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P0AGA2 (SECY_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 73. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Protein translocase subunit SecY
Gene names
Name:secY
Synonyms:prlA
Ordered Locus Names:b3300, JW3262
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length443 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently. SecY is required to insert newly synthesized SecY into the inner membrane. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true, overexpression also results in FtsH-mediated degradation of SecY. HAMAP-Rule MF_01465

Subunit structure

Component of the Sec protein translocase complex. Heterotrimer consisting of SecY, SecE and SecG subunits. The heterotrimers can form oligomers, although 1 heterotrimer is thought to be able to translocate proteins. Interacts with the ribosome. Interacts with SecDF-YajC and YidC; YidC interacts with nascent inner membrane proteins after SecY. SecY probably contacts the 23S rRNA and possibly also ribosomal protein L23 during ribosome docking. A single SecY molecule forms the translocating pore, although interaction with SecA may require oligomers. Ref.14 Ref.16

Subcellular location

Cell inner membrane; Multi-pass membrane protein HAMAP-Rule MF_01465.

Post-translational modification

SecY that is not part of the protein translocation apparatus is degraded by FtsH. Also degraded by FtsH when the SecYEG complex is jammed, or upon treatment with antibiotics that block translation elongation such as chloramphenicol. HAMAP-Rule MF_01465

Sequence similarities

Belongs to the SecY/SEC61-alpha family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

secAP104084EBI-761422,EBI-543213

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 443443Protein translocase subunit SecY HAMAP-Rule MF_01465
PRO_0000131721

Regions

Topological domain1 – 2222Cytoplasmic Probable
Transmembrane23 – 3513Helical; Name=1; Probable
Topological domain36 – 6025Periplasmic By similarity
Transmembrane61 – 9636Discontinuously helical; Name=2; By similarity
Intramembrane61 – 7010Helical; Name=Helix 2A; Probable
Intramembrane71 – 766 Probable
Intramembrane77 – 9620Helical; Name=Helix 2B; Probable
Topological domain97 – 11519Cytoplasmic Probable
Transmembrane116 – 13116Helical; Name=3; Probable
Topological domain132 – 16433Periplasmic Probable
Transmembrane165 – 17814Helical; Name=4; Probable
Topological domain179 – 1835Cytoplasmic Probable
Transmembrane184 – 20017Helical; Name=5; Probable
Topological domain201 – 22323Periplasmic Probable
Transmembrane224 – 23714Helical; Name=6; Probable
Topological domain238 – 27336Cytoplasmic Probable
Transmembrane274 – 28714Helical; Name=7; Probable
Topological domain288 – 31326Periplasmic Probable
Transmembrane314 – 32916Helical; Name=8; Probable
Topological domain330 – 38051Cytoplasmic Probable
Transmembrane381 – 39515Helical; Name=9; Probable
Topological domain3961Periplasmic Probable
Transmembrane397 – 41317Helical; Name=10; Probable
Topological domain414 – 44330Cytoplasmic Probable

Experimental info

Mutagenesis401P → S in secY100; temperature-sensitive.
Mutagenesis60 – 7415Missing: Some loss of viability, supports protein translocation; strongly suppresses defective and missing signal sequences; transient transmembrane channels open. Ref.18 Ref.19
Mutagenesis65 – 706Missing: Grows almost as well as wild-type, supports protein translocation; strongly suppresses defective and missing signal sequences; transient transmembrane channels open. Ref.18 Ref.19
Mutagenesis671F → C in prlA3; altered signal sequence interaction, transient channel opening and closing in presence of oxidant; massive ion flux when cross-linked to SecE C-120 mutation. Ref.18
Mutagenesis1671G → E in secY100; temperature-sensitive.
Mutagenesis2401G → D in secY24; temperature-sensitive at 42 degrees Celsius, impairs interaction with SecE even at 30 degrees in vitro. Ref.11
Mutagenesis2821S → R in prlA401; altered signal sequence interaction, transient transmembrane channels open.
Mutagenesis2861F → Y in prlA4-1; altered signal sequence interaction.
Mutagenesis2871P → L in secY161; altered signal sequence interaction.
Mutagenesis2901I → T in secY121; altered signal sequence interaction.
Mutagenesis3571R → H in secY39; cold-sensitive.
Mutagenesis3631A → S in secY40; cold-sensitive.
Mutagenesis4081I → N in prlA4-2; altered signal sequence interaction. Ref.18
Mutagenesis424 – 44320Missing: No longer complements secY24, a temperature-sensitive secY mutation. Ref.20

Sequences

Sequence LengthMass (Da)Tools
P0AGA2 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: 711CA63CD8809763

FASTA44348,512
        10         20         30         40         50         60 
MAKQPGLDFQ SAKGGLGELK RRLLFVIGAL IVFRIGSFIP IPGIDAAVLA KLLEQQRGTI 

        70         80         90        100        110        120 
IEMFNMFSGG ALSRASIFAL GIMPYISASI IIQLLTVVHP TLAEIKKEGE SGRRKISQYT 

