|Gene:||secD||Accession Numbers: EG10938 (EcoCyc), b0408, ECK0402|
SecD is a membrane component of the SecD/SecF/YajC/YidC complex, which is itself a subclass of the Sec protein secretion complex. Deletions of secD result in cold-sensitive mutants which could be complemented by plasmids expressing the gene [Gardel87]. SecD/SecF/YajC/YidC are believed to stabilize the SecYEG complex, facilitating the insertion of SecA and its bound preprotein into the inner membrane.
Gene Citations: [Pogliano94]
Locations: inner membrane
|Map Position: [426,871 -> 428,718] (9.2 centisomes, 33°)||Length: 1848 bp / 615 aa|
Molecular Weight of Polypeptide: 66.632 kD (from nucleotide sequence)
Unification Links: ASAP:ABE-0001417 , CGSC:17893 , DIP:DIP-35837N , EchoBASE:EB0931 , EcoGene:EG10938 , EcoliWiki:b0408 , Mint:MINT-1309074 , ModBase:P0AG90 , OU-Microarray:b0408 , PortEco:secD , PR:PRO_000023925 , Pride:P0AG90 , Protein Model Portal:P0AG90 , RefSeq:NP_414942 , RegulonDB:EG10938 , SMR:P0AG90 , String:511145.b0408 , UniProt:P0AG90
Relationship Links: InterPro:IN-FAMILY:IPR005791 , InterPro:IN-FAMILY:IPR022645 , InterPro:IN-FAMILY:IPR022646 , InterPro:IN-FAMILY:IPR022813 , InterPro:IN-FAMILY:IPR027398 , Pfam:IN-FAMILY:PF02355 , Pfam:IN-FAMILY:PF07549 , Pfam:IN-FAMILY:PF13721
|Biological Process:||GO:0015031 - protein transport
GO:0006605 - protein targeting [GOA06]
GO:0006810 - transport [UniProtGOA11a]
GO:0006886 - intracellular protein transport [GOA01a]
GO:0043952 - protein transport by the Sec complex [GOA06]
GO:0065002 - intracellular protein transmembrane transport [GOA06]
|Molecular Function:||GO:0005515 - protein binding
GO:0015450 - P-P-bond-hydrolysis-driven protein transmembrane transporter activity [GOA01a]
|Cellular Component:||GO:0005886 - plasma membrane
[UniProtGOA11, UniProtGOA11a, GOA06, DiazMejia09, Zhang07, Daley05]
GO:0005622 - intracellular [GOA06]
GO:0016020 - membrane [UniProtGOA11a]
GO:0016021 - integral component of membrane [UniProtGOA11a]
|MultiFun Terms:||cell structure → membrane|
|transport → Channel-type Transporters → Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters → The Type II (General) Secretory Pathway (IISP) Family|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||No||37||Aerobic||7||No [Baba06, Comment 1]|
Subunit of: SecD-SecF-YajC-YidC Secretion Complex
Component of: Sec Holo-Translocon (extended summary available)
SecD/SecF/YajC and YidC are all components of the Sec protein secretion pathway. They are believed to work in conjunction with SecYEG to stabilize the insertion of SecA and its bound preprotein into the inner membrane.
In studies of conditional lethal mutations of secD and secF genes, secA transcription was found to be stimulated due to severe general protein translocation defects. Deletions of secD result in cold-sensitive mutations which could be complemented by plasmids containing the gene [Gardel87]. Overexpression of SecD and SecF increases translocation in wild-type cells [Pogliano94a]. Within the same operon as secD and secF is a third gene known as yajC which may also have a role in protein translocation [Pogliano94]. Co-purification studies [Samuelson00] indicate that YidC is associated with the SecYEG translocase complex and plays a role in the assembly of inner membrane proteins. Subsequent studies [Nouwen02] show that, under conditions of SecD/SecF/YajC overproduction, YidC forms a heterotetrameric complex with SecD/SecF/YajC.
In vitro reconstitution studies demonstrated that the presence of SecD/SecF/YajC stabilizes the SecA insertion complex and inhibits movement of the SecA bound precursor in either direction [Duong97]. If this model holds true, then the SecD/SecF/YajC/YidC stabilization complex must be released from the SecYEG complex or be otherwise inactivated in order for SecA to de-insert from the complex and to begin another round of stepwise translocation powered by ATP hydrolysis [Danese98].
Subunit of: Sec Holo-Translocon
Synonyms: Sec translocation complex
Subunit composition of
Sec Holo-Translocon = [(YidC)(YajC)(SecF)(SecD)][(SecE)(SecG)(SecY)]
SecD-SecF-YajC-YidC Secretion Complex = (YidC)(YajC)(SecF)(SecD) (extended summary available)
inner-membrane protein insertion factor = YidC (extended summary available)
SecYEG translocase = (SecE)(SecG)(SecY) (extended summary available)
The Sec 'holo-translocon' (HