P0AGA2 (SECY_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protein translocase subunit SecY

Gene names

Name:	secY
Synonyms:	prlA
Ordered Locus Names:	b3300, JW3262

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	443 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	Protein transport Translocation Transport
Cellular component	Cell inner membrane Cell membrane Membrane
Domain	Transmembrane Transmembrane helix
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	intracellular protein transmembrane transport Inferred from mutant phenotype Ref.7. Source: EcoliWiki protein targeting Inferred from electronic annotation. Source: HAMAP protein transport by the Sec complex Inferred from mutant phenotype Ref.7. Source: EcoliWiki
Cellular_component	integral to membrane Inferred from direct assay PubMed 3004955. Source: EcoliWiki plasma membrane Inferred from direct assay PubMed 3004955. Source: EcoliWiki
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
secA	P10408	4	EBI-761422,EBI-543213

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 443	443	Protein translocase subunit SecY HAMAP-Rule MF_01465		PRO_0000131721
Regions
	Topological domain	1 – 22	22	Cytoplasmic Probable
	Transmembrane	23 – 35	13	Helical; Name=1; Probable
	Topological domain	36 – 60	25	Periplasmic By similarity
	Transmembrane	61 – 96	36	Discontinuously helical; Name=2; By similarity
	Intramembrane	61 – 70	10	Helical; Name=Helix 2A; Probable
	Intramembrane	71 – 76	6	Probable
	Intramembrane	77 – 96	20	Helical; Name=Helix 2B; Probable
	Topological domain	97 – 115	19	Cytoplasmic Probable
	Transmembrane	116 – 131	16	Helical; Name=3; Probable
	Topological domain	132 – 164	33	Periplasmic Probable
	Transmembrane	165 – 178	14	Helical; Name=4; Probable
	Topological domain	179 – 183	5	Cytoplasmic Probable
	Transmembrane	184 – 200	17	Helical; Name=5; Probable
	Topological domain	201 – 223	23	Periplasmic Probable
	Transmembrane	224 – 237	14	Helical; Name=6; Probable
	Topological domain	238 – 273	36	Cytoplasmic Probable
	Transmembrane	274 – 287	14	Helical; Name=7; Probable
	Topological domain	288 – 313	26	Periplasmic Probable
	Transmembrane	314 – 329	16	Helical; Name=8; Probable
	Topological domain	330 – 380	51	Cytoplasmic Probable
	Transmembrane	381 – 395	15	Helical; Name=9; Probable
	Topological domain	396	1	Periplasmic Probable
	Transmembrane	397 – 413	17	Helical; Name=10; Probable
	Topological domain	414 – 443	30	Cytoplasmic Probable
Experimental info
	Mutagenesis	40	1	P → S in secY100; temperature-sensitive.
	Mutagenesis	60 – 74	15	Missing: Some loss of viability, supports protein translocation; strongly suppresses defective and missing signal sequences; transient transmembrane channels open. Ref.18 Ref.19
	Mutagenesis	65 – 70	6	Missing: 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
	Mutagenesis	67	1	F → 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
	Mutagenesis	167	1	G → E in secY100; temperature-sensitive.
	Mutagenesis	240	1	G → D in secY24; temperature-sensitive at 42 degrees Celsius, impairs interaction with SecE even at 30 degrees in vitro. Ref.11
	Mutagenesis	282	1	S → R in prlA401; altered signal sequence interaction, transient transmembrane channels open.
	Mutagenesis	286	1	F → Y in prlA4-1; altered signal sequence interaction.
	Mutagenesis	287	1	P → L in secY161; altered signal sequence interaction.
	Mutagenesis	290	1	I → T in secY121; altered signal sequence interaction.
	Mutagenesis	357	1	R → H in secY39; cold-sensitive.
	Mutagenesis	363	1	A → S in secY40; cold-sensitive.
	Mutagenesis	408	1	I → N in prlA4-2; altered signal sequence interaction. Ref.18
	Mutagenesis	424 – 443	20	Missing: No longer complements secY24, a temperature-sensitive secY mutation. Ref.20

Sequences

	Sequence		Length	Mass (Da)
	P0AGA2 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 711CA63CD8809763	FASTA	443	48,512
	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

References

	« Hide 'large scale' referencesShow '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 277:1453-1474(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.

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.

PIR

QQECSY. A04473.

RefSeq

NP_417759.1. NC_000913.2.
YP_492132.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2AKH	electron microscopy	14.90	B/Y	1-436	[»]
2AKI	electron microscopy	14.90	B/Y	1-436	[»]
3J01	electron microscopy	-	A	8-442	[»]

ProteinModelPortal

P0AGA2.

SMR

P0AGA2. Positions 8-442.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-59302N.

IntAct

P0AGA2. 2 interactions.

STRING

511145.b3300.

Protein family/group databases

TCDB

3.A.5.1.1. general secretory pathway (Sec) family.

Proteomic databases

PaxDb

P0AGA2.

PRIDE

P0AGA2.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76325; AAC76325; b3300.
BAE77991; BAE77991; BAE77991.

GeneID

12934410.
947799.

KEGG

ecj:Y75_p3876.
eco:b3300.

PATRIC

32122032. VBIEscCol129921_3393.

Organism-specific databases

EchoBASE

EB0759.

EcoGene

EG10766. secY.

Phylogenomic databases

eggNOG

COG0201.

HOGENOM

HOG000080585.

KO

K03076.

OMA

FIMWLGE.

ProtClustDB

PRK09204.

Enzyme and pathway databases

BioCyc

EcoCyc:SECY.
ECOL316407:JW3262-MONOMER.

Gene expression databases

Genevestigator

P0AGA2.

Family and domain databases

Gene3D

1.10.3370.10. 1 hit.

HAMAP

MF_01465. SecY.

InterPro

IPR026593. SecY.
IPR002208. SecY/SEC61-alpha.
IPR023201. SecY_su_dom.
[Graphical view]

PANTHER

PTHR10906. PTHR10906. 1 hit.

Pfam

PF00344. SecY. 1 hit.
[Graphical view]

PIRSF

PIRSF004557. SecY. 1 hit.

SUPFAM

SSF103491. SecY. 1 hit.

TIGRFAMs

TIGR00967. 3a0501s007. 1 hit.

PROSITE

PS00755. SECY_1. 1 hit.
PS00756. SECY_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0AGA2.

Entry information

Entry name

SECY_ECOLI

Accession

Primary (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:	May 1, 2013
This is version 66 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program