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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

  • intracellular protein transmembrane transport Source: EcoliWiki
  • intracellular protein transport Source: EcoliWiki
  • protein transport by the Sec complex Source: EcoCyc

Keywordsi

Biological processProtein transport, Translocation, Transport

Enzyme and pathway databases

BioCyciEcoCyc:SECY.

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10766. secY.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 22CytoplasmicCuratedAdd BLAST22
Transmembranei23 – 35Helical; Name=1CuratedAdd BLAST13
Topological domaini36 – 60PeriplasmicBy similarityAdd BLAST25
Transmembranei61 – 96Discontinuously helical; Name=2By similarityAdd BLAST36
Intramembranei61 – 70Helical; Name=Helix 2ACurated10
Intramembranei71 – 76Curated6
Intramembranei77 – 96Helical; Name=Helix 2BCuratedAdd BLAST20
Topological domaini97 – 115CytoplasmicCuratedAdd BLAST19
Transmembranei116 – 131Helical; Name=3CuratedAdd BLAST16
Topological domaini132 – 164PeriplasmicCuratedAdd BLAST33
Transmembranei165 – 178Helical; Name=4CuratedAdd BLAST14
Topological domaini179 – 183CytoplasmicCurated5
Transmembranei184 – 200Helical; Name=5CuratedAdd BLAST17
Topological domaini201 – 223PeriplasmicCuratedAdd BLAST23
Transmembranei224 – 237Helical; Name=6CuratedAdd BLAST14
Topological domaini238 – 273CytoplasmicCuratedAdd BLAST36
Transmembranei274 – 287Helical; Name=7CuratedAdd BLAST14
Topological domaini288 – 313PeriplasmicCuratedAdd BLAST26
Transmembranei314 – 329Helical; Name=8CuratedAdd BLAST16
Topological domaini330 – 380CytoplasmicCuratedAdd BLAST51
Transmembranei381 – 395Helical; Name=9CuratedAdd BLAST15
Topological domaini396PeriplasmicCurated1
Transmembranei397 – 413Helical; Name=10CuratedAdd BLAST17
Topological domaini414 – 443CytoplasmicCuratedAdd BLAST30

GO - Cellular componenti

  • integral component of membrane Source: EcoliWiki
  • integral component of plasma membrane Source: CACAO
  • intracellular Source: GOC
  • plasma membrane Source: EcoCyc

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi40P → S in secY100; temperature-sensitive. 1
Mutagenesisi60 – 74Missing : Some loss of viability, supports protein translocation; strongly suppresses defective and missing signal sequences; transient transmembrane channels open. 2 PublicationsAdd BLAST15
Mutagenesisi65 – 70Missing : Grows almost as well as wild-type, supports protein translocation; strongly suppresses defective and missing signal sequences; transient transmembrane channels open. 2 Publications6
Mutagenesisi67F → 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 Publication1
Mutagenesisi167G → E in secY100; temperature-sensitive. 1
Mutagenesisi240G → D in secY24; temperature-sensitive at 42 degrees Celsius, impairs interaction with SecE even at 30 degrees in vitro. 1 Publication1
Mutagenesisi282S → R in prlA401; altered signal sequence interaction, transient transmembrane channels open. 1
Mutagenesisi286F → Y in prlA4-1; altered signal sequence interaction. 1
Mutagenesisi287P → L in secY161; altered signal sequence interaction. 1
Mutagenesisi290I → T in secY121; altered signal sequence interaction. 1
Mutagenesisi357R → H in secY39; cold-sensitive. 1
Mutagenesisi363A → S in secY40; cold-sensitive. 1
Mutagenesisi408I → N in prlA4-2; altered signal sequence interaction. 1 Publication1
Mutagenesisi424 – 443Missing : No longer complements secY24, a temperature-sensitive secY mutation. 1 PublicationAdd BLAST20

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001317211 – 443Protein translocase subunit SecYAdd BLAST443

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.

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

BioGridi4263404. 321 interactors.
DIPiDIP-59302N.
IntActiP0AGA2. 2 interactors.
STRINGi511145.b3300.

