PDEF_ECOLI
ID PDEF_ECOLI Reviewed; 747 AA.
AC P77172;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=Cyclic di-GMP phosphodiesterase PdeF {ECO:0000305};
DE EC=3.1.4.52 {ECO:0000269|PubMed:20522491};
GN Name=pdeF {ECO:0000303|PubMed:26148715}; Synonyms=yfgF;
GN OrderedLocusNames=b2503, JW2488;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP TOPOLOGY [LARGE SCALE ANALYSIS], AND SUBCELLULAR LOCATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=15919996; DOI=10.1126/science.1109730;
RA Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G.;
RT "Global topology analysis of the Escherichia coli inner membrane
RT proteome.";
RL Science 308:1321-1323(2005).
RN [5]
RP CHARACTERIZATION AS A C-DI-GMP PHOSPHODIESTERASE, FUNCTION, CATALYTIC
RP ACTIVITY, COFACTOR, PH OPTIMUM, ACTIVITY REGULATION, INDUCTION, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MC1000 / ATCC 39531, K12 / MG1655 / ATCC 47076, and
RC K12 / W3110;
RX PubMed=20522491; DOI=10.1099/mic.0.037887-0;
RA Lacey M.M., Partridge J.D., Green J.;
RT "Escherichia coli K-12 YfgF is an anaerobic cyclic di-GMP phosphodiesterase
RT with roles in cell surface remodelling and the oxidative stress response.";
RL Microbiology 156:2873-2886(2010).
RN [6]
RP NOMENCLATURE.
RX PubMed=26148715; DOI=10.1128/jb.00424-15;
RA Hengge R., Galperin M.Y., Ghigo J.M., Gomelsky M., Green J., Hughes K.T.,
RA Jenal U., Landini P.;
RT "Systematic nomenclature for GGDEF and EAL domain-containing cyclic di-GMP
RT turnover proteins of Escherichia coli.";
RL J. Bacteriol. 198:7-11(2015).
CC -!- FUNCTION: Phosphodiesterase (PDE) that catalyzes the hydrolysis of
CC cyclic-di-GMP (c-di-GMP) to 5'-pGpG. Truncated proteins consisting of
CC the GGDEF/EAL domains (residues 319-747) or of the EAL domain alone
CC (481-747) have c-di-GMP phosphodiesterase activity. They do not have
CC diguanylate cyclase activity. Cyclic-di-GMP is a second messenger which
CC controls cell surface-associated traits in bacteria.
CC {ECO:0000269|PubMed:20522491}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cyclic di-3',5'-guanylate + H2O = 5'-
CC phosphoguanylyl(3'->5')guanosine + H(+); Xref=Rhea:RHEA:24902,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:58754,
CC ChEBI:CHEBI:58805; EC=3.1.4.52;
CC Evidence={ECO:0000269|PubMed:20522491};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:20522491};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:20522491};
CC Note=Mg(2+), and possibly also Mn(2+). {ECO:0000269|PubMed:20522491};
CC -!- ACTIVITY REGULATION: Inhibited by pGpG. {ECO:0000269|PubMed:20522491}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7.5 for the truncated enzyme.
CC {ECO:0000269|PubMed:20522491};
CC -!- SUBCELLULAR LOCATION: Cell inner membrane
CC {ECO:0000269|PubMed:15919996}; Multi-pass membrane protein
CC {ECO:0000255}.
CC -!- INDUCTION: Induced by FNR. Expression is highest under anaerobic
CC conditions at 28 degrees Celsius in stationary phase.
CC {ECO:0000269|PubMed:20522491}.
CC -!- DISRUPTION PHENOTYPE: Increased biofilm formation but a decreased
CC tendency to sediment and aggregate. Cells are more sensitive to
CC peroxide. {ECO:0000269|PubMed:20522491}.
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DR EMBL; U00096; AAC75556.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16393.1; -; Genomic_DNA.
DR PIR; F65026; F65026.
DR RefSeq; NP_416998.1; NC_000913.3.
DR RefSeq; WP_000772731.1; NZ_LN832404.1.
DR AlphaFoldDB; P77172; -.
DR SMR; P77172; -.
DR BioGRID; 4260585; 25.
DR DIP; DIP-12038N; -.
DR IntAct; P77172; 1.
DR STRING; 511145.b2503; -.
DR PaxDb; P77172; -.
DR PRIDE; P77172; -.
DR EnsemblBacteria; AAC75556; AAC75556; b2503.
DR EnsemblBacteria; BAA16393; BAA16393; BAA16393.
