PDER_ECOLI
ID PDER_ECOLI Reviewed; 661 AA.
AC P77334;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 163.
DE RecName: Full=Cyclic di-GMP phosphodiesterase PdeR {ECO:0000305};
DE EC=3.1.4.52 {ECO:0000269|PubMed:17010156, ECO:0000269|PubMed:23708798};
GN Name=pdeR {ECO:0000303|PubMed:26148715}; Synonyms=gmr, yciR;
GN OrderedLocusNames=b1285, JW1278;
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=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-557.
RA Rita Z.R., Arraiano C.A.;
RL Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, INDUCTION, RPOS-DEPENDENCE, H-NS-REPRESSION,
RP AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MC4100;
RX PubMed=17010156; DOI=10.1111/j.1365-2958.2006.05440.x;
RA Weber H., Pesavento C., Possling A., Tischendorf G., Hengge R.;
RT "Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia
RT coli.";
RL Mol. Microbiol. 62:1014-1034(2006).
RN [6]
RP INDUCTION, AND RPOS-DEPENDENCE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=19332833; DOI=10.1099/mic.0.024257-0;
RA Sommerfeldt N., Possling A., Becker G., Pesavento C., Tschowri N.,
RA Hengge R.;
RT "Gene expression patterns and differential input into curli fimbriae
RT regulation of all GGDEF/EAL domain proteins in Escherichia coli.";
RL Microbiology 155:1318-1331(2009).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND INTERACTION WITH DGCM AND MLRA.
RX PubMed=23708798; DOI=10.1038/emboj.2013.120;
RA Lindenberg S., Klauck G., Pesavento C., Klauck E., Hengge R.;
RT "The EAL domain protein YciR acts as a trigger enzyme in a c-di-GMP
RT signalling cascade in E. coli biofilm control.";
RL EMBO J. 32:2001-2014(2013).
RN [8]
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: Part of a signaling cascade that regulates curli
CC biosynthesis. The cascade is composed of two cyclic-di-GMP (c-di-GMP)
CC control modules, in which c-di-GMP controlled by the DgcE/PdeH pair
CC (module I) regulates the activity of the DgcM/PdeR pair (module II),
CC which in turn regulates activity of the transcription factor MlrA and
CC expression of the master biofilm regulator csgD (PubMed:23708798). PdeR
CC acts as a trigger enzyme that connects modules I and II. It inhibits
CC DgcM and MlrA by direct interaction. Inhibition is relieved when PdeR
CC binds and degrades c-di-GMP generated by module I (PubMed:17010156,
CC PubMed:23708798). {ECO:0000269|PubMed:17010156,
CC ECO:0000269|PubMed:23708798}.
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:17010156, ECO:0000269|PubMed:23708798};
CC -!- SUBUNIT: Interacts with DgcM and MlrA. {ECO:0000269|PubMed:23708798}.
CC -!- INTERACTION:
CC P77334; P77302: dgcM; NbExp=5; IntAct=EBI-548149, EBI-544662;
CC P77334; P33358: mlrA; NbExp=2; IntAct=EBI-548149, EBI-1127668;
CC -!- INDUCTION: Constitutively expressed at both 28 and 37 degrees Celsius,
CC during transition into stationary phase, more highly expressed on
CC plates than in liquid medium. Expression is RpoS dependent and
CC repressed by H-NS. {ECO:0000269|PubMed:17010156,
CC ECO:0000269|PubMed:19332833}.
CC -!- DISRUPTION PHENOTYPE: Leads to overproduction of curli fimbrae and
CC autoaggregation in cultures grown at 28 degrees Celsius.
CC {ECO:0000269|PubMed:17010156}.
CC -!- SEQUENCE CAUTION:
CC Sequence=L40788; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U00096; AAC74367.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA14839.1; -; Genomic_DNA.
DR EMBL; L40788; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; H64876; H64876.
DR RefSeq; NP_415801.1; NC_000913.3.
DR RefSeq; WP_000859945.1; NZ_SSZK01000012.1.
DR AlphaFoldDB; P77334; -.
DR SMR; P77334; -.
DR BioGRID; 4261961; 47.
DR DIP; DIP-11590N; -.
DR IntAct; P77334; 6.
DR MINT; P77334; -.
