UniProtKB - P21514 (PDEL_ECOLI)
Protein
Cyclic di-GMP phosphodiesterase PdeL
Gene
pdeL
Organism
Escherichia coli (strain K12)
Status
Functioni
Acts both as an enzyme and as a c-di-GMP sensor to couple transcriptional activity to the c-di-GMP status of the cell (PubMed:26553851). Phosphodiesterase (PDE) that catalyzes the hydrolysis of cyclic-di-GMP (c-di-GMP) to 5'-pGpG (PubMed:15995192, PubMed:24451384, PubMed:26553851). Also acts as a transcription factor to control its own expression (PubMed:26553851).3 Publications
Miscellaneous
An overexpressed EAL domain (residues 77-362) has similar KM, Vmax, pH and metal dependence and subunit composition as the full-length protein.1 Publication
Catalytic activityi
- EC:3.1.4.523 Publications
Cofactori
Activity regulationi
Strongly inhibited by Ca2+.2 Publications
Kineticsi
- KM=25 µM for c-di-GMP1 Publication
pH dependencei
Optimum pH is 9.35.1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 127 | SubstrateCombined sources1 Publication | 1 | |
Metal bindingi | 141 | Magnesium or manganeseCombined sources1 Publication | 1 | |
Metal bindingi | 200 | Magnesium or manganeseCombined sources1 Publication | 1 | |
Binding sitei | 200 | SubstrateCombined sources1 Publication | 1 | |
Metal bindingi | 232 | Magnesium or manganeseCombined sources1 Publication | 1 | |
Metal bindingi | 262 | Magnesium or manganeseCombined sources1 Publication | 1 | |
Binding sitei | 262 | SubstrateCombined sources1 Publication | 1 | |
Binding sitei | 286 | SubstrateCombined sources1 Publication | 1 | |
Binding sitei | 341 | SubstrateCombined sources1 Publication | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
DNA bindingi | 42 – 61 | H-T-H motifPROSITE-ProRule annotationAdd BLAST | 20 |
GO - Molecular functioni
- bacterial-type RNA polymerase regulatory region sequence-specific DNA binding Source: EcoCyc
- cyclic-guanylate-specific phosphodiesterase activity Source: EcoCyc
- metal ion binding Source: UniProtKB-KW
GO - Biological processi
- positive regulation of transcription, DNA-templated Source: EcoCyc
Keywordsi
Molecular function | DNA-binding, Hydrolase |
Biological process | Transcription, Transcription regulation |
Ligand | c-di-GMP, Magnesium, Manganese, Metal-binding |
Enzyme and pathway databases
BioCyci | EcoCyc:EG11236-MONOMER ECOL316407:JW0307-MONOMER MetaCyc:EG11236-MONOMER |
SABIO-RKi | P21514 |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Name:pdeL1 Publication Synonyms:yahA Ordered Locus Names:b0315, JW0307 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 60 | K → A: Does not bind to the PdeL box. 1 Publication | 1 | |
Mutagenesisi | 206 | F → S: Increases catalytic activity. 1 Publication | 1 | |
Mutagenesisi | 249 | F → L: Increases catalytic activity. 1 Publication | 1 | |
Mutagenesisi | 263 | D → N: Loss of activity. 1 Publication | 1 | |
Mutagenesisi | 298 | S → W: Slow monomer-dimer exchange. Equilibrium largely on the monomeric side, in particular in the presence of substrate. Strong decrease in activity. 1 Publication | 1 | |
Mutagenesisi | 299 | G → S: Increases catalytic activity. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000168573 | 1 – 362 | Cyclic di-GMP phosphodiesterase PdeLAdd BLAST | 362 |
Proteomic databases
jPOSTi | P21514 |
PaxDbi | P21514 |
PRIDEi | P21514 |
Expressioni
Inductioni
Autoregulated. Directly regulates its own expression in a c-di-GMP-dependent manner.1 Publication
Interactioni
Subunit structurei
Is in a fast thermodynamic monomer-homodimer equilibrium. Dimerization is required for PDE activity. Dimerization affinity is increased about 100-fold upon substrate binding.
1 PublicationProtein-protein interaction databases
BioGridi | 4262803, 8 interactors |
IntActi | P21514, 3 interactors |
STRINGi | 511145.b0315 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P21514 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 18 – 83 | HTH luxR-typePROSITE-ProRule annotationAdd BLAST | 66 | |
Domaini | 106 – 360 | EALPROSITE-ProRule annotationAdd BLAST | 255 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 144 – 145 | Substrate bindingCombined sources1 Publication | 2 | |
Regioni | 319 – 322 | Substrate bindingCombined sources1 Publication | 4 |
Phylogenomic databases
eggNOGi | ENOG4105BZU Bacteria COG2200 LUCA COG2771 LUCA |
HOGENOMi | HOG000117345 |
InParanoidi | P21514 |
KOi | K13244 |
PhylomeDBi | P21514 |
Family and domain databases
CDDi | cd01948 EAL, 1 hit cd06170 LuxR_C_like, 1 hit |
Gene3Di | 1.10.10.10, 1 hit 3.20.20.450, 1 hit |
InterProi | View protein in InterPro IPR001633 EAL_dom IPR035919 EAL_sf IPR016032 Sig_transdc_resp-reg_C-effctor IPR000792 Tscrpt_reg_LuxR_C IPR036388 WH-like_DNA-bd_sf |
Pfami | View protein in Pfam PF00563 EAL, 1 hit PF00196 GerE, 1 hit |
SMARTi | View protein in SMART SM00052 EAL, 1 hit SM00421 HTH_LUXR, 1 hit |
SUPFAMi | SSF141868 SSF141868, 1 hit SSF46894 SSF46894, 1 hit |
PROSITEi | View protein in PROSITE PS50883 EAL, 1 hit PS50043 HTH_LUXR_2, 1 hit |
i Sequence
Sequence statusi: Complete.
