P13518 (CSRD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
RNase E specificity factor CsrD

Alternative name(s):
Regulator of CsrB and CsrC decay CsrD

Gene names

Name:	csrD
Synonyms:	yhdA
Ordered Locus Names:	b3252, JW3221

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	646 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.4 Ref.5 Ref.6
Subcellular location	Cell membrane; Multi-pass membrane protein Potential.
Induction	Expressed at low levels at both 28 and 37 degrees Celsius. Ref.6
Domain	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. Ref.5
Disruption phenotype	Dramatically stabilizes CsrB and CsrC RNAs, small RNAs that sequester the global carbon storage regulator CsrA; also decreased transcription of CsrB/C (Ref.5). Decreased biofilm formation, decreased expression of AdrA, a probable diguanylate cyclase and of the curli regulator CsgD. Decreased expression of the curlin subunit CsgB, decreased curli expression at 28 degrees Celsius (Ref.6). Ref.4 Ref.5 Ref.6
Sequence similarities	Contains 1 EAL domain. Contains 1 GGDEF domain.
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.

Ontologies

Keywords
Cellular component	Cell membrane Membrane
Domain	Coiled coil Transmembrane Transmembrane helix
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cyclic nucleotide biosynthetic process Inferred from electronic annotation. Source: InterPro intracellular signal transduction Inferred from electronic annotation. Source: InterPro
Cellular_component	integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	RNA binding Inferred from direct assay Ref.5. Source: EcoCyc phosphorus-oxygen lyase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 646	646	RNase E specificity factor CsrD		PRO_0000169492
Regions
	Transmembrane	10 – 30	21	Helical; Potential
	Transmembrane	135 – 155	21	Helical; Potential
	Domain	254 – 387	134	GGDEF
	Domain	396 – 644	249	EAL
	Region	152 – 219	68	HAMP-like
	Coiled coil	194 – 224	31	Potential
Experimental info
	Mutagenesis	584	1	L → A: Decreased transcription of csrB. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	P13518 [UniParc]. Last modified November 1, 1995. Version 2. Checksum: 0387E011BC4D06B8	FASTA	646	73,339
	10 20 30 40 50 60 MRLTTKFSAF VTLLTGLTIF VTLLGCSLSF YNAIQYKFSH RVQAVATAID THLVSNDFSV 70 80 90 100 110 120 LRPQITELMM SADIVRVDLL HGDKQVYTLA RNGSYRPVGS SDLFRELSVP LIKHPGMSLR 130 140 150 160 170 180 LVYQDPMGNY FHSLMTTAPL TGAIGFIIVM LFLAVRWLQR QLAGQELLET RATRILNGER 190 200 210 220 230 240 GSNVLGTIYE WPPRTSSALD TLLREIQNAR EQHSRLDTLI RSYAAQDVKT GLNNRLFFDN 250 260 270 280 290 300 QLATLLEDQE KVGTHGIVMM IRLPDFNMLS DTWGHSQVEE QFFTLTNLLS TFMMRYPGAL 310 320 330 340 350 360 LARYHRSDFA ALLPHRTLKE AESIAGQLIK AVDTLPNNKM LDRDDMIHIG ICAWRSGQDT 370 380 390 400 410 420 EQVMEHAESA TRNAGLQGGN SWAIYDDSLP EKGRGNVRWR TLIEQMLSRG GPRLYQKPAV 430 440 450 460 470 480 TREGQVHHRE LMCRIFDGNE EVSSAEYMPM VLQFGLSEEY DRLQISRLIP LLRYWPEENL 490 500 510 520 530 540 AIQVTVESLI RPRFQRWLRD TLMQCEKSQR KRIIIELAEA DVGQHISRLQ PVIRLVNALG 550 560 570 580 590 600 VRVAVNQAGL TLVSTSWIKE LNVELLKLHP GLVRNIEKRT ENQLLVQSLV EACSGTSTQV 610 620 630 640 YATGVRSRSE WQTLIQRGVT GGQGDFFASS QPLDTNVKKY SQRYSV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"Determinations of the DNA sequence of the mreB gene and of the gene products of the mre region that function in formation of the rod shape of Escherichia coli cells." Doi M., Wachi M., Ishino F., Tomioka S., Ito M., Sakagami Y., Suzuki A., Matsuhashi M. J. Bacteriol. 170:4619-4624(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 545-646. Strain: K12.
[4]	"Identification of YhdA as a regulator of the Escherichia coli carbon storage regulation system." Jonas K., Tomenius H., Romling U., Georgellis D., Melefors O. FEMS Microbiol. Lett. 264:232-237(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN REGULATION OF CARBON STORAGE REGULATION SYSTEM, DISRUPTION PHENOTYPE. Strain: K12 / MG1655 / CF7789.
[5]	"Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E." Suzuki K., Babitzke P., Kushner S.R., Romeo T. Genes Dev. 20:2605-2617(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF LEU-584, DOMAIN EAL AND GGDEF, DISRUPTION PHENOTYPE. Strain: K12 / MG1655 / CF7789.
[6]	"Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli." Sommerfeldt N., Possling A., Becker G., Pesavento C., Tschowri N., Hengge R. Microbiology 155:1318-1331(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN CURLI EXPRESSION, INDUCTION, DISRUPTION PHENOTYPE. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U18997 Genomic DNA. Translation: AAA58055.1. U00096 Genomic DNA. Translation: AAC76284.1. AP009048 Genomic DNA. Translation: BAE77294.1. M22055 Genomic DNA. Translation: AAA83890.1.
PIR	QQECE5. F65117.
RefSeq	NP_417718.1. NC_000913.2. YP_491435.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P13518.
SMR	P13518. Positions 210-634.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-12292N.
IntAct	P13518. 1 interaction.
MINT	MINT-1286606.
STRING	511145.b3252.
Proteomic databases
PaxDb	P13518.
PRIDE	P13518.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC76284; AAC76284; b3252. BAE77294; BAE77294; BAE77294.
GeneID	12932949. 947702.
KEGG	ecj:Y75_p3171. eco:b3252.
PATRIC	32121930. VBIEscCol129921_3349.
Organism-specific databases
EchoBASE	EB0018.
EcoGene	EG10018. csrD.
Phylogenomic databases
eggNOG	COG2199.
HOGENOM	HOG000270419.
OMA	RMDTLIR.
ProtClustDB	PRK11059.
Enzyme and pathway databases
BioCyc	EcoCyc:EG10018-MONOMER. ECOL316407:JW3221-MONOMER.
Gene expression databases
Genevestigator	P13518.
Family and domain databases
Gene3D	3.20.20.450. 1 hit.
InterPro	IPR001054. A/G_cyclase. IPR001633. Diguanylate_PEstase_EAL_dom. IPR000160. GGDEF_dom. [Graphical view]
Pfam	PF00563. EAL. 1 hit. PF00990. GGDEF. 1 hit. [Graphical view]
SMART	SM00052. EAL. 1 hit. SM00267. GGDEF. 1 hit. [Graphical view]
SUPFAM	SSF55073. A/G_cyclase. 1 hit. SSF141868. SSF141868. 1 hit.
TIGRFAMs	TIGR00254. GGDEF. 1 hit.
PROSITE	PS50883. EAL. 1 hit. PS50887. GGDEF. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

CSRD_ECOLI

Accession

Primary (citable) accession number: P13518
Secondary accession number(s): Q2M8W2

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	November 1, 1995
Last modified:	May 1, 2013
This is version 106 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program