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Entry version 98 (02 Jun 2021)
Sequence version 1 (05 Jul 2005)
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Protein

Cyclic di-GMP phosphodiesterase response regulator RpfG

Gene

rpfG

Organism
Xanthomonas campestris pv. campestris (strain 8004)
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

Member of the two-component regulatory system RpfG/RpfC, which is involved in the perception and response to the diffusible signaling factor (DSF), which is essential for cell-cell signaling (PubMed:11123673, PubMed:12960398).

Detection of DSF leads to the positive regulation of biofilm dispersal and the production of virulence factors (PubMed:12960398).

Activated RpfG degrades cyclic di-GMP to GMP, leading to the activation of Clp, a global transcriptional regulator that regulates a large set of genes in DSF pathway. May also directly control genes involved in biofilm dispersal (PubMed:15158198, PubMed:17378922, PubMed:20231439).

5 Publications

Caution

The article describing the function and the phosphodiesterase activity has been retracted due to duplications and irregularities in some figures, but repeated experiments using the original strains support the findings.2 Publications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, Transducer
Biological processTwo-component regulatory system, Virulence
Ligandc-di-GMP

<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 response regulator RpfG (EC:3.1.4.-By similarity)
<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:rpfG
Ordered Locus Names:XC_2335
<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>OrganismiXanthomonas campestris pv. campestris (strain 8004)
<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 identifieri314565 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
<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
  • UP000000420 <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

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

Cytoplasm

<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

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi231H → A: Does not affect interaction with GGDEF domain. 1 Publication1
Mutagenesisi232D → A: Does not affect interaction with GGDEF domain. 1 Publication1
Mutagenesisi294G → A: Decreases interaction with GGDEF domain. 1 Publication1
Mutagenesisi295Y → A: Decreases interaction with GGDEF domain. 1 Publication1
Mutagenesisi296P → A: Decreases interaction with GGDEF domain. 1 Publication1

<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_00000812191 – 378Cyclic di-GMP phosphodiesterase response regulator RpfGAdd BLAST378

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei804-aspartylphosphatePROSITE-ProRule annotation1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Phosphorylated and activated by RpfC.1 Publication

Keywords - PTMi

Phosphoprotein

<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 a subset of GGDEF domain-containing proteins.

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

Database of interacting proteins

More...
DIPi
DIP-58626N

Protein interaction database and analysis system

More...
IntActi
Q4UU85, 10 interactors

<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

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SMRi
Q4UU85

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>Domaini29 – 147Response regulatoryPROSITE-ProRule annotationAdd BLAST119
Domaini174 – 371HD-GYPPROSITE-ProRule annotationAdd BLAST198

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Contains a C-terminal HD-GYP (modified HD) domain, which is involved in degradation of cyclic di-GMP. The GYP motif is required for interaction with GGDEF domain-containing proteins.1 Publication

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_000445_92_10_6

Identification of Orthologs from Complete Genome Data

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OMAi
RCANTQF

Database of Orthologous Groups

More...
OrthoDBi
1755994at2

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00077, HDc, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR011006, CheY-like_superfamily
IPR003607, HD/PDEase_dom
IPR037522, HD_GYP_dom
IPR001789, Sig_transdc_resp-reg_receiver

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00072, Response_reg, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00471, HDc, 1 hit
SM00448, REC, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF52172, SSF52172, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51832, HD_GYP, 1 hit
PS50110, RESPONSE_REGULATORY, 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.

Q4UU85-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MQDVLGNPAG VSSAETWGSW SEKADLGLNI VIVDDQMSAR TMLRHVIEDI
60 70 80 90 100
APELKVYDFG DPLDALSWCE AGRVDLLLLD YRMPGMDGLE FARRLRRLPS
110 120 130 140 150
HRDIPIILIT IVGDEPIRQA ALEAGVIDFL VKPIRPRELR ARCSNLLQLR
160 170 180 190 200
QQSESVKQRA LSLEQRLLAS MNEVEERERE TLSRLARAIE YRDGGTSAFL
210 220 230 240 250
ERMSHVAGLV AEQLGLSEEE VRIIEMAAPL HDMGKIAIPD SVLLKPGKLT
260 270 280 290 300
EDEMNVMKRH PRIGYELLSG SQNRFIQVGA LIALRHHERY DGSGYPDGLV
310 320 330 340 350
GEAIPLEARI VAVADVFDAL LSARPYKEAW TMDAALAYLY AQRGRLFDPR
360 370
CVDALLRGRA QLEQICGQFS TASARPGV
Length:378
Mass (Da):42,173
Last modified:July 5, 2005 - 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:iD360BCFEFD52D3A1
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AJ251547 Genomic DNA Translation: CAB89843.1
CP000050 Genomic DNA Translation: AAY49388.1

NCBI Reference Sequences

More...
RefSeqi
WP_011037024.1, NC_007086.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAY49388; AAY49388; XC_2335

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
58013597

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
xcb:XC_2335

<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
AJ251547 Genomic DNA Translation: CAB89843.1
CP000050 Genomic DNA Translation: AAY49388.1
RefSeqiWP_011037024.1, NC_007086.1

3D structure databases

SMRiQ4UU85
ModBaseiSearch...

Protein-protein interaction databases

DIPiDIP-58626N
IntActiQ4UU85, 10 interactors

Genome annotation databases

EnsemblBacteriaiAAY49388; AAY49388; XC_2335
GeneIDi58013597
KEGGixcb:XC_2335

Phylogenomic databases

HOGENOMiCLU_000445_92_10_6
OMAiRCANTQF
OrthoDBi1755994at2

Family and domain databases

CDDicd00077, HDc, 1 hit
InterProiView protein in InterPro
IPR011006, CheY-like_superfamily
IPR003607, HD/PDEase_dom
IPR037522, HD_GYP_dom
IPR001789, Sig_transdc_resp-reg_receiver
PfamiView protein in Pfam
PF00072, Response_reg, 1 hit
SMARTiView protein in SMART
SM00471, HDc, 1 hit
SM00448, REC, 1 hit
SUPFAMiSSF52172, SSF52172, 1 hit
PROSITEiView protein in PROSITE
PS51832, HD_GYP, 1 hit
PS50110, RESPONSE_REGULATORY, 1 hit

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 nameiRPFG_XANC8
<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: Q4UU85
Secondary accession number(s): Q9L433
<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: December 20, 2005
Last sequence update: July 5, 2005
Last modified: June 2, 2021
This is version 98 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
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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