       130        140        150        160        170        180 
RYGTLVLAIF QSIGIATGLP NMPGMQGLVI NPGFAFYFTA VVSLVTGTMF LMWLGEQITE 

       190        200        210        220        230        240 
RGIGNGISII IFAGIVAGLP PAIAHTIEQA RQGDLHFLVL LLVAVLVFAV TFFVVFVERG 

       250        260        270        280        290        300 
QRRIVVNYAK RQQGRRVYAA QSTHLPLKVN MAGVIPAIFA SSIILFPATI ASWFGGGTGW 

       310        320        330        340        350        360 
NWLTTISLYL QPGQPLYVLL YASAIIFFCF FYTALVFNPR ETADNLKKSG AFVPGIRPGE 

       370        380        390        400        410        420 
QTAKYIDKVM TRLTLVGALY ITFICLIPEF MRDAMKVPFY FGGTSLLIVV VVIMDFMAQV 

       430        440 
QTLMMSSQYE SALKKANLKG YGR 

« Hide

References

« Hide 'large scale' references
[1]"The spc ribosomal protein operon of Escherichia coli: sequence and cotranscription of the ribosomal protein genes and a protein export gene."
Cerretti D.P., Dean D., Davis G.R., Bedwell D.M., Nomura M.
Nucleic Acids Res. 11:2599-2616(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"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.
[3]"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.
[4]"Topology analysis of the SecY protein, an integral membrane protein involved in protein export in Escherichia coli."
Akiyama Y., Ito K.
EMBO J. 6:3465-3470(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: TOPOLOGY.
[5]"Temperature-sensitive sec mutants of Escherichia coli: inhibition of protein export at the permissive temperature."
Ito K., Hirota Y., Akiyama Y.
J. Bacteriol. 171:1742-1743(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTANT SECY100.
[6]"Export of Escherichia coli alkaline phosphatase attached to an integral membrane protein, SecY."
Akiyama Y., Ito K.
J. Biol. Chem. 264:437-442(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: REQUIRED FOR ITS OWN INSERTION INTO MEMBRANES.
Strain: K12 / MC4100.
[7]"Characterization of cold-sensitive secY mutants of Escherichia coli."
Baba T., Jacq A., Brickman E., Beckwith J., Taura T., Ueguchi C., Akiyama Y., Ito K.
J. Bacteriol. 172:7005-7010(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTANTS SECY39 AND SECY40.
[8]"Novel prlA alleles defective in supporting staphylokinase processing in Escherichia coli."
Sako T.
J. Bacteriol. 173:2289-2296(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTANTS SECY121 AND SECY161.
[9]"Biochemical analysis of the biogenesis and function of the Escherichia coli export factor SecY."
Swidersky U.E., Rienhoefer-Schweer A., Werner P.K., Ernst F., Benson S.A., Hoffschulte H.K., Mueller M.
Eur. J. Biochem. 207:803-811(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
[10]"PrlA suppressor mutations cluster in regions corresponding to three distinct topological domains."
Osborne R.S., Silhavy T.J.
EMBO J. 12:3391-3398(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTANTS.
[11]"A cytoplasmic domain is important for the formation of a SecY-SecE translocator complex."
Baba T., Taura T., Shimoike T., Akiyama Y., Yoshihisa T., Ito K.
Proc. Natl. Acad. Sci. U.S.A. 91:4539-4543(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF GLY-240.
Strain: K12 / MC4100.
[12]"The allele-specific synthetic lethality of prlA-prlG double mutants predicts interactive domains of SecY and SecE."
Flower A.M., Osborne R.S., Silhavy T.J.
EMBO J. 14:884-893(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTANTS.
[13]"FtsH is required for proteolytic elimination of uncomplexed forms of SecY, an essential protein translocase subunit."
Kihara A., Akiyama Y., Ito K.
Proc. Natl. Acad. Sci. U.S.A. 92:4532-4536(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: DEGRADATION BY FTSH.
[14]"Sec-dependent membrane protein insertion: sequential interaction of nascent FtsQ with SecY and YidC."
Urbanus M.L., Scotti P.A., Froderberg L., Saaf A., de Gier J.W., Brunner J., Samuelson J.C., Dalbey R.E., Oudega B., Luirink J.
EMBO Rep. 2:524-529(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH FTSQ BEFORE YIDC.
[15]"Global topology analysis of the Escherichia coli inner membrane proteome."
Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G.
Science 308:1321-1323(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: TOPOLOGY [LARGE SCALE ANALYSIS].
Strain: K12 / MG1655 / ATCC 47076.
[16]"Protein translocation is mediated by oligomers of the SecY complex with one SecY copy forming the channel."
Osborne A.R., Rapoport T.A.
Cell 129:97-110(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH SECA, CHARACTERIZATION OF THE TRANSLOCATING PORE.
[17]"Effects of antibiotics and a proto-oncogene homolog on destruction of protein translocator SecY."
van Stelten J., Silva F., Belin D., Silhavy T.J.
Science 325:753-756(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: COMPLEX DEGRADATION.
Strain: K12 / MC4100.
[18]"Determining the conductance of the SecY protein translocation channel for small molecules."
Saparov S.M., Erlandson K., Cannon K., Schaletzky J., Schulman S., Rapoport T.A., Pohl P.
Mol. Cell 26:501-509(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION OF CHANNEL OPENING, MUTAGENESIS OF 60-ILE--ARG-74; 65-ASN--GLY-70; PHE-67 AND ILE-408.
[19]"The plug domain of the SecY protein stabilizes the closed state of the translocation channel and maintains a membrane seal."
Li W., Schulman S., Boyd D., Erlandson K., Beckwith J., Rapoport T.A.
Mol. Cell 26:511-521(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF 60-ILE--ARG-74 AND 65-ASN--GLY-70.
[20]"Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes."
Egea P.F., Stroud R.M.
Proc. Natl. Acad. Sci. U.S.A. 107:17182-17187(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF 424-MET--ARG-443.
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[21]"Structure of the E. coli protein-conducting channel bound to a translating ribosome."
Mitra K., Schaffitzel C., Shaikh T., Tama F., Jenni S., Brooks C.L. III, Ban N., Frank J.
Nature 438:318-324(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY ELECTRON MICROSCOPY (14.9 ANGSTROMS) OF 1-436 IN COMPLEX WITH THE RIBOSOME AND A NASCENT POLYPEPTIDE CHAIN.
Strain: MRE-600.
[22]"Cryo-EM structure of the ribosome-SecYE complex in the membrane environment."
Frauenfeld J., Gumbart J., Sluis E.O., Funes S., Gartmann M., Beatrix B., Mielke T., Berninghausen O., Becker T., Schulten K., Beckmann R.
Nat. Struct. Mol. Biol. 18:614-621(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY CRYOELECTRON MICROSCOPY IN COMPLEX WITH THE RIBOSOME AND A NASCENT POLYPEPTIDE CHAIN.
[23]"Structure, function, and biogenesis of SecY, an integral membrane protein involved in protein export."
Ito K.
J. Bioenerg. Biomembr. 22:353-367(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[24]"Protein translocation across the bacterial cytoplasmic membrane."
Driessen A.J., Nouwen N.
Annu. Rev. Biochem. 77:643-667(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X01563 Genomic DNA. Translation: CAA25725.1.
U18997 Genomic DNA. Translation: AAA58097.1.
U00096 Genomic DNA. Translation: AAC76325.1.
AP009048 Genomic DNA. Translation: BAE77991.1.
PIRQQECSY. A04473.
RefSeqNP_417759.1. NC_000913.3.
YP_492132.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2AKHelectron microscopy14.90B/Y1-436[»]
2AKIelectron microscopy14.90B/Y1-436[»]
3J01electron microscopy-A8-442[»]
3J45electron microscopy9.50y6-440[»]
3J46electron microscopy10.10y6-440[»]
ProteinModelPortalP0AGA2.
SMRP0AGA2. Positions 8-442.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-59302N.
IntActP0AGA2. 2 interactions.
STRING511145.b3300.

