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Protein

Cyclic di-GMP phosphodiesterase PdeR

Gene

pdeR

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

Functioni

Part of a signaling cascade that regulates curli biosynthesis. The cascade is composed of two cyclic-di-GMP (c-di-GMP) control modules, in which c-di-GMP controlled by the DgcE/PdeH pair (module I) regulates the activity of the DgcM/PdeR pair (module II), which in turn regulates activity of the transcription factor MlrA and expression of the master biofilm regulator csgD (PubMed:23708798). PdeR acts as a trigger enzyme that connects modules I and II. It inhibits DgcM and MlrA by direct interaction. Inhibition is relieved when PdeR binds and degrades c-di-GMP generated by module I (PubMed:17010156, PubMed:23708798).2 Publications

Catalytic activityi

Cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine.2 Publications

GO - Molecular functioni

  • cyclic-guanylate-specific phosphodiesterase activity Source: EcoCyc
  • GTP binding Source: EcoCyc

GO - Biological processi

  • negative regulation of cyclase activity Source: EcoCyc
  • posttranscriptional regulation of gene expression Source: EcoCyc

Keywordsi

Molecular functionHydrolase
Ligandc-di-GMP

Enzyme and pathway databases

BioCyciEcoCyc:G6639-MONOMER
MetaCyc:G6639-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
Cyclic di-GMP phosphodiesterase PdeRCurated (EC:3.1.4.522 Publications)
Gene namesi
Name:pdeR1 Publication
Synonyms:gmr, yciR
Ordered Locus Names:b1285, JW1278
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13415 gmr

Pathology & Biotechi

Disruption phenotypei

Leads to overproduction of curli fimbrae and autoaggregation in cultures grown at 28 degrees Celsius.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001688851 – 661Cyclic di-GMP phosphodiesterase PdeRAdd BLAST661

Proteomic databases

PaxDbiP77334
PRIDEiP77334

Expressioni

Inductioni

Constitutively expressed at both 28 and 37 degrees Celsius, during transition into stationary phase, more highly expressed on plates than in liquid medium. Expression is RpoS dependent and repressed by H-NS.2 Publications

Interactioni

Subunit structurei

Interacts with DgcM and MlrA.1 Publication

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi4261961, 47 interactors
DIPiDIP-11590N
IntActiP77334, 6 interactors
MINTiP77334
STRINGi316385.ECDH10B_1402

Structurei

3D structure databases

ProteinModelPortaliP77334
SMRiP77334
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini109 – 179PASPROSITE-ProRule annotationAdd BLAST71
Domaini265 – 397GGDEFPROSITE-ProRule annotationAdd BLAST133
Domaini406 – 658EALPROSITE-ProRule annotationAdd BLAST253

Phylogenomic databases

eggNOGiENOG4105BZU Bacteria
COG2199 LUCA
COG2200 LUCA
COG2202 LUCA
HOGENOMiHOG000136248
InParanoidiP77334
KOiK14051
OMAiHKRPRSQ
PhylomeDBiP77334

Family and domain databases

CDDicd01948 EAL, 1 hit
cd01949 GGDEF, 1 hit
cd00130 PAS, 1 hit
Gene3Di3.20.20.450, 1 hit
InterProiView protein in InterPro
IPR001633 EAL_dom
IPR035919 EAL_sf
IPR000160 GGDEF_dom
IPR029787 Nucleotide_cyclase
IPR000014 PAS
IPR035965 PAS-like_dom_sf
PfamiView protein in Pfam
PF00563 EAL, 1 hit
PF00990 GGDEF, 1 hit
PF13426 PAS_9, 1 hit
SMARTiView protein in SMART
SM00052 EAL, 1 hit
SM00267 GGDEF, 1 hit
SM00091 PAS, 1 hit
SUPFAMiSSF141868 SSF141868, 1 hit
SSF55073 SSF55073, 1 hit
SSF55785 SSF55785, 1 hit
TIGRFAMsiTIGR00254 GGDEF, 1 hit
TIGR00229 sensory_box, 1 hit
PROSITEiView protein in PROSITE
PS50883 EAL, 1 hit
PS50887 GGDEF, 1 hit
PS50112 PAS, 1 hit

Sequencei

Sequence statusi: Complete.

P77334-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKTVRESTTL YNFLGSHNPY WRLTESSDVL RFSTTETTEP DRTLQLSAEQ
60 70 80 90 100
AARIREMTVI TSSLMMSLTV DESDLSVHLV GRKINKREWA GNASAWHDTP
110 120 130 140 150
AVARDLSHGL SFAEQVVSEA HSAIVILDSR GNIQRFNRLC EDYTGLKEHD
160 170 180 190 200
VIGQSVFKLF MSRREAAASR RNNRVFFRSG NAYEVELWIP TCKGQRLFLF
210 220 230 240 250
RNKFVHSGSG KNEIFLICSG TDITEERRAQ ERLRILANTD SITGLPNRNA
260 270 280 290 300
MQDLIDHAIN HADNNKVGVV YLDLDNFKKV NDAYGHLFGD QLLRDVSLAI
310 320 330 340 350
LSCLEHDQVL ARPGGDEFLV LASNTSQSAL EAMASRILTR LRLPFRIGLI
360 370 380 390 400
EVYTSCSVGI ALSPEHGSDS TAIIRHADTA MYTAKEGGRG QFCVFTPEMN
410 420 430 440 450
QRVFEYLWLD TNLRKALEND QLVIHYQPKI TWRGEVRSLE ALVRWQSPER
460 470 480 490 500
GLIPPLDFIS YAEESGLIVP LGRWVILDVV RQVAKWRDKG INLRVAVNIS
510 520 530 540 550
ARQLADQTIF TALKQVLQEL NFEYCPIDVE LTESCLIEND ELALSVIQQF
560 570 580 590 600
SQLGAQVHLD DFGTGYSSLS QLARFPIDAI KLDQVFVRDI HKQPVSQSLV
610 620 630 640 650
RAIVAVAQAL NLQVIAEGVE SAKEDAFLTK NGINERQGFL FAKPMPAVAF
660
ERWYKRYLKR A
Length:661
Mass (Da):74,665
Last modified:February 1, 1997 - v1
Checksum:i991D47CDE46A8F01
GO

Sequence cautioni

The sequence L40788 differs from that shown. Reason: Frameshift at positions 5, 25, 365, 392 and 451.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti4V → L in L40788 (Ref. 4) Curated1
Sequence conflicti113A → P in L40788 (Ref. 4) Curated1
Sequence conflicti175V → L in L40788 (Ref. 4) Curated1
Sequence conflicti256D → H in L40788 (Ref. 4) Curated1
Sequence conflicti344P → G in L40788 (Ref. 4) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC74367.1
AP009048 Genomic DNA Translation: BAA14839.1
L40788 Genomic DNA No translation available.
PIRiH64876
RefSeqiNP_415801.1, NC_000913.3
WP_000859945.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC74367; AAC74367; b1285
BAA14839; BAA14839; BAA14839
GeneIDi945868
KEGGiecj:JW1278
eco:b1285
PATRICifig|1411691.4.peg.994

Entry informationi

Entry nameiPDER_ECOLI
AccessioniPrimary (citable) accession number: P77334
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: February 1, 1997
Last modified: May 23, 2018
This is version 143 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

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