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 YfgF

Gene

yfgF

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.

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
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

c-di-GMP, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7314-MONOMER.
ECOL316407:JW2488-MONOMER.
MetaCyc:G7314-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Cyclic di-GMP phosphodiesterase YfgF (EC:3.1.4.52)
Gene namesi
Name:yfgF
Ordered Locus Names:b2503, JW2488
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14202. yfgF.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 1414PeriplasmicSequence analysisAdd
BLAST
Transmembranei15 – 3622HelicalSequence analysisAdd
BLAST
Topological domaini37 – 426CytoplasmicSequence analysis
Transmembranei43 – 6523HelicalSequence analysisAdd
BLAST
Topological domaini66 – 7914PeriplasmicSequence analysisAdd
BLAST
Transmembranei80 – 10223HelicalSequence analysisAdd
BLAST
Topological domaini103 – 12826CytoplasmicSequence analysisAdd
BLAST
Transmembranei129 – 15123HelicalSequence analysisAdd
BLAST
Topological domaini152 – 16514PeriplasmicSequence analysisAdd
BLAST
Transmembranei166 – 18823HelicalSequence analysisAdd
BLAST
Topological domaini189 – 21527CytoplasmicSequence analysisAdd
BLAST
Transmembranei216 – 23520HelicalSequence analysisAdd
BLAST
Topological domaini236 – 2394PeriplasmicSequence analysis
Transmembranei240 – 25920HelicalSequence analysisAdd
BLAST
Topological domaini260 – 2656CytoplasmicSequence analysis
Transmembranei266 – 28520HelicalSequence analysisAdd
BLAST
Topological domaini286 – 2949PeriplasmicSequence analysis
Transmembranei295 – 31723HelicalSequence analysisAdd
BLAST
Topological domaini318 – 747430CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • integral component of membrane Source: EcoCyc
  • plasma membrane Source: EcoCyc
Complete GO annotation...

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 747747Cyclic di-GMP phosphodiesterase YfgFPRO_0000169241Add
BLAST

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. 23 interactions.
DIPiDIP-12038N.
IntActiP77172. 1 interaction.
STRINGi511145.b2503.

Structurei

3D structure databases

ProteinModelPortaliP77172.
SMRiP77172. Positions 329-732.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini493 – 744252EALPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 EAL domain.PROSITE-ProRule annotation

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105BZU. Bacteria.
ENOG410XNMH. LUCA.
HOGENOMiHOG000123041.
InParanoidiP77172.
OMAiFRLIWNG.
OrthoDBiEOG69GZGV.
PhylomeDBiP77172.

Family and domain databases

Gene3Di3.20.20.450. 1 hit.
InterProiIPR001633. EAL_dom.
IPR000160. GGDEF_dom.
IPR007895. MASE1.
[Graphical view]
PfamiPF00563. EAL. 1 hit.
PF05231. MASE1. 1 hit.
[Graphical view]
SMARTiSM00052. EAL. 1 hit.
SM00267. GGDEF. 1 hit.
[Graphical view]
SUPFAMiSSF141868. SSF141868. 1 hit.
PROSITEiPS50883. EAL. 1 hit.
[Graphical view]

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.
PATRICi32120395. VBIEscCol129921_2600.

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

ProteinModelPortaliP77172.
SMRiP77172. Positions 329-732.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260585. 23 interactions.
DIPiDIP-12038N.
IntActiP77172. 1 interaction.
STRINGi511145.b2503.

Proteomic databases

PaxDbiP77172.
PRIDEiP77172.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75556; AAC75556; b2503.
BAA16393; BAA16393; BAA16393.
GeneIDi946968.
KEGGiecj:JW2488.
eco:b2503.
PATRICi32120395. VBIEscCol129921_2600.

Organism-specific databases

EchoBASEiEB3954.
EcoGeneiEG14202. yfgF.

Phylogenomic databases

eggNOGiENOG4105BZU. Bacteria.
ENOG410XNMH. LUCA.
HOGENOMiHOG000123041.
InParanoidiP77172.
OMAiFRLIWNG.
OrthoDBiEOG69GZGV.
PhylomeDBiP77172.

Enzyme and pathway databases

BioCyciEcoCyc:G7314-MONOMER.
ECOL316407:JW2488-MONOMER.
MetaCyc:G7314-MONOMER.

Miscellaneous databases

PROiP77172.

Family and domain databases

Gene3Di3.20.20.450. 1 hit.
InterProiIPR001633. EAL_dom.
IPR000160. GGDEF_dom.
IPR007895. MASE1.
[Graphical view]
PfamiPF00563. EAL. 1 hit.
PF05231. MASE1. 1 hit.
[Graphical view]
SMARTiSM00052. EAL. 1 hit.
SM00267. GGDEF. 1 hit.
[Graphical view]
SUPFAMiSSF141868. SSF141868. 1 hit.
PROSITEiPS50883. EAL. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
    Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
    , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
    DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Global topology analysis of the Escherichia coli inner membrane proteome."
    Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G.
    Science 308:1321-1323(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: TOPOLOGY [LARGE SCALE ANALYSIS].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Escherichia coli K-12 YfgF is an anaerobic cyclic di-GMP phosphodiesterase with roles in cell surface remodelling and the oxidative stress response."
    Lacey M.M., Partridge J.D., Green J.
    Microbiology 156:2873-2886(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION AS A C-DI-GMP PHOSPHODIESTERASE, FUNCTION, COFACTOR, PH OPTIMUM, ENZYME REGULATION, INDUCTION, DISRUPTION PHENOTYPE.
    Strain: K12 / MC1000 / ATCC 39531, K12 / MG1655 / ATCC 47076 and K12 / W3110.

Entry informationi

Entry nameiYFGF_ECOLI
AccessioniPrimary (citable) accession number: P77172
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: February 1, 1997
Last modified: March 16, 2016
This is version 122 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.