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19  structures 5237  species 3  interactions 6369  sequences 14  architectures

Family: SecY (PF00344)

Summary: SecY translocase

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This is the Wikipedia entry entitled "SecY protein". More...

SecY protein Edit Wikipedia article

eubacterial secY protein
PDB 1rh5 EBI.jpg
Structure of a protein-conducting channel.[1]
Identifiers
Symbol SecY
Pfam PF00344
InterPro IPR002208
PROSITE PDOC00612
SCOP 1rh5
SUPERFAMILY 1rh5
TCDB 3.A.5
OPM superfamily 19
OPM protein 1rh5

The SecY protein is the main transmembrane subunit of the eubacterial Sec or Type II secretory pathway and a protein-secreting ATPase complex, also known as a translocon.

Secretion of some proteins carrying a signal-peptide across the inner membrane in Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component within the membrane.[2] From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.

The translocase pathway comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF).[2] The chaperone protein SecB[3] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion.[4] The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains.[5] Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices.

The eubacterial secY protein[6] interacts with the signal sequences of secretory proteins as well as with two other components of the protein translocation system: secA and secE. SecY is an integral plasma membrane protein of 419 to 492 amino acid residues that apparently contains 10 transmembrane (TM), 6 cytoplasmic and 5 periplasmic regions.

Cytoplasmic regions 2 and 3, and TM domains 1, 2, 4, 5, 7 and 10 are well conserved: the conserved cytoplasmic regions are believed to interact with cytoplasmic secretion factors, while the TM domains may participate in protein export.[7] Homologs of secY are found in archaebacteria.[8] SecY is also encoded in the chloroplast genome of some algae[9] where it could be involved in a prokaryotic-like protein export system across the two membranes of the chloroplast endoplasmic reticulum (CER) which is present in chromophyte and cryptophyte algae.

Subfamilies[edit]

Human proteins containing this domain[edit]

SEC61A1; SEC61A2;

References[edit]

  1. ^ Van den Berg B, Clemons WM, Collinson I, et al. (January 2004). "X-ray structure of a protein-conducting channel". Nature 427 (6969): 36–44. doi:10.1038/nature02218. PMID 14661030. 
  2. ^ a b Bieker KL, Phillips GJ, Silhavy TJ (1990). "The sec and prl genes of Escherichia coli". J. Bioenerg. Biomembr. 22 (3): 291–310. doi:10.1007/BF00763169. PMID 2202721. 
  3. ^ Driessen AJ (2001). "SecB, a molecular chaperone with two faces". Trends Microbiol. 9 (5): 193–196. doi:10.1016/S0966-842X(01)01980-1. PMID 11336818. 
  4. ^ Muller JP (1999). "Effects of pre-protein overexpression on SecB synthesis in Escherichia coli". FEMS Microbiol. Lett. 176 (1): 219–227. PMID 10418149. 
  5. ^ Rapoport TA, Breyton C, Haase W, Kuhlbrandt W, Collinson I (2002). "Three-dimensional structure of the bacterial protein-translocation complex SecYEG". Nature 418 (6898): 662–665. doi:10.1038/nature00827. PMID 12167867. 
  6. ^ Ito K (1992). "SecY and integral membrane components of the Escherichia coli protein translocation system". Mol. Microbiol. 6 (17): 2423–2428. doi:10.1111/j.1365-2958.1992.tb01417.x. PMID 1406280. 
  7. ^ Oliver DB, Suh JW, Thomas SM, Dolan KM, Price CW, Boylan SA (1990). "Isolation of a secY homologue from Bacillus subtilis: evidence for a common protein export pathway in eubacteria". Mol. Microbiol. 4 (2): 305–314. doi:10.1111/j.1365-2958.1990.tb00597.x. PMID 2110998. 
  8. ^ Auer J, Spicker G, Bock A (1991). "Presence of a gene in the archaebacterium Methanococcus vannielii homologous to secY of eubacteria". Biochimie 73 (6): 683–688. doi:10.1016/0300-9084(91)90048-6. PMID 1764515. 
  9. ^ Douglas SE (1992). "A secY homologue is found in the plastid genome of Cryptomonas phi". FEBS Lett. 298 (1): 93–96. doi:10.1016/0014-5793(92)80029-G. PMID 1544427. 

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SecY translocase Provide feedback

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002208

Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component [PUBMED:2202721]. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.

The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) [PUBMED:2202721]. The chaperone protein SecB [PUBMED:11336818] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion [PUBMED:10418149]. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains [PUBMED:12167867]. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices.

The eubacterial secY protein [PUBMED:1406280] interacts with the signal sequences of secretory proteins as well as with two other components of the protein translocation system: secA and secE. SecY is an integral plasma membrane protein of 419 to 492 amino acid residues that apparently contains 10 transmembrane (TM), 6 cytoplasmic and 5 periplasmic regions.

Cytoplasmic regions 2 and 3, and TM domains 1, 2, 4, 5, 7 and 10 are well conserved: the conserved cytoplasmic regions are believed to interact with cytoplasmic secretion factors, while the TM domains may participate in protein export [PUBMED:2110998]. Homologs of secY are found in archaebacteria [PUBMED:1764515]. SecY is also encoded in the chloroplast genome of some algae [PUBMED:1544427] where it could be involved in a prokaryotic-like protein export system across the two membranes of the chloroplast endoplasmic reticulum (CER) which is present in chromophyte and cryptophyte algae.

Gene Ontology

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Domain organisation

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Alignments

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(157)
Full
(6369)
Representative proteomes NCBI
(4121)
Meta
(3873)
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(523)
RP35
(976)
RP55
(1295)
RP75
(1533)
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  Seed
(157)
Full
(6369)
Representative proteomes NCBI
(4121)
Meta
(3873)
RP15
(523)
RP35
(976)
RP55
(1295)
RP75
(1533)
Alignment:
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  Seed
(157)
Full
(6369)
Representative proteomes NCBI
(4121)
Meta
(3873)
RP15
(523)
RP35
(976)
RP55
(1295)
RP75
(1533)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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Curation and family details

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Seed source: Prosite
Previous IDs: secY;
Type: Family
Author: Finn RD
Number in seed: 157
Number in full: 6369
Average length of the domain: 333.00 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 79.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.2 22.2
Trusted cut-off 22.3 22.2
Noise cut-off 21.8 21.7
Model length: 346
Family (HMM) version: 15
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Species distribution

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Interactions

There are 3 interactions for this family. More...

Sec61_beta SecY Plug_translocon

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SecY domain has been found. There are 19 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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