PDEB_SHEON
ID PDEB_SHEON Reviewed; 856 AA.
AC Q8EJM6;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=Cyclic di-GMP phosphodiesterase PdeB;
DE EC=3.1.4.52;
DE AltName: Full=Phosphodiesterase biofilm protein;
GN Name=pdeB; OrderedLocusNames=SO_0437;
OS Shewanella oneidensis (strain MR-1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC Shewanellaceae; Shewanella.
OX NCBI_TaxID=211586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MR-1;
RX PubMed=12368813; DOI=10.1038/nbt749;
RA Heidelberg J.F., Paulsen I.T., Nelson K.E., Gaidos E.J., Nelson W.C.,
RA Read T.D., Eisen J.A., Seshadri R., Ward N.L., Methe B.A., Clayton R.A.,
RA Meyer T., Tsapin A., Scott J., Beanan M.J., Brinkac L.M., Daugherty S.C.,
RA DeBoy R.T., Dodson R.J., Durkin A.S., Haft D.H., Kolonay J.F., Madupu R.,
RA Peterson J.D., Umayam L.A., White O., Wolf A.M., Vamathevan J.J.,
RA Weidman J.F., Impraim M., Lee K., Berry K.J., Lee C., Mueller J.,
RA Khouri H.M., Gill J., Utterback T.R., McDonald L.A., Feldblyum T.V.,
RA Smith H.O., Venter J.C., Nealson K.H., Fraser C.M.;
RT "Genome sequence of the dissimilatory metal ion-reducing bacterium
RT Shewanella oneidensis.";
RL Nat. Biotechnol. 20:1118-1123(2002).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, GENE NAME, AND
RP MUTAGENESIS OF GLU-634.
RC STRAIN=MR-1;
RX PubMed=23794617; DOI=10.1128/jb.00498-13;
RA Chao L., Rakshe S., Leff M., Spormann A.M.;
RT "PdeB, a cyclic di-GMP-specific phosphodiesterase that regulates Shewanella
RT oneidensis MR-1 motility and biofilm formation.";
RL J. Bacteriol. 195:3827-3833(2013).
CC -!- FUNCTION: Affects motility and biofilm formation, and is linked to the
CC regulation of sulfate uptake and assimilation.
CC {ECO:0000269|PubMed:23794617}.
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:23794617};
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Multi-pass membrane
CC protein {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Deletion mutant shows decreased swimming motility
CC and increased biofilm formation under rich growth medium conditions.
CC {ECO:0000269|PubMed:23794617}.
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DR EMBL; AE014299; AAN53519.1; -; Genomic_DNA.
DR RefSeq; NP_716074.1; NC_004347.2.
DR RefSeq; WP_011070793.1; NZ_CP053946.1.
DR AlphaFoldDB; Q8EJM6; -.
DR SMR; Q8EJM6; -.
DR STRING; 211586.SO_0437; -.
DR PaxDb; Q8EJM6; -.
DR KEGG; son:SO_0437; -.
DR PATRIC; fig|211586.12.peg.426; -.
DR eggNOG; COG5001; Bacteria.
DR eggNOG; COG5002; Bacteria.
DR HOGENOM; CLU_000445_79_0_6; -.
DR OMA; EYLNPVA; -.
DR OrthoDB; 1635706at2; -.
DR PhylomeDB; Q8EJM6; -.
DR BioCyc; SONE211586:G1GMP-418-MON; -.
DR BRENDA; 3.1.4.52; 5706.
DR Proteomes; UP000008186; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0071111; F:cyclic-guanylate-specific phosphodiesterase activity; IEA:UniProtKB-EC.
DR CDD; cd01948; EAL; 1.
DR CDD; cd01949; GGDEF; 1.
DR CDD; cd00130; PAS; 1.
DR Gene3D; 3.20.20.450; -; 1.
DR Gene3D; 3.30.70.270; -; 1.
DR InterPro; IPR001633; EAL_dom.
