Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Cyclic di-GMP phosphodiesterase PdeF

Gene

pdeF

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

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

Catalytic activityi

Cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine.1 Publication

Cofactori

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

Enzyme regulationi

Inhibited by pGpG.1 Publication

pH dependencei

Optimum pH is 7.5 for the truncated enzyme.1 Publication

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

Keywordsi

Molecular functionHydrolase
Ligandc-di-GMP, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7314-MONOMER
MetaCyc:G7314-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
Cyclic di-GMP phosphodiesterase PdeFCurated (EC:3.1.4.521 Publication)
Gene namesi
Name:pdeF1 Publication
Synonyms:yfgF
Ordered Locus Names:b2503, JW2488
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14202 yfgF

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 14PeriplasmicCuratedAdd BLAST14
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

  • integral component of membrane Source: EcoCyc
  • plasma membrane Source: EcoCyc

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

Increased biofilm formation but a decreased tendency to sediment and aggregate. Cells are more sensitive to peroxide.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001692411 – 747Cyclic di-GMP phosphodiesterase PdeFAdd BLAST747

Proteomic databases

PaxDbiP77172
PRIDEiP77172

Expressioni

Inductioni

Induced by FNR. Expression is highest under anaerobic conditions at 28 degrees Celsius in stationary phase.1 Publication

Interactioni

Protein-protein interaction databases

BioGridi4260585, 25 interactors
DIPiDIP-12038N
IntActiP77172, 1 interactor
STRINGi316385.ECDH10B_2669

Structurei

3D structure databases

ProteinModelPortaliP77172
SMRiP77172
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini493 – 744EALPROSITE-ProRule annotationAdd BLAST252

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105BZU Bacteria
ENOG410XNMH LUCA
HOGENOMiHOG000123041
InParanoidiP77172
OMAiLWGAMRF
PhylomeDBiP77172

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

Sequencei

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
Checksum:i7D5E8B0E646C8EDF
GO

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

Genome annotation databases

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

Similar proteinsi

Entry informationi

Entry nameiPDEF_ECOLI
AccessioniPrimary (citable) accession number: P77172
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: February 1, 1997
Last modified: March 28, 2018
This is version 131 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health