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Protein

Protein translocase subunit SecY

Gene

secY

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.

GO - Biological processi

  1. intracellular protein transmembrane transport Source: EcoliWiki
  2. intracellular protein transport Source: EcoliWiki
  3. protein targeting Source: UniProtKB-HAMAP
  4. protein transport by the Sec complex Source: EcoCyc
Complete GO annotation...

Keywords - Biological processi

Protein transport, Translocation, Transport

Enzyme and pathway databases

BioCyciEcoCyc:SECY.
ECOL316407:JW3262-MONOMER.

Protein family/group databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Protein translocase subunit SecY
Gene namesi
Name:secY
Synonyms:prlA
Ordered Locus Names:b3300, JW3262
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10766. secY.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 2222CytoplasmicCuratedAdd
BLAST
Transmembranei23 – 3513Helical; Name=1CuratedAdd
BLAST
Topological domaini36 – 6025PeriplasmicBy similarityAdd
BLAST
Transmembranei61 – 9636Discontinuously helical; Name=2By similarityAdd
BLAST
Intramembranei61 – 7010Helical; Name=Helix 2ACurated
Intramembranei71 – 766Curated
Intramembranei77 – 9620Helical; Name=Helix 2BCuratedAdd
BLAST
Topological domaini97 – 11519CytoplasmicCuratedAdd
BLAST
Transmembranei116 – 13116Helical; Name=3CuratedAdd
BLAST
Topological domaini132 – 16433PeriplasmicCuratedAdd
BLAST
Transmembranei165 – 17814Helical; Name=4CuratedAdd
BLAST
Topological domaini179 – 1835CytoplasmicCurated
Transmembranei184 – 20017Helical; Name=5CuratedAdd
BLAST
Topological domaini201 – 22323PeriplasmicCuratedAdd
BLAST
Transmembranei224 – 23714Helical; Name=6CuratedAdd
BLAST
Topological domaini238 – 27336CytoplasmicCuratedAdd
BLAST
Transmembranei274 – 28714Helical; Name=7CuratedAdd
BLAST
Topological domaini288 – 31326PeriplasmicCuratedAdd
BLAST
Transmembranei314 – 32916Helical; Name=8CuratedAdd
BLAST
Topological domaini330 – 38051CytoplasmicCuratedAdd
BLAST
Transmembranei381 – 39515Helical; Name=9CuratedAdd
BLAST
Topological domaini396 – 3961PeriplasmicCurated
Transmembranei397 – 41317Helical; Name=10CuratedAdd
BLAST
Topological domaini414 – 44330CytoplasmicCuratedAdd
BLAST

GO - Cellular componenti

  1. integral component of membrane Source: EcoliWiki
  2. integral component of plasma membrane Source: EcoCyc
  3. intracellular Source: GOC
  4. plasma membrane Source: EcoliWiki
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi40 – 401P → S in secY100; temperature-sensitive.
Mutagenesisi60 – 7415Missing: Some loss of viability, supports protein translocation; strongly suppresses defective and missing signal sequences; transient transmembrane channels open. 2 PublicationsAdd
BLAST
Mutagenesisi65 – 706Missing: Grows almost as well as wild-type, supports protein translocation; strongly suppresses defective and missing signal sequences; transient transmembrane channels open. 2 Publications
Mutagenesisi67 – 671F → 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. 1 Publication
Mutagenesisi167 – 1671G → E in secY100; temperature-sensitive.
Mutagenesisi240 – 2401G → D in secY24; temperature-sensitive at 42 degrees Celsius, impairs interaction with SecE even at 30 degrees in vitro. 1 Publication
Mutagenesisi282 – 2821S → R in prlA401; altered signal sequence interaction, transient transmembrane channels open.
Mutagenesisi286 – 2861F → Y in prlA4-1; altered signal sequence interaction.
Mutagenesisi287 – 2871P → L in secY161; altered signal sequence interaction.
Mutagenesisi290 – 2901I → T in secY121; altered signal sequence interaction.
Mutagenesisi357 – 3571R → H in secY39; cold-sensitive.
Mutagenesisi363 – 3631A → S in secY40; cold-sensitive.
Mutagenesisi408 – 4081I → N in prlA4-2; altered signal sequence interaction. 1 Publication
Mutagenesisi424 – 44320Missing: No longer complements secY24, a temperature-sensitive secY mutation. 1 PublicationAdd
BLAST

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 443443Protein translocase subunit SecYPRO_0000131721Add
BLAST

Post-translational modificationi

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.

Proteomic databases

PaxDbiP0AGA2.
PRIDEiP0AGA2.

Expressioni

Gene expression databases

GenevestigatoriP0AGA2.

Interactioni

Subunit structurei

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.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
secAP104084EBI-761422,EBI-543213

Protein-protein interaction databases

DIPiDIP-59302N.
IntActiP0AGA2. 2 interactions.
STRINGi511145.b3300.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AKHelectron microscopy14.90B/Y1-436[»]
2AKIelectron microscopy14.90B/Y1-436[»]
3J45electron microscopy9.50y6-440[»]
3J46electron microscopy10.10y6-440[»]
4V6Melectron microscopy-A8-442[»]
ProteinModelPortaliP0AGA2.
SMRiP0AGA2. Positions 8-442.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AGA2.

Family & Domainsi

Sequence similaritiesi

Belongs to the SecY/SEC61-alpha family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0201.
HOGENOMiHOG000080585.
InParanoidiP0AGA2.
KOiK03076.
OMAiQTYVISQ.
OrthoDBiEOG651SWP.
PhylomeDBiP0AGA2.