DR InterPro; IPR035919; EAL_sf.
DR InterPro; IPR000160; GGDEF_dom.
DR InterPro; IPR029787; Nucleotide_cyclase.
DR InterPro; IPR000014; PAS.
DR InterPro; IPR035965; PAS-like_dom_sf.
DR InterPro; IPR013656; PAS_4.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR Pfam; PF00563; EAL; 1.
DR Pfam; PF00990; GGDEF; 1.
DR Pfam; PF08448; PAS_4; 1.
DR SMART; SM00052; EAL; 1.
DR SMART; SM00267; GGDEF; 1.
DR SMART; SM00091; PAS; 1.
DR SUPFAM; SSF141868; SSF141868; 1.
DR SUPFAM; SSF55073; SSF55073; 1.
DR SUPFAM; SSF55785; SSF55785; 1.
DR TIGRFAMs; TIGR00254; GGDEF; 1.
DR PROSITE; PS50883; EAL; 1.
DR PROSITE; PS50887; GGDEF; 1.
DR PROSITE; PS50112; PAS; 1.
PE 1: Evidence at protein level;
KW c-di-GMP; Cell membrane; Hydrolase; Membrane; Reference proteome;
KW Transmembrane; Transmembrane helix.
FT CHAIN 1..856
FT /note="Cyclic di-GMP phosphodiesterase PdeB"
FT /id="PRO_0000429746"
FT TRANSMEM 7..27
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 230..250
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 303..350
FT /note="PAS"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 454..587
FT /note="GGDEF"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00095"
FT DOMAIN 598..852
FT /note="EAL"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00074"
FT MUTAGEN 634
FT /note="E->A: Lack of activity."
FT /evidence="ECO:0000269|PubMed:23794617"
SQ SEQUENCE 856 AA; 95807 MW; 20263CD22438D3E2 CRC64;
MRIGNKILVF IVGFCLPAVV LVSYCLGVWF DHRVELLRQD NVRHELANIQ QQFRIDVDRL
GFLTNIYASP LSHLDSEQLK SLESSWLESS MSGNLSWFIL RDGNLQNVFQ NEQPIAEANR
QEIAKAITTQ AKPEFASAYL IGDKGYVVTA VASHLGEYVL LVRQLTERDL LEYAQTSLVA
RVSMSNVVTA HHSSHSSSVA LPSLISQQPI YLHVEFSDDP FRDVKLSLDW VSLAVILLGI
LIVALGYVWL RACLLQPFKS LMQQLALVDP MASVYRPVTS EGNEELSVLA NRVNSLLARI
YQQKERGKIT LESIAEAVIL TDIEAKVIYM NPKAETLLEV ASSNAVGESL ASLLKAGEQL
NQAVFHCIRL GETMPQVAKI KLLTTMPRII ERSISNVLNH EKEIVGTVVV LRDITQEELL
KHQLQKRANF DGITGLLNRQ AFEEQLPEFA SQARSLAVCY LDLEQFKLIN DSCGHTAGDR
MLAMVARAIQ SCLGPQELLA RIGGDEFGLV ICDRTALAVA QLLKQIIAQV SLQVLHDKNC
NYKVGLSIGV AFGRAPYINA QELLKDADIA CIAAKAKGTN QIHIYDDKDK ELTYQRNAPK
WAVRIAQAIE ENELLLYYQP IRGLGASSKR QRMEVLLRIQ EPCGRILAPA QFIAAAERFK
LMPEIDKEVI RKAFLWLSLN SQLWQDHCIS INLSGNSLGA EGMVEYIAKQ QQIFDIPSQC
VCFEITETTA IQNRHRGMEM LRQLRKLGFS FALDDFGSGF ASYGYLRELP VDYVKIDGCF
VKNLAVNAKD YAIVKSIQDV CRVMGIETVA EFVENQEIID RLQTIGINYA QGYAIGRPQP
LASYCEQFET RLAQRA
