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P0AGD7

- SRP54_ECOLI

UniProt

P0AGD7 - SRP54_ECOLI

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Protein
Signal recognition particle protein
Gene
ffh, b2610, JW5414
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY. Interaction with FtsY leads to the transfer of the RNC complex to the Sec translocase for insertion into the membrane, the hydrolysis of GTP by both Ffh and FtsY, and the dissociation of the SRP-FtsY complex into the individual components.7 Publications

Enzyme regulationi

Conformation of the Ffh-FtsY complex and regulation of its GTPase activity are modulated by the 4.5S RNA. Formation of the FfH-FtsY complex leads to a mutual stimulation of both GTPases.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi107 – 1148GTP By similarity
Nucleotide bindingi190 – 1945GTP By similarity
Nucleotide bindingi248 – 2514GTP By similarity

GO - Molecular functioni

  1. 7S RNA binding Source: InterPro
  2. GTP binding Source: EcoliWiki
  3. GTPase activity Source: EcoCyc

GO - Biological processi

  1. GTP catabolic process Source: GOC
  2. SRP-dependent cotranslational protein targeting to membrane Source: InterPro
  3. protein targeting to membrane Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Ligandi

GTP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10300-MONOMER.
ECOL316407:JW5414-MONOMER.

Protein family/group databases

TCDBi3.A.5.1.1. the general secretory pathway (sec) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Signal recognition particle protein
Alternative name(s):
Fifty-four homolog
Short name:
Ffh
p48
Gene namesi
Name:ffh
Ordered Locus Names:b2610, JW5414
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10300. ffh.

Subcellular locationi

Cytoplasm
Note: The SRP-RNC complex is targeted to the cytoplasmic membrane.UniRule annotation

GO - Cellular componenti

  1. ribonucleoprotein complex Source: EcoliWiki
  2. signal recognition particle Source: EcoliWiki
  3. signal recognition particle, endoplasmic reticulum targeting Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Signal recognition particle

Pathology & Biotechi

Disruption phenotypei

Essential; deletion experiments lead to loss of inner membrane protein targeting. Also leads to reduced targeting of lipoproteins Lpp and BRP.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 453453Signal recognition particle proteinUniRule annotation
PRO_0000101153Add
BLAST

Proteomic databases

PaxDbiP0AGD7.
PRIDEiP0AGD7.

Expressioni

Gene expression databases

GenevestigatoriP0AGD7.

Interactioni

Subunit structurei

Part of the signal recognition particle protein translocation system, which is composed of SRP and FtsY. SRP is a ribonucleoprotein composed of Ffh and a 4.5S RNA molecule. Metal ions are essential for the formation and stability of the SRP complex. Interacts with the ribosomes, via ribosomal protein L23. Interacts with FtsY.6 Publications

Protein-protein interaction databases

DIPiDIP-31865N.
IntActiP0AGD7. 19 interactions.
MINTiMINT-1218614.
STRINGi511145.b2610.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 1511
Helixi24 – 4017
Helixi45 – 6016
Helixi70 – 8617
Beta strandi96 – 10611
Helixi113 – 12614
Beta strandi132 – 1365
Helixi144 – 15512
Beta strandi158 – 1603
Helixi168 – 18114
Beta strandi185 – 1906
Helixi199 – 21214
Beta strandi215 – 2228
Helixi229 – 23911
Beta strandi244 – 2485
Helixi258 – 2669
Beta strandi270 – 2745
Beta strandi276 – 2783
Beta strandi282 – 2843
Helixi287 – 2959
Helixi331 – 3388
Helixi373 – 3819
Helixi385 – 3895
Helixi391 – 3933
Helixi396 – 40510
Helixi410 – 43021

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DULX-ray1.80A329-430[»]
1HQ1X-ray1.52A328-432[»]
2J28electron microscopy8.0092-431[»]
2PXBX-ray2.00A329-430[»]
2PXDX-ray2.00A329-430[»]
2PXEX-ray2.00A329-430[»]
2PXFX-ray2.00A329-430[»]
2PXKX-ray2.00A329-430[»]
2PXLX-ray2.50A329-430[»]
2PXPX-ray2.50A329-430[»]
2PXQX-ray2.50A329-430[»]
2PXTX-ray2.50A329-430[»]
2PXUX-ray2.50A329-430[»]
2PXVX-ray2.00A329-430[»]
2XKVelectron microscopy13.50C329-430[»]
2XXAX-ray3.94A/C1-433[»]
3LQXX-ray1.93A329-428[»]
4C7OX-ray2.60A/C1-298[»]
ProteinModelPortaliP0AGD7.