DR GeneID; 946968; -.
DR KEGG; ecj:JW2488; -.
DR KEGG; eco:b2503; -.
DR PATRIC; fig|1411691.4.peg.4235; -.
DR EchoBASE; EB3954; -.
DR eggNOG; COG2200; Bacteria.
DR HOGENOM; CLU_023566_2_0_6; -.
DR InParanoid; P77172; -.
DR OMA; WDGMPLQ; -.
DR PhylomeDB; P77172; -.
DR BioCyc; EcoCyc:G7314-MON; -.
DR BioCyc; MetaCyc:G7314-MON; -.
DR PRO; PR:P77172; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IDA:EcoCyc.
DR GO; GO:0005886; C:plasma membrane; IDA:EcoCyc.
DR GO; GO:0071111; F:cyclic-guanylate-specific phosphodiesterase activity; IDA:EcoCyc.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0071454; P:cellular response to anoxia; IMP:EcoCyc.
DR GO; GO:0070301; P:cellular response to hydrogen peroxide; IMP:EcoCyc.
DR GO; GO:1900190; P:regulation of single-species biofilm formation; IMP:EcoCyc.
DR CDD; cd01948; EAL; 1.
DR Gene3D; 3.20.20.450; -; 1.
DR InterPro; IPR001633; EAL_dom.
DR InterPro; IPR035919; EAL_sf.
DR InterPro; IPR000160; GGDEF_dom.
DR InterPro; IPR007895; MASE1.
DR Pfam; PF00563; EAL; 1.
DR Pfam; PF05231; MASE1; 1.
DR SMART; SM00052; EAL; 1.
DR SMART; SM00267; GGDEF; 1.
DR SUPFAM; SSF141868; SSF141868; 1.
DR PROSITE; PS50883; EAL; 1.
PE 1: Evidence at protein level;
KW c-di-GMP; Cell inner membrane; Cell membrane; Hydrolase; Membrane;
KW Nucleotide-binding; Reference proteome; Transmembrane; Transmembrane helix.
FT CHAIN 1..747
FT /note="Cyclic di-GMP phosphodiesterase PdeF"
FT /id="PRO_0000169241"
FT TOPO_DOM 1..14
FT /note="Periplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 15..36
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 37..42
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 43..65
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 66..79
FT /note="Periplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 80..102
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 103..128
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 129..151
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 152..165
FT /note="Periplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 166..188
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 189..215
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 216..235
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 236..239
FT /note="Periplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 240..259
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 260..265
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 266..285
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 286..294
FT /note="Periplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 295..317
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 318..747
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:15919996"
FT DOMAIN 493..744
FT /note="EAL"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00074"
SQ SEQUENCE 747 AA; 85608 MW; 7D5E8B0E646C8EDF CRC64;
MKLNATYIKI RDKWWGLPLF LPSLILPIFA HINTFAHISS GEVFLFYLPL ALMISMMMFF
SWAALPGIAL GIFVRKYAEL GFYETLSLTA NFIIIIILCW GGYRVFTPRR NNVSHGDTRL
ISQRIFWQIV FPATLFLILF QFAAFVGLLA SRENLVGVMP FNLGTLINYQ ALLVGNLIGV
PLCYFIIRVV RNPFYLRSYY SQLKQQVDAK VTKKEFALWL LALGALLLLL CMPLNEKSTI
FSTNYTLSLL LPLMMWGAMR YGYKLISLLW AVVLMISIHS YQNYIPIYPG YTTQLTITSS
SYLVFSFIVN YMAVLATRQR AVVRRIQRLA YVDPVVHLPN VRALNRALRD APWSALCYLR
IPGMEMLVKN YGIMLRIQYK QKLSHWLSPL LEPGEDVYQL SGNDLALRLN TESHQERITA
LDSHLKQFRF FWDGMPMQPQ IGVSYCYVRS PVNHIYLLLG ELNTVAELSI VTNAPENMQR
RGAMYLQREL KDKVAMMNRL QQALEHNHFF LMAQPITGMR GDVYHEILLR MKGENDELIS
PDSFLPVAHE FGLSSSIDMW VIEHTLQFMA ENRAKMPAHR FAINLSPTSV CQARFPVEVS
QLLAKYQIEA WQLIFEVTES NALTNVKQAQ ITLQHLQELG CQIAIDDFGT GYASYARLKN
VNADLLKIDG SFIRNIVSNS LDYQIVASIC HLARMKKMLV VAEYVENEEI REAVLSLGID
YMQGYLIGKP QPLIDTLNEI EPIRESA
