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Entry version 150 (07 Oct 2020)
Sequence version 2 (01 Nov 1995)
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Protein

RNase E specificity factor CsrD

Gene

csrD

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

Serves as a specificity factor required for RNase E-mediated decay of the small global regulatory RNAs CsrB and CsrC, it is probably not a nuclease. Nor does its activity involve c-di-GMP, despite its domain composition. Positively modulates motility gene expression, is also required for curli expression.3 Publications

Caution

Although this protein contains both EAL and GGDEF domains it is unlikely to have either c-di-GMP phosphodiesterase or diguanylate cyclase activities as amino acids known to be important to these activities are not conserved.Curated

<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 - Biological processi

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG10018-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:
RNase E specificity factor CsrD
Alternative name(s):
Regulator of CsrB and CsrC decay CsrD
<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:csrD
Synonyms:yhdA
Ordered Locus Names:b3252, JW3221
<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 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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei10 – 30HelicalSequence analysisAdd BLAST21
Transmembranei135 – 155HelicalSequence analysisAdd BLAST21

GO - Cellular componenti

<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>Keywords - Cellular componenti

Cell membrane, Membrane

<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

Dramatically stabilizes CsrB and CsrC RNAs, small RNAs that sequester the global carbon storage regulator CsrA; also decreased transcription of CsrB/C (PubMed:16980588). Decreased biofilm formation, decreased expression of DgcC, a probable diguanylate cyclase and of the curli regulator CsgD. Decreased expression of the curlin subunit CsgB, decreased curli expression at 28 degrees Celsius (PubMed:19332833).3 Publications

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>Mutagenesisi584L → A: Decreased transcription of csrB. 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_00001694921 – 646RNase E specificity factor CsrDAdd BLAST646

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P13518

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

More...
PaxDbi
P13518

PRoteomics IDEntifications database

More...
PRIDEi
P13518

<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

Expressed at low levels at both 28 and 37 degrees Celsius.1 Publication

<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

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4261943, 11 interactors

Database of interacting proteins

More...
DIPi
DIP-12292N

Protein interaction database and analysis system

More...
IntActi
P13518, 1 interactor

STRING: functional protein association networks

More...
STRINGi
511145.b3252

<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
P13518

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>Domaini254 – 387GGDEFPROSITE-ProRule annotationAdd BLAST134
Domaini396 – 644EALPROSITE-ProRule annotationAdd BLAST249

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni152 – 219HAMP-likeAdd BLAST68

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and domains' section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili194 – 224Sequence analysisAdd BLAST31

<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

Removal of the transmembrane regions (residues 1-156) has no effect on csrB translation, however removal of either the HAMP-like region, EAL or GGDEF domains obviates the activity of CsrD.1 Publication

Keywords - Domaini

Coiled coil, Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG2199, Bacteria
COG2200, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_028330_0_0_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P13518

KEGG Orthology (KO)

More...
KOi
K18765

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P13518

Family and domain databases

Conserved Domains Database

More...
CDDi
cd01948, EAL, 1 hit
cd01949, GGDEF, 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
IPR033423, GAPES4
IPR000160, GGDEF_dom
IPR029787, Nucleotide_cyclase
IPR043128, Rev_trsase/Diguanyl_cyclase

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00563, EAL, 1 hit
PF17157, GAPES4, 1 hit
PF00990, GGDEF, 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