Structurei

Secondary structure

1443
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi17 – 36Combined sources20
Beta strandi41 – 44Combined sources4
Helixi46 – 52Combined sources7
Helixi59 – 65Combined sources7
Turni66 – 69Combined sources4
Turni71 – 75Combined sources5
Helixi83 – 98Combined sources16
Helixi100 – 106Combined sources7
Helixi110 – 138Combined sources29
Helixi155 – 176Combined sources22
Turni178 – 181Combined sources4
Beta strandi182 – 184Combined sources3
Helixi186 – 196Combined sources11
Helixi200 – 208Combined sources9
Turni209 – 213Combined sources5
Helixi217 – 239Combined sources23
Beta strandi242 – 251Combined sources10
Beta strandi258 – 267Combined sources10
Beta strandi269 – 272Combined sources4
Helixi274 – 290Combined sources17
Turni291 – 294Combined sources4
Helixi301 – 309Combined sources9
Helixi315 – 336Combined sources22
Helixi339 – 348Combined sources10
Helixi360 – 394Combined sources35
Beta strandi401 – 403Combined sources3
Helixi404 – 426Combined sources23

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5ABBelectron microscopy8.00A1-443[»]
5GAEelectron microscopy3.33g1-443[»]
5MG3electron microscopy14.00Y1-443[»]
ProteinModelPortaliP0AGA2.
SMRiP0AGA2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AGA2.

Family & Domainsi

Sequence similaritiesi

Belongs to the SecY/SEC61-alpha family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105CGG. Bacteria.
COG0201. LUCA.
HOGENOMiHOG000080585.
InParanoidiP0AGA2.
KOiK03076.
OMAiQTYVISQ.
PhylomeDBiP0AGA2.

Family and domain databases

Gene3Di1.10.3370.10. 1 hit.
HAMAPiMF_01465. SecY. 1 hit.
InterProiView protein in InterPro
IPR026593. SecY.
IPR002208. SecY/SEC61-alpha.
IPR030659. SecY_CS.
IPR023201. SecY_su_dom.
PANTHERiPTHR10906. PTHR10906. 1 hit.
PfamiView protein in Pfam
PF00344. SecY. 1 hit.
PIRSFiPIRSF004557. SecY. 1 hit.
SUPFAMiSSF103491. SSF103491. 1 hit.
TIGRFAMsiTIGR00967. 3a0501s007. 1 hit.
PROSITEiView protein in PROSITE
PS00755. SECY_1. 1 hit.
PS00756. SECY_2. 1 hit.

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.
WP_001118861.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76325; AAC76325; b3300.
BAE77991; BAE77991; BAE77991.
GeneIDi947799.
KEGGiecj:JW3262.
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.
WP_001118861.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5ABBelectron microscopy8.00A1-443[»]
5GAEelectron microscopy3.33g1-443[»]
5MG3electron microscopy14.00Y1-443[»]
ProteinModelPortaliP0AGA2.
SMRiP0AGA2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263404. 321 interactors.
DIPiDIP-59302N.
IntActiP0AGA2. 2 interactors.
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.
GeneIDi947799.
KEGGiecj:JW3262.
eco:b3300.
PATRICi32122032. VBIEscCol129921_3393.

Organism-specific databases

EchoBASEiEB0759.
EcoGeneiEG10766. secY.

Phylogenomic databases

eggNOGiENOG4105CGG. Bacteria.
COG0201. LUCA.
HOGENOMiHOG000080585.
InParanoidiP0AGA2.
KOiK03076.
OMAiQTYVISQ.
PhylomeDBiP0AGA2.

Enzyme and pathway databases

BioCyciEcoCyc:SECY.

Miscellaneous databases

EvolutionaryTraceiP0AGA2.
PROiP0AGA2.

Family and domain databases

Gene3Di1.10.3370.10. 1 hit.
HAMAPiMF_01465. SecY. 1 hit.
InterProiView protein in InterPro
IPR026593. SecY.
IPR002208. SecY/SEC61-alpha.
IPR030659. SecY_CS.
IPR023201. SecY_su_dom.
PANTHERiPTHR10906. PTHR10906. 1 hit.
PfamiView protein in Pfam
PF00344. SecY. 1 hit.
PIRSFiPIRSF004557. SecY. 1 hit.
SUPFAMiSSF103491. SSF103491. 1 hit.
TIGRFAMsiTIGR00967. 3a0501s007. 1 hit.
PROSITEiView protein in PROSITE
PS00755. SECY_1. 1 hit.
PS00756. SECY_2. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSECY_ECOLI
AccessioniPrimary (citable) accession number: P0AGA2
Secondary accession number(s): P03844, Q2M6W5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: February 15, 2017
This is version 93 of the entry and version 1 of the sequence. See 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

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 one 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.