Summary: Protein export membrane protein
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This is the Wikipedia entry entitled "SecDF protein-export membrane protein". More...
SecDF protein-export membrane protein Edit Wikipedia article
| SecD_SecF | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | SecD_SecF | ||||||||
| Pfam | PF02355 | ||||||||
| Pfam clan | CL0322 | ||||||||
| InterPro | IPR022645 | ||||||||
| TCDB | 3.A.5 | ||||||||
| OPM superfamily | 16 | ||||||||
| OPM protein | 3aqp | ||||||||
| |||||||||
SecD and SecF are prokaryotic protein export membrane proteins. They are a part of the larger multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC.[1] SecD and SecF are required to maintain a proton motive force.[2]
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.[3] 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).[3] The chaperone protein SecB [4] 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.[5] Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains.[6] Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices.
This family consists of various prokaryotic SecD and SecF protein export membrane proteins. The SecD and SecF equivalents of the Gram-positive bacterium Bacillus subtilis are jointly present in one polypeptide, denoted SecDF, that is required to maintain a high capacity for protein secretion. Unlike the SecD subunit of the pre-protein translocase of E. coli, SecDF of B. subtilis was not required for the release of a mature secretory protein from the membrane, indicating that SecDF is involved in earlier translocation steps.[1] Comparison with SecD and SecF proteins from other organisms revealed the presence of 10 conserved regions in SecDF, some of which appear to be important for SecDF function. Interestingly, the SecDF protein of B. subtilis has 12 putative transmembrane domains. Thus, SecDF does not only show sequence similarity but also structural similarity to secondary solute transporters.[1]
References
- ^ a b c Bolhuis A, Broekhuizen CP, Sorokin A, van Roosmalen ML, Venema G, Bron S, Quax WJ, van Dijl JM (1998). "SecDF of Bacillus subtilis, a molecular Siamese twin required for the efficient secretion of proteins". J. Biol. Chem. 273 (33): 21217–24. PMID 9694879.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ Arkowitz RA, Wickner W (1994). "SecD and SecF are required for the proton electrochemical gradient stimulation of preprotein translocation". EMBO J. 13 (4): 954–63. PMC 394897. PMID 8112309.
{{cite journal}}: Unknown parameter|month=ignored (help) - ^ a b Bieker KL, Phillips GJ, Silhavy TJ (1990). "The sec and prl genes of Escherichia coli". J. Bioenerg. Biomembr. 22 (3): 291–310. PMID 2202721.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ Driessen AJ (2001). "SecB, a molecular chaperone with two faces". Trends Microbiol. 9 (5): 193–6. PMID 11336818.
{{cite journal}}: Unknown parameter|month=ignored (help) - ^ Müller JP (1999). "Effects of pre-protein overexpression on SecB synthesis in Escherichia coli". FEMS Microbiol. Lett. 176 (1): 219–27. PMID 10418149.
{{cite journal}}: Unknown parameter|month=ignored (help) - ^ Breyton C, Haase W, Rapoport TA, Kühlbrandt W, Collinson I (2002). "Three-dimensional structure of the bacterial protein-translocation complex SecYEG". Nature. 418 (6898): 662–5. doi:10.1038/nature00827. PMID 12167867.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link)
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Protein export membrane protein Provide feedback
This family consists of various prokaryotic SecD and SecF protein export membrane proteins. This SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC [1]. SecD and SecF are required to maintain a proton motive force [2].
Literature references
-
Bolhuis A, Broekhuizen CP, Sorokin A, van Roosmalen ML, Venema G, Bron S, Quax WJ, van Dijl JM; , J Biol Chem 1998;273:21217-21224.: SecDF of Bacillus subtilis, a molecular Siamese twin required for the efficient secretion of proteins. PUBMED:9694879 EPMC:9694879
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Arkowitz RA, Wickner W; , EMBO J 1994;13:954-963.: SecD and SecF are required for the proton electrochemical gradient stimulation of preprotein translocation. PUBMED:8112309 EPMC:8112309
Internal database links
| SCOOP: | ACR_tran DUF5693 MMPL Patched Sterol-sensing |
External database links
| Transporter classification: | 3.A.5 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR022813
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 ]. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. 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 SecD and SecF equivalents of the Gram-positive bacterium Bacillus subtilis are jointly present in one polypeptide, denoted SecDF, that is required to maintain a high capacity for protein secretion. Unlike the SecD subunit of the pre-protein translocase of E. coli, SecDF of B. subtilis was not required for the release of a mature secretory protein from the membrane, indicating that SecDF is involved in earlier translocation steps [ PUBMED:9694879 ]. Comparison with SecD and SecF proteins from other organisms revealed the presence of 10 conserved regions in SecDF, some of which appear to be important for SecDF function. Interestingly, the SecDF protein of B. subtilis has 12 putative transmembrane domains. Thus, SecDF does not only show sequence similarity but also structural similarity to secondary solute transporters [ PUBMED:9694879 ].
This entry represents archaeal and bacterial SecD and SecF protein export membrane proteins and their archaeal homologues [ PUBMED:16452406 ]. It is found in association with SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC [ PUBMED:9694879 ]. SecD and SecF are required to maintain a proton motive force [ PUBMED:8112309 ].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan RND_permease (CL0322), which has the following description:
Different members of the RND superfamily have been shown to transport hydrophobic drugs, fatty acids, bile salts, organic solvents, heavy metals, autoinducers and lipooligosaccharides in bacteria [1].
The clan contains the following 5 members:
ACR_tran MMPL Patched SecD_SecF Sterol-sensingAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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| Seed (17) |
Full (15904) |
Representative proteomes | UniProt (84444) |
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| RP15 (2213) |
RP35 (7870) |
RP55 (16698) |
RP75 (28962) |
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| PP/heatmap | 1 | ||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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| Seed (17) |
Full (15904) |
Representative proteomes | UniProt (84444) |
||||
|---|---|---|---|---|---|---|---|
| RP15 (2213) |
RP35 (7870) |
RP55 (16698) |
RP75 (28962) |
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| Raw Stockholm | |||||||
| Gzipped | |||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
| Seed source: | Pfam-B_844 (release 5.2) |
| Previous IDs: | none |
| Type: | Family |
| Sequence Ontology: | SO:0100021 |
| Author: |
Bashton M  , Bateman A
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| Number in seed: | 17 |
| Number in full: | 15904 |
| Average length of the domain: | 185.4 aa |
| Average identity of full alignment: | 28 % |
| Average coverage of the sequence by the domain: | 42.08 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 189 | ||||||||||||
| Family (HMM) version: | 19 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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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 SecD_SecF domain has been found. There are 23 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 sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