Superfamily database of structural and functional annotation

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

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00254, GGDEF, 1 hit

PROSITE; a protein domain and family database

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

P13518-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRLTTKFSAF VTLLTGLTIF VTLLGCSLSF YNAIQYKFSH RVQAVATAID
60 70 80 90 100
THLVSNDFSV LRPQITELMM SADIVRVDLL HGDKQVYTLA RNGSYRPVGS
110 120 130 140 150
SDLFRELSVP LIKHPGMSLR LVYQDPMGNY FHSLMTTAPL TGAIGFIIVM
160 170 180 190 200
LFLAVRWLQR QLAGQELLET RATRILNGER GSNVLGTIYE WPPRTSSALD
210 220 230 240 250
TLLREIQNAR EQHSRLDTLI RSYAAQDVKT GLNNRLFFDN QLATLLEDQE
260 270 280 290 300
KVGTHGIVMM IRLPDFNMLS DTWGHSQVEE QFFTLTNLLS TFMMRYPGAL
310 320 330 340 350
LARYHRSDFA ALLPHRTLKE AESIAGQLIK AVDTLPNNKM LDRDDMIHIG
360 370 380 390 400
ICAWRSGQDT EQVMEHAESA TRNAGLQGGN SWAIYDDSLP EKGRGNVRWR
410 420 430 440 450
TLIEQMLSRG GPRLYQKPAV TREGQVHHRE LMCRIFDGNE EVSSAEYMPM
460 470 480 490 500
VLQFGLSEEY DRLQISRLIP LLRYWPEENL AIQVTVESLI RPRFQRWLRD
510 520 530 540 550
TLMQCEKSQR KRIIIELAEA DVGQHISRLQ PVIRLVNALG VRVAVNQAGL
560 570 580 590 600
TLVSTSWIKE LNVELLKLHP GLVRNIEKRT ENQLLVQSLV EACSGTSTQV
610 620 630 640
YATGVRSRSE WQTLIQRGVT GGQGDFFASS QPLDTNVKKY SQRYSV
Length:646
Mass (Da):73,339
Last modified:November 1, 1995 - v2
<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:i0387E011BC4D06B8
GO

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
U18997 Genomic DNA Translation: AAA58055.1
U00096 Genomic DNA Translation: AAC76284.1
AP009048 Genomic DNA Translation: BAE77294.1
M22055 Genomic DNA Translation: AAA83890.1

Protein sequence database of the Protein Information Resource

More...
PIRi
F65117, QQECE5

NCBI Reference Sequences

More...
RefSeqi
NP_417718.1, NC_000913.3
WP_001241469.1, NZ_SSZK01000034.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC76284; AAC76284; b3252
BAE77294; BAE77294; BAE77294

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
947702

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW3221
eco:b3252

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.3477

<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
U18997 Genomic DNA Translation: AAA58055.1
U00096 Genomic DNA Translation: AAC76284.1
AP009048 Genomic DNA Translation: BAE77294.1
M22055 Genomic DNA Translation: AAA83890.1
PIRiF65117, QQECE5
RefSeqiNP_417718.1, NC_000913.3
WP_001241469.1, NZ_SSZK01000034.1

3D structure databases

SMRiP13518
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4261943, 11 interactors
DIPiDIP-12292N
IntActiP13518, 1 interactor
STRINGi511145.b3252

Proteomic databases

jPOSTiP13518
PaxDbiP13518
PRIDEiP13518

Genome annotation databases

EnsemblBacteriaiAAC76284; AAC76284; b3252
BAE77294; BAE77294; BAE77294
GeneIDi947702
KEGGiecj:JW3221
eco:b3252
PATRICifig|1411691.4.peg.3477

Organism-specific databases

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

More...
EchoBASEi
EB0018

Phylogenomic databases

eggNOGiCOG2199, Bacteria
COG2200, Bacteria
HOGENOMiCLU_028330_0_0_6
InParanoidiP13518
KOiK18765
PhylomeDBiP13518

Enzyme and pathway databases

BioCyciEcoCyc:EG10018-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P13518

Family and domain databases

CDDicd01948, EAL, 1 hit
cd01949, GGDEF, 1 hit
Gene3Di3.20.20.450, 1 hit
3.30.70.270, 1 hit
InterProiView protein in InterPro
IPR001633, EAL_dom
IPR035919, EAL_sf
IPR033423, GAPES4
IPR000160, GGDEF_dom
IPR029787, Nucleotide_cyclase
IPR043128, Rev_trsase/Diguanyl_cyclase
PfamiView protein in Pfam
PF00563, EAL, 1 hit
PF17157, GAPES4, 1 hit
PF00990, GGDEF, 1 hit
SMARTiView protein in SMART
SM00052, EAL, 1 hit
SM00267, GGDEF, 1 hit
SUPFAMiSSF141868, SSF141868, 1 hit
SSF55073, SSF55073, 1 hit
TIGRFAMsiTIGR00254, GGDEF, 1 hit
PROSITEiView protein in PROSITE
PS50883, EAL, 1 hit
PS50887, GGDEF, 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 nameiCSRD_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: P13518
Secondary accession number(s): Q2M8W2
<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: January 1, 1990
Last sequence update: November 1, 1995
Last modified: October 7, 2020
This is version 150 of the entry and version 2 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

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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