P21514-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MNSCDFRVFL QEFGTTVHLS LPGSVSEKER LLLKLLMQGM SVTEISQYRN
60 70 80 90 100
RSAKTISHQK KQLFEKLGIQ SDITFWRDIF FQYNPEIISA TGSNSHRYIN
110 120 130 140 150
DNHYHHIVTP EAISLALENH EFKPWIQPVF CAQTGVLTGC EVLVRWEHPQ
160 170 180 190 200
TGIIPPDQFI PLAESSGLIV IMTRQLMKQT ADILMPVKHL LPDNFHIGIN
210 220 230 240 250
VSAGCFLAAG FEKECLNLVN KLGNDKIKLV LELTERNPIP VTPEARAIFD
260 270 280 290 300
SLHQHNITFA LDDFGTGYAT YRYLQAFPVD FIKIDKSFVQ MASVDEISGH
310 320 330 340 350
IVDNIVELAR KPGLSIVAEG VETQEQADLM IGKGVHFLQG YLYSPPVPGN
360
KFISEWVMKA GG
Sequence cautioni
The sequence AAB18041 differs from that shown. Reason: Erroneous initiation.Curated
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U73857 Genomic DNA Translation: AAB18041.1 Different initiation. U00096 Genomic DNA Translation: AAC73418.1 AP009048 Genomic DNA Translation: BAE76098.1 X52905 Genomic DNA Translation: CAA37089.1 |
PIRi | C64758 |
RefSeqi | NP_414849.1, NC_000913.3 WP_001301264.1, NZ_SSZK01000075.1 |
Genome annotation databases
EnsemblBacteriai | AAC73418; AAC73418; b0315 BAE76098; BAE76098; BAE76098 |
GeneIDi | 947459 |
KEGGi | ecj:JW0307 eco:b0315 |
PATRICi | fig|1411691.4.peg.1962 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U73857 Genomic DNA Translation: AAB18041.1 Different initiation. U00096 Genomic DNA Translation: AAC73418.1 AP009048 Genomic DNA Translation: BAE76098.1 X52905 Genomic DNA Translation: CAA37089.1 |
PIRi | C64758 |
RefSeqi | NP_414849.1, NC_000913.3 WP_001301264.1, NZ_SSZK01000075.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
4KIE | X-ray | 1.70 | A | 96-362 | [»] | |
4LJ3 | X-ray | 1.70 | A/B | 101-362 | [»] | |
4LYK | X-ray | 2.40 | A/B/C/D | 101-362 | [»] | |
SMRi | P21514 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGridi | 4262803, 8 interactors |
IntActi | P21514, 3 interactors |
STRINGi | 511145.b0315 |
Proteomic databases
jPOSTi | P21514 |
PaxDbi | P21514 |
PRIDEi | P21514 |
Genome annotation databases
EnsemblBacteriai | AAC73418; AAC73418; b0315 BAE76098; BAE76098; BAE76098 |
GeneIDi | 947459 |
KEGGi | ecj:JW0307 eco:b0315 |
PATRICi | fig|1411691.4.peg.1962 |
Organism-specific databases
EchoBASEi | EB1218 |
Phylogenomic databases
eggNOGi | ENOG4105BZU Bacteria COG2200 LUCA COG2771 LUCA |
HOGENOMi | HOG000117345 |
InParanoidi | P21514 |
KOi | K13244 |
PhylomeDBi | P21514 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG11236-MONOMER ECOL316407:JW0307-MONOMER MetaCyc:EG11236-MONOMER |
SABIO-RKi | P21514 |
Miscellaneous databases
PROi | PR:P21514 |
Family and domain databases
CDDi | cd01948 EAL, 1 hit cd06170 LuxR_C_like, 1 hit |
Gene3Di | 1.10.10.10, 1 hit 3.20.20.450, 1 hit |
InterProi | View protein in InterPro IPR001633 EAL_dom IPR035919 EAL_sf IPR016032 Sig_transdc_resp-reg_C-effctor IPR000792 Tscrpt_reg_LuxR_C IPR036388 WH-like_DNA-bd_sf |
Pfami | View protein in Pfam PF00563 EAL, 1 hit PF00196 GerE, 1 hit |
SMARTi | View protein in SMART SM00052 EAL, 1 hit SM00421 HTH_LUXR, 1 hit |
SUPFAMi | SSF141868 SSF141868, 1 hit SSF46894 SSF46894, 1 hit |
PROSITEi | View protein in PROSITE PS50883 EAL, 1 hit PS50043 HTH_LUXR_2, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | PDEL_ECOLI | |
Accessioni | P21514Primary (citable) accession number: P21514 Secondary accession number(s): P75689, Q2MCA8 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | May 1, 1991 |
Last sequence update: | November 1, 1997 | |
Last modified: | November 13, 2019 | |
This is version 147 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Complete proteome, Reference proteomeDocuments
- Escherichia coli
Escherichia coli (strain K12): entries and cross-references to EcoGene - PDB cross-references
Index of Protein Data Bank (PDB) cross-references