Family and domain databases

Gene3Di1.10.3370.10. 1 hit.
HAMAPiMF_01465. SecY.
InterProiIPR026593. SecY.
IPR002208. SecY/SEC61-alpha.
IPR023201. SecY_su_dom.
[Graphical view]
PANTHERiPTHR10906. PTHR10906. 1 hit.
PfamiPF00344. SecY. 1 hit.
[Graphical view]
PIRSFiPIRSF004557. SecY. 1 hit.
SUPFAMiSSF103491. SSF103491. 1 hit.
TIGRFAMsiTIGR00967. 3a0501s007. 1 hit.
PROSITEiPS00755. SECY_1. 1 hit.
PS00756. SECY_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0AGA2-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAKQPGLDFQ SAKGGLGELK RRLLFVIGAL IVFRIGSFIP IPGIDAAVLA
60 70 80 90 100
KLLEQQRGTI IEMFNMFSGG ALSRASIFAL GIMPYISASI IIQLLTVVHP
110 120 130 140 150
TLAEIKKEGE SGRRKISQYT RYGTLVLAIF QSIGIATGLP NMPGMQGLVI
160 170 180 190 200
NPGFAFYFTA VVSLVTGTMF LMWLGEQITE RGIGNGISII IFAGIVAGLP
210 220 230 240 250
PAIAHTIEQA RQGDLHFLVL LLVAVLVFAV TFFVVFVERG QRRIVVNYAK
260 270 280 290 300
RQQGRRVYAA QSTHLPLKVN MAGVIPAIFA SSIILFPATI ASWFGGGTGW
310 320 330 340 350
NWLTTISLYL QPGQPLYVLL YASAIIFFCF FYTALVFNPR ETADNLKKSG
360 370 380 390 400
AFVPGIRPGE QTAKYIDKVM TRLTLVGALY ITFICLIPEF MRDAMKVPFY
410 420 430 440
FGGTSLLIVV VVIMDFMAQV QTLMMSSQYE SALKKANLKG YGR
Length:443
Mass (Da):48,512
Last modified:July 21, 1986 - v1
Checksum:i711CA63CD8809763
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01563 Genomic DNA. Translation: CAA25725.1.
U18997 Genomic DNA. Translation: AAA58097.1.
U00096 Genomic DNA. Translation: AAC76325.1.
AP009048 Genomic DNA. Translation: BAE77991.1.
PIRiA04473. QQECSY.
RefSeqiNP_417759.1. NC_000913.3.
YP_492132.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76325; AAC76325; b3300.
BAE77991; BAE77991; BAE77991.
GeneIDi12934410.
947799.
KEGGiecj:Y75_p3876.
eco:b3300.
PATRICi32122032. VBIEscCol129921_3393.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01563 Genomic DNA. Translation: CAA25725.1.
U18997 Genomic DNA. Translation: AAA58097.1.
U00096 Genomic DNA. Translation: AAC76325.1.
AP009048 Genomic DNA. Translation: BAE77991.1.
PIRiA04473. QQECSY.
RefSeqiNP_417759.1. NC_000913.3.
YP_492132.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AKHelectron microscopy14.90B/Y1-436[»]
2AKIelectron microscopy14.90B/Y1-436[»]
3J45electron microscopy9.50y6-440[»]
3J46electron microscopy10.10y6-440[»]
4V6Melectron microscopy-A8-442[»]
ProteinModelPortaliP0AGA2.
SMRiP0AGA2. Positions 8-442.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59302N.
IntActiP0AGA2. 2 interactions.
STRINGi511145.b3300.

Protein family/group databases

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

Proteomic databases

PaxDbiP0AGA2.
PRIDEiP0AGA2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76325; AAC76325; b3300.
BAE77991; BAE77991; BAE77991.
GeneIDi12934410.
947799.
KEGGiecj:Y75_p3876.
eco:b3300.
PATRICi32122032. VBIEscCol129921_3393.

Organism-specific databases

EchoBASEiEB0759.
EcoGeneiEG10766. secY.

Phylogenomic databases

eggNOGiCOG0201.
HOGENOMiHOG000080585.
InParanoidiP0AGA2.
KOiK03076.
OMAiQTYVISQ.
OrthoDBiEOG651SWP.
PhylomeDBiP0AGA2.

Enzyme and pathway databases

BioCyciEcoCyc:SECY.
ECOL316407:JW3262-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AGA2.
PROiP0AGA2.

Gene expression databases

GenevestigatoriP0AGA2.

Family and domain databases

Gene3Di1.10.3370.10. 1 hit.
HAMAPiMF_01465. SecY.
InterProiIPR026593. SecY.
IPR002208. SecY/SEC61-alpha.
IPR023201. SecY_su_dom.
[Graphical view]
PANTHERiPTHR10906. PTHR10906. 1 hit.
PfamiPF00344. SecY. 1 hit.
[Graphical view]
PIRSFiPIRSF004557. SecY. 1 hit.
SUPFAMiSSF103491. SSF103491. 1 hit.
TIGRFAMsiTIGR00967. 3a0501s007. 1 hit.
PROSITEiPS00755. SECY_1. 1 hit.
PS00756. SECY_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. 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. 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.

Entry informationi

Entry nameiSECY_ECOLI
AccessioniPrimary (citable) accession number: P0AGA2
Secondary accession number(s): P03844, Q2M6W5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: February 4, 2015
This is version 79 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

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.