DR STRING; 511145.b1285; -.
DR jPOST; P77334; -.
DR PaxDb; P77334; -.
DR PRIDE; P77334; -.
DR DNASU; 945868; -.
DR EnsemblBacteria; AAC74367; AAC74367; b1285.
DR EnsemblBacteria; BAA14839; BAA14839; BAA14839.
DR GeneID; 66674889; -.
DR GeneID; 945868; -.
DR KEGG; ecj:JW1278; -.
DR KEGG; eco:b1285; -.
DR PATRIC; fig|1411691.4.peg.994; -.
DR EchoBASE; EB3191; -.
DR eggNOG; COG5001; Bacteria.
DR HOGENOM; CLU_000445_70_50_6; -.
DR InParanoid; P77334; -.
DR OMA; RFCCAFQ; -.
DR PhylomeDB; P77334; -.
DR BioCyc; EcoCyc:G6639-MON; -.
DR BioCyc; MetaCyc:G6639-MON; -.
DR PRO; PR:P77334; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0071111; F:cyclic-guanylate-specific phosphodiesterase activity; IDA:EcoCyc.
DR GO; GO:0005525; F:GTP binding; IDA:EcoCyc.
DR GO; GO:0031280; P:negative regulation of cyclase activity; IDA:EcoCyc.
DR GO; GO:0010608; P:post-transcriptional regulation of gene expression; IMP:EcoCyc.
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; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR Pfam; PF00563; EAL; 1.
DR Pfam; PF00990; GGDEF; 1.
DR Pfam; PF13426; PAS_9; 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 TIGRFAMs; TIGR00229; sensory_box; 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; Hydrolase; Reference proteome.
FT CHAIN 1..661
FT /note="Cyclic di-GMP phosphodiesterase PdeR"
FT /id="PRO_0000168885"
FT DOMAIN 109..179
FT /note="PAS"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT DOMAIN 265..397
FT /note="GGDEF"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00095"
FT DOMAIN 406..658
FT /note="EAL"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00074"
FT CONFLICT 4
FT /note="V -> L (in Ref. 4; L40788)"
FT /evidence="ECO:0000305"
FT CONFLICT 113
FT /note="A -> P (in Ref. 4; L40788)"
FT /evidence="ECO:0000305"
FT CONFLICT 175
FT /note="V -> L (in Ref. 4; L40788)"
FT /evidence="ECO:0000305"
FT CONFLICT 256
FT /note="D -> H (in Ref. 4; L40788)"
FT /evidence="ECO:0000305"
FT CONFLICT 344
FT /note="P -> G (in Ref. 4; L40788)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 661 AA; 74665 MW; 991D47CDE46A8F01 CRC64;
MKTVRESTTL YNFLGSHNPY WRLTESSDVL RFSTTETTEP DRTLQLSAEQ AARIREMTVI
TSSLMMSLTV DESDLSVHLV GRKINKREWA GNASAWHDTP AVARDLSHGL SFAEQVVSEA
HSAIVILDSR GNIQRFNRLC EDYTGLKEHD VIGQSVFKLF MSRREAAASR RNNRVFFRSG
NAYEVELWIP TCKGQRLFLF RNKFVHSGSG KNEIFLICSG TDITEERRAQ ERLRILANTD
SITGLPNRNA MQDLIDHAIN HADNNKVGVV YLDLDNFKKV NDAYGHLFGD QLLRDVSLAI
LSCLEHDQVL ARPGGDEFLV LASNTSQSAL EAMASRILTR LRLPFRIGLI EVYTSCSVGI
ALSPEHGSDS TAIIRHADTA MYTAKEGGRG QFCVFTPEMN QRVFEYLWLD TNLRKALEND
QLVIHYQPKI TWRGEVRSLE ALVRWQSPER GLIPPLDFIS YAEESGLIVP LGRWVILDVV
RQVAKWRDKG INLRVAVNIS ARQLADQTIF TALKQVLQEL NFEYCPIDVE LTESCLIEND
ELALSVIQQF SQLGAQVHLD DFGTGYSSLS QLARFPIDAI KLDQVFVRDI HKQPVSQSLV
RAIVAVAQAL NLQVIAEGVE SAKEDAFLTK NGINERQGFL FAKPMPAVAF ERWYKRYLKR
A
