEA WQLIFEVTES NALTNVKQAQ ITLQHLQELG CQIAIDDFGT
660 670 680 690 700
GYASYARLKN VNADLLKIDG SFIRNIVSNS LDYQIVASIC HLARMKKMLV
710 720 730 740
VAEYVENEEI REAVLSLGID YMQGYLIGKP QPLIDTLNEI EPIRESA
Length:747
Mass (Da):85,608
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:i7D5E8B0E646C8EDF
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: AAC75556.1
AP009048 Genomic DNA Translation: BAA16393.1

Protein sequence database of the Protein Information Resource

More...
PIRi
F65026

NCBI Reference Sequences

More...
RefSeqi
NP_416998.1, NC_000913.3
WP_000772731.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC75556; AAC75556; b2503
BAA16393; BAA16393; BAA16393

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
946968

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW2488
eco:b2503

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.4235

<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: AAC75556.1
AP009048 Genomic DNA Translation: BAA16393.1
PIRiF65026
RefSeqiNP_416998.1, NC_000913.3
WP_000772731.1, NZ_LN832404.1

3D structure databases

SMRiP77172
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4260585, 25 interactors
DIPiDIP-12038N
IntActiP77172, 1 interactor
STRINGi511145.b2503

Proteomic databases

PaxDbiP77172
PRIDEiP77172

Genome annotation databases

EnsemblBacteriaiAAC75556; AAC75556; b2503
BAA16393; BAA16393; BAA16393
GeneIDi946968
KEGGiecj:JW2488
eco:b2503
PATRICifig|1411691.4.peg.4235

Organism-specific databases

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

More...
EchoBASEi
EB3954

Phylogenomic databases

eggNOGiCOG2200, Bacteria
HOGENOMiCLU_023566_2_0_6
InParanoidiP77172
PhylomeDBiP77172

Enzyme and pathway databases

BioCyciEcoCyc:G7314-MONOMER
MetaCyc:G7314-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P77172

Family and domain databases

CDDicd01948, EAL, 1 hit
Gene3Di3.20.20.450, 1 hit
InterProiView protein in InterPro
IPR001633, EAL_dom
IPR035919, EAL_sf
IPR000160, GGDEF_dom
IPR007895, MASE1
PfamiView protein in Pfam
PF00563, EAL, 1 hit
PF05231, MASE1, 1 hit
SMARTiView protein in SMART
SM00052, EAL, 1 hit
SM00267, GGDEF, 1 hit
SUPFAMiSSF141868, SSF141868, 1 hit
PROSITEiView protein in PROSITE
PS50883, EAL, 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 nameiPDEF_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: P77172
<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: April 27, 2001
Last sequence update: February 1, 1997
Last modified: October 7, 2020
This is version 144 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

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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