Protein family/group databases

TCDB3.A.5.1.1. the general secretory pathway (sec) family.

Proteomic databases

PaxDbP0AGA2.
PRIDEP0AGA2.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76325; AAC76325; b3300.
BAE77991; BAE77991; BAE77991.
GeneID12934410.
947799.
KEGGecj:Y75_p3876.
eco:b3300.
PATRIC32122032. VBIEscCol129921_3393.

Organism-specific databases

EchoBASEEB0759.
EcoGeneEG10766. secY.

Phylogenomic databases

eggNOGCOG0201.
HOGENOMHOG000080585.
KOK03076.
OMAQTYVISQ.
OrthoDBEOG651SWP.
PhylomeDBP0AGA2.
ProtClustDBPRK09204.

Enzyme and pathway databases

BioCycEcoCyc:SECY.
ECOL316407:JW3262-MONOMER.

Gene expression databases

GenevestigatorP0AGA2.

Family and domain databases

Gene3D1.10.3370.10. 1 hit.
HAMAPMF_01465. SecY.
InterProIPR026593. SecY.
IPR002208. SecY/SEC61-alpha.
IPR023201. SecY_su_dom.
[Graphical view]
PANTHERPTHR10906. PTHR10906. 1 hit.
PfamPF00344. SecY. 1 hit.
[Graphical view]
PIRSFPIRSF004557. SecY. 1 hit.
SUPFAMSSF103491. SSF103491. 1 hit.
TIGRFAMsTIGR00967. 3a0501s007. 1 hit.
PROSITEPS00755. SECY_1. 1 hit.
PS00756. SECY_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0AGA2.
PROP0AGA2.

Entry information

Entry nameSECY_ECOLI
AccessionPrimary (citable) accession number: P0AGA2
Secondary accession number(s): P03844, Q2M6W5
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: April 16, 2014
This is version 73 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

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