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Entry version 159 (02 Dec 2020)
Sequence version 1 (01 Feb 1997)
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Protein

Cyclic di-GMP phosphodiesterase PdeR

Gene

pdeR

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionHydrolase
Ligandc-di-GMP

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:G6639-MONOMER
MetaCyc:G6639-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Cyclic di-GMP phosphodiesterase PdeRCurated (EC:3.1.4.522 Publications)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:pdeR1 Publication
Synonyms:gmr, yciR
Ordered Locus Names:b1285, JW1278
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

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

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001688851 – 661Cyclic di-GMP phosphodiesterase PdeRAdd BLAST661

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P77334

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P77334

PRoteomics IDEntifications database

More...
PRIDEi
P77334

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>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

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Interacts with DgcM and MlrA.

1 Publication

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection">Interaction</a>' section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Hide details

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4261961, 47 interactors

Database of interacting proteins

More...
DIPi
DIP-11590N

Protein interaction database and analysis system

More...
IntActi
P77334, 6 interactors

Molecular INTeraction database

More...
MINTi
P77334

STRING: functional protein association networks

More...
STRINGi
511145.b1285

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P77334

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini109 – 179PASPROSITE-ProRule annotationAdd BLAST71
Domaini265 – 397GGDEFPROSITE-ProRule annotationAdd BLAST133
Domaini406 – 658EALPROSITE-ProRule annotationAdd BLAST253

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG5001, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_000445_70_50_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P77334

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P77334

Family and domain databases

Conserved Domains Database

More...
CDDi
cd01948, EAL, 1 hit
cd01949, GGDEF, 1 hit
cd00130, PAS, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.20.20.450, 1 hit
3.30.70.270, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001633, EAL_dom
IPR035919, EAL_sf
IPR000160, GGDEF_dom
IPR029787, Nucleotide_cyclase
IPR000014, PAS
IPR035965, PAS-like_dom_sf
IPR043128, Rev_trsase/Diguanyl_cyclase

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00563, EAL, 1 hit
PF00990, GGDEF, 1 hit
PF13426, PAS_9, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00052, EAL, 1 hit
SM00267, GGDEF, 1 hit
SM00091, PAS, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF141868, SSF141868, 1 hit
SSF55073, SSF55073, 1 hit
SSF55785, SSF55785, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00254, GGDEF, 1 hit
TIGR00229, sensory_box, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50883, EAL, 1 hit
PS50887, GGDEF, 1 hit
PS50112, PAS, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i991D47CDE46A8F01
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence L40788 differs from that shown. Reason: Frameshift.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>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:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC74367.1
AP009048 Genomic DNA Translation: BAA14839.1
L40788 Genomic DNA No translation available.

Protein sequence database of the Protein Information Resource

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PIRi
H64876

NCBI Reference Sequences

More...
RefSeqi
NP_415801.1, NC_000913.3
WP_000859945.1, NZ_SSZK01000012.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC74367; AAC74367; b1285
BAA14839; BAA14839; BAA14839

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
945868

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW1278
eco:b1285

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.994

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

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_SSZK01000012.1

3D structure databases

SMRiP77334
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4261961, 47 interactors
DIPiDIP-11590N
IntActiP77334, 6 interactors
MINTiP77334
STRINGi511145.b1285

Proteomic databases

jPOSTiP77334
PaxDbiP77334
PRIDEiP77334

Genome annotation databases

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

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB3191

Phylogenomic databases

eggNOGiCOG5001, Bacteria
HOGENOMiCLU_000445_70_50_6
InParanoidiP77334
PhylomeDBiP77334

Enzyme and pathway databases

BioCyciEcoCyc:G6639-MONOMER
MetaCyc:G6639-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P77334

Family and domain databases

CDDicd01948, EAL, 1 hit
cd01949, GGDEF, 1 hit
cd00130, PAS, 1 hit
Gene3Di3.20.20.450, 1 hit
3.30.70.270, 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
IPR043128, Rev_trsase/Diguanyl_cyclase
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

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPDER_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P77334
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: February 1, 1997
Last modified: December 2, 2020
This is version 159 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome
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