Miscellaneous databases

EvolutionaryTraceiP0AGD7.

Family & Domainsi

Domaini

Composed of three domains: the N-terminal N domain, which is responsible for interactions with the ribosome, the central G domain, which binds GTP, and the C-terminal M domain, which binds the RNA and the signal sequence of the RNC.2 Publications

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0541.
HOGENOMiHOG000036164.
KOiK03106.
OMAiLKQHKQM.
OrthoDBiEOG62K1ZH.
PhylomeDBiP0AGD7.

Family and domain databases

Gene3Di1.10.260.30. 1 hit.
3.40.50.300. 1 hit.
HAMAPiMF_00306. SRP54.
InterProiIPR003593. AAA+_ATPase.
IPR027417. P-loop_NTPase.
IPR013822. Signal_recog_particl_SRP54_hlx.
IPR004125. Signal_recog_particle_SRP54_M.
IPR022941. SRP54.
IPR000897. SRP54_GTPase_dom.
IPR004780. SRP_Ffh.
[Graphical view]
PANTHERiPTHR11564:SF7. PTHR11564:SF7. 1 hit.
PfamiPF00448. SRP54. 1 hit.
PF02881. SRP54_N. 1 hit.
PF02978. SRP_SPB. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
SM00962. SRP54. 1 hit.
SM00963. SRP54_N. 1 hit.
[Graphical view]
SUPFAMiSSF47446. SSF47446. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00959. ffh. 1 hit.
PROSITEiPS00300. SRP54. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0AGD7-1 [UniParc]FASTAAdd to Basket

« Hide

MFDNLTDRLS RTLRNISGRG RLTEDNVKDT LREVRMALLE ADVALPVVRE    50
FINRVKEKAV GHEVNKSLTP GQEFVKIVRN ELVAAMGEEN QTLNLAAQPP 100
AVVLMAGLQG AGKTTSVGKL GKFLREKHKK KVLVVSADVY RPAAIKQLET 150
LAEQVGVDFF PSDVGQKPVD IVNAALKEAK LKFYDVLLVD TAGRLHVDEA 200
MMDEIKQVHA SINPVETLFV VDAMTGQDAA NTAKAFNEAL PLTGVVLTKV 250
DGDARGGAAL SIRHITGKPI KFLGVGEKTE ALEPFHPDRI ASRILGMGDV 300
LSLIEDIESK VDRAQAEKLA SKLKKGDGFD LNDFLEQLRQ MKNMGGMASL 350
MGKLPGMGQI PDNVKSQMDD KVLVRMEAII NSMTMKERAK PEIIKGSRKR 400
RIAAGCGMQV QDVNRLLKQF DDMQRMMKKM KKGGMAKMMR SMKGMMPPGF 450
PGR 453
Length:453
Mass (Da):49,787
Last modified:December 20, 2005 - v1
Checksum:iE9C7A7101CC04D66
GO

Sequence cautioni

The sequence CAA25957.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X01818 Genomic DNA. Translation: CAA25957.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75659.1.
AP009048 Genomic DNA. Translation: BAA16495.2.
PIRiE65039.
RefSeqiNP_417101.1. NC_000913.3.
YP_490833.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75659; AAC75659; b2610.
BAA16495; BAA16495; BAA16495.
GeneIDi12933092.
947102.
KEGGiecj:Y75_p2558.
eco:b2610.
PATRICi32120619. VBIEscCol129921_2708.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X01818 Genomic DNA. Translation: CAA25957.1 . Different initiation.
U00096 Genomic DNA. Translation: AAC75659.1 .
AP009048 Genomic DNA. Translation: BAA16495.2 .
PIRi E65039.
RefSeqi NP_417101.1. NC_000913.3.
YP_490833.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1DUL X-ray 1.80 A 329-430 [» ]
1HQ1 X-ray 1.52 A 328-432 [» ]
2J28 electron microscopy 8.00 9 2-431 [» ]
2PXB X-ray 2.00 A 329-430 [» ]
2PXD X-ray 2.00 A 329-430 [» ]
2PXE X-ray 2.00 A 329-430 [» ]
2PXF X-ray 2.00 A 329-430 [» ]
2PXK X-ray 2.00 A 329-430 [» ]
2PXL X-ray 2.50 A 329-430 [» ]
2PXP X-ray 2.50 A 329-430 [» ]
2PXQ X-ray 2.50 A 329-430 [» ]
2PXT X-ray 2.50 A 329-430 [» ]
2PXU X-ray 2.50 A 329-430 [» ]
2PXV X-ray 2.00 A 329-430 [» ]
2XKV electron microscopy 13.50 C 329-430 [» ]
2XXA X-ray 3.94 A/C 1-433 [» ]
3LQX X-ray 1.93 A 329-428 [» ]
4C7O X-ray 2.60 A/C 1-298 [» ]
ProteinModelPortali P0AGD7.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-31865N.
IntActi P0AGD7. 19 interactions.
MINTi MINT-1218614.
STRINGi 511145.b2610.

Protein family/group databases

TCDBi 3.A.5.1.1. the general secretory pathway (sec) family.

Proteomic databases

PaxDbi P0AGD7.
PRIDEi P0AGD7.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75659 ; AAC75659 ; b2610 .
BAA16495 ; BAA16495 ; BAA16495 .
GeneIDi 12933092.
947102.
KEGGi ecj:Y75_p2558.
eco:b2610.
PATRICi 32120619. VBIEscCol129921_2708.

Organism-specific databases

EchoBASEi EB0296.
EcoGenei EG10300. ffh.

Phylogenomic databases

eggNOGi COG0541.
HOGENOMi HOG000036164.
KOi K03106.
OMAi LKQHKQM.
OrthoDBi EOG62K1ZH.
PhylomeDBi P0AGD7.

Enzyme and pathway databases

BioCyci EcoCyc:EG10300-MONOMER.
ECOL316407:JW5414-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0AGD7.
PROi P0AGD7.

Gene expression databases

Genevestigatori P0AGD7.

