P0AGD7 (SRP54_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Signal recognition particle protein

Alternative name(s):
Fifty-four homolog
Short name=Ffh
p48

Gene names

Name:	ffh
Ordered Locus Names:	b2610, JW5414

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	453 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.13
Enzyme regulation	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. Ref.9
Subunit structure	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. Ref.6 Ref.7 Ref.8 Ref.11 Ref.12 Ref.18
Subcellular location	Cytoplasm. Note: The SRP-RNC complex is targeted to the cytoplasmic membrane. HAMAP-Rule MF_00306
Domain	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. Ref.12 Ref.17
Disruption phenotype	Essential; deletion experiments lead to loss of inner membrane protein targeting. Also leads to reduced targeting of lipoproteins Lpp and BRP. Ref.10 Ref.13
Sequence similarities	Belongs to the GTP-binding SRP family. SRP54 subfamily.
Sequence caution	The sequence CAA25957.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Cellular component	Cytoplasm Signal recognition particle
Ligand	GTP-binding Nucleotide-binding RNA-binding
Molecular function	Ribonucleoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	GTP catabolic process Inferred from direct assay PubMed 7612669. Source: GOC SRP-dependent cotranslational protein targeting to membrane Inferred from electronic annotation. Source: InterPro protein targeting to membrane Inferred from mutant phenotype Ref.7. Source: EcoliWiki
Cellular_component	ribonucleoprotein complex Inferred from direct assay PubMed 1701272. Source: EcoliWiki signal recognition particle Inferred from mutant phenotype Ref.7PubMed 1701272. Source: EcoliWiki signal recognition particle, endoplasmic reticulum targeting Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	7S RNA binding Inferred from electronic annotation. Source: InterPro GTP binding Inferred from direct assay PubMed 7612669. Source: EcoliWiki GTPase activity Inferred from mutant phenotype PubMed 7612669. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 453

453

Signal recognition particle protein HAMAP-Rule MF_00306

PRO_0000101153

Regions

Nucleotide binding

107 – 114

8

GTP By similarity

Nucleotide binding

190 – 194

5

GTP By similarity

Nucleotide binding

248 – 251

4

GTP By similarity

Secondary structure

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453

Helix Strand Turn

Details...

Helix

5 – 15

11

Helix

24 – 40

17

Helix

45 – 60

16

Helix

70 – 86

17

Beta strand

96 – 106

11

Helix

113 – 126

14

Beta strand

132 – 136

5

Helix

144 – 155

12

Beta strand

158 – 160

3

Helix

168 – 181

14

Beta strand

185 – 190

6

Helix

199 – 212

14

Beta strand

215 – 222

8

Helix

229 – 239

11

Beta strand

244 – 248

5

Helix

258 – 266

9

Beta strand

270 – 274

5

Beta strand

276 – 278

3

Beta strand

282 – 284

3

Helix

287 – 295

9

Helix

331 – 338

8

Helix

373 – 381

9

Helix

385 – 389

5

Helix

391 – 393

3

Helix

396 – 405

10

Helix

410 – 430

21

Sequences

	Sequence		Length	Mass (Da)
	P0AGD7 [UniParc]. Last modified December 20, 2005. Version 1. Checksum: E9C7A7101CC04D66	FASTA	453	49,787
	10 20 30 40 50 60 MFDNLTDRLS RTLRNISGRG RLTEDNVKDT LREVRMALLE ADVALPVVRE FINRVKEKAV 70 80 90 100 110 120 GHEVNKSLTP GQEFVKIVRN ELVAAMGEEN QTLNLAAQPP AVVLMAGLQG AGKTTSVGKL 130 140 150 160 170 180 GKFLREKHKK KVLVVSADVY RPAAIKQLET LAEQVGVDFF PSDVGQKPVD IVNAALKEAK 190 200 210 220 230 240 LKFYDVLLVD TAGRLHVDEA MMDEIKQVHA SINPVETLFV VDAMTGQDAA NTAKAFNEAL 250 260 270 280 290 300 PLTGVVLTKV DGDARGGAAL SIRHITGKPI KFLGVGEKTE ALEPFHPDRI ASRILGMGDV 310 320 330 340 350 360 LSLIEDIESK VDRAQAEKLA SKLKKGDGFD LNDFLEQLRQ MKNMGGMASL MGKLPGMGQI 370 380 390 400 410 420 PDNVKSQMDD KVLVRMEAII NSMTMKERAK PEIIKGSRKR RIAAGCGMQV QDVNRLLKQF 430 440 450 DDMQRMMKKM KKGGMAKMMR SMKGMMPPGF PGR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"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 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X01818 Genomic DNA. Translation: CAA25957.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75659.1.
AP009048 Genomic DNA. Translation: BAA16495.2.

PIR

E65039.

RefSeq

NP_417101.1. NC_000913.3.
YP_490833.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj

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	[»]

ProteinModelPortal

P0AGD7.

ModBase

Search...

MobiDB

Search...

Protein-protein interaction databases

DIP

DIP-31865N.

IntAct

P0AGD7. 19 interactions.

MINT

MINT-1218614.

STRING

511145.b2610.

Protein family/group databases

TCDB

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

Proteomic databases

PaxDb

P0AGD7.

PRIDE

P0AGD7.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75659; AAC75659; b2610.
BAA16495; BAA16495; BAA16495.

GeneID

12933092.
947102.

KEGG

ecj:Y75_p2558.
eco:b2610.

PATRIC

32120619. VBIEscCol129921_2708.

Organism-specific databases

EchoBASE

EB0296.

EcoGene

EG10300. ffh.

Phylogenomic databases

eggNOG

COG0541.

HOGENOM

HOG000036164.

KO

K03106.

OMA

LKQHKQM.

OrthoDB

EOG62K1ZH.

PhylomeDB

P0AGD7.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P0AGD7.

Family and domain databases

Gene3D

1.10.260.30. 1 hit.
3.40.50.300. 1 hit.

HAMAP

MF_00306. SRP54.

InterPro

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]

PANTHER

PTHR11564:SF7. PTHR11564:SF7. 1 hit.

Pfam

PF00448. SRP54. 1 hit.
PF02881. SRP54_N. 1 hit.
PF02978. SRP_SPB. 1 hit.
[Graphical view]

SMART

SM00382. AAA. 1 hit.
SM00962. SRP54. 1 hit.
SM00963. SRP54_N. 1 hit.
[Graphical view]

SUPFAM

SSF47446. SSF47446. 1 hit.
SSF52540. SSF52540. 1 hit.

TIGRFAMs

TIGR00959. ffh. 1 hit.

PROSITE

PS00300. SRP54. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0AGD7.

PRO

P0AGD7.

Entry information

Entry name

SRP54_ECOLI

Accession

Primary (citable) accession number: P0AGD7
Secondary accession number(s): P07019, P77007, P77008

Entry history

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 status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program