Family and domain databases

Gene3Di 1.10.260.30. 1 hit.
3.40.50.300. 1 hit.
HAMAPi MF_00306. SRP54.
InterProi IPR003593. AAA+_ATPase.
IPR027417. P-loop_NTPase.
IPR013822. Signal_recog_particl_SRP54_hlx.
IPR004125. Signal_recog_particle_SRP54_M.
IPR022941. SRP54.
IPR000897. SRP54_GTPase_dom.
IPR004780. SRP_Ffh.
[Graphical view ]
PANTHERi PTHR11564:SF7. PTHR11564:SF7. 1 hit.
Pfami PF00448. SRP54. 1 hit.
PF02881. SRP54_N. 1 hit.
PF02978. SRP_SPB. 1 hit.
[Graphical view ]
SMARTi SM00382. AAA. 1 hit.
SM00962. SRP54. 1 hit.
SM00963. SRP54_N. 1 hit.
[Graphical view ]
SUPFAMi SSF47446. SSF47446. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsi TIGR00959. ffh. 1 hit.
PROSITEi PS00300. SRP54. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of an Escherichia coli operon containing genes for the tRNA(m1G)methyltransferase, the ribosomal proteins S16 and L19 and a 21-K polypeptide."
    Bystroem A.S., Hjalmarsson K.J., Wikstroem P.M., Bjoerk G.R.
    EMBO J. 2:899-905(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
    Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
    , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
    DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "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], SEQUENCE REVISION.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "E. coli 4.5S RNA is part of a ribonucleoprotein particle that has properties related to signal recognition particle."
    Ribes V., Roemisch K., Giner A., Dobberstein B., Tollervey D.
    Cell 63:591-600(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "Signal-sequence recognition by an Escherichia coli ribonucleoprotein complex."
    Luirink J., High S., Wood H., Giner A., Tollervey D., Dobberstein B.
    Nature 359:741-743(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT.
  7. "The E. coli ffh gene is necessary for viability and efficient protein export."
    Phillips G.J., Silhavy T.J.
    Nature 359:744-746(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT.
  8. "Co-translational protein targeting catalyzed by the Escherichia coli signal recognition particle and its receptor."
    Powers T., Walter P.
    EMBO J. 16:4880-4886(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT.
  9. "Role of SRP RNA in the GTPase cycles of Ffh and FtsY."
    Peluso P., Shan S.O., Nock S., Herschlag D., Walter P.
    Biochemistry 40:15224-15233(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, GTPASE ACTIVITY, ENZYME REGULATION.
  10. "Genetic screen yields mutations in genes encoding all known components of the Escherichia coli signal recognition particle pathway."
    Tian H., Beckwith J.
    J. Bacteriol. 184:111-118(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    Strain: K12.
  11. "Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome."
    Ullers R.S., Houben E.N.G., Raine A., ten Hagen-Jongman C.M., Ehrenberg M., Brunner J., Oudega B., Harms N., Luirink J.
    J. Cell Biol. 161:679-684(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RIBOSOMAL PROTEIN L23 AND NASCENT PROTEIN CHAINS.
    Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
  12. "The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome."
    Gu S.-Q., Peske F., Wieden H.-J., Rodnina M.V., Wintermeyer W.
    RNA 9:566-573(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RIBOSOMAL PROTEIN L23, DOMAIN.
    Strain: MRE-600.
  13. "Targeting and translocation of two lipoproteins in Escherichia coli via the SRP/Sec/YidC pathway."
    Froderberg L., Houben E.N., Baars L., Luirink J., de Gier J.W.
    J. Biol. Chem. 279:31026-31032(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN LIPOPROTEIN EXPORT, DISRUPTION PHENOTYPE.
  14. "Trigger factor binds to ribosome-signal-recognition particle (SRP) complexes and is excluded by binding of the SRP receptor."
    Buskiewicz I., Deuerling E., Gu S.-Q., Joeckel J., Rodnina M.V., Bukau B., Wintermeyer W.
    Proc. Natl. Acad. Sci. U.S.A. 101:7902-7906(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SIMULTANEOUS BINDING OF TRIGGER FACTOR AND SRP TO THE RIBOSOME.
    Strain: MRE-600.
  15. "Early targeting events during membrane protein biogenesis in Escherichia coli."
    Bibi E.
    Biochim. Biophys. Acta 1808:841-850(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  16. "Structure of a methionine-rich segment of Escherichia coli Ffh protein."
    Oh D.-B., Yi G.-S., Chi S.-W., Kim H.
    FEBS Lett. 395:160-164(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 410-434.
  17. "Crystal structure of the ribonucleoprotein core of the signal recognition particle."
    Batey R.T., Rambo R.P., Lucast L., Rha B., Doudna J.A.
    Science 287:1232-1239(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 371-430 IN COMPLEX WITH 4.5S RNA, DOMAIN.
  18. "Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly."
    Batey R.T., Doudna J.A.
    Biochemistry 41:11703-11710(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.93 ANGSTROMS) OF 328-432, SUBUNIT.
  19. "Following the signal sequence from ribosomal tunnel exit to signal recognition particle."
    Halic M., Blau M., Becker T., Mielke T., Pool M.R., Wild K., Sinning I., Beckmann R.
    Nature 444:507-511(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (8.00 ANGSTROMS) OF 2-431.
  20. "A general strategy to solve the phase problem in RNA crystallography."
    Keel A.Y., Rambo R.P., Batey R.T., Kieft J.S.
    Structure 15:761-772(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 329-430.
  21. "Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor."
    Estrozi L.F., Boehringer D., Shan S.O., Ban N., Schaffitzel C.
    Nat. Struct. Mol. Biol. 18:88-90(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (13.50 ANGSTROMS) OF 371-430.
  22. "The crystal structure of the signal recognition particle in complex with its receptor."
    Ataide S.F., Schmitz N., Shen K., Ke A., Shan S.O., Doudna J.A., Ban N.
    Science 331:881-886(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.94 ANGSTROMS) OF 1-433.

Entry informationi

Entry nameiSRP54_ECOLI
AccessioniPrimary (citable) accession number: P0AGD7
Secondary accession number(s): P07019, P77007, P77008
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: December 20, 2005
Last modified: July 9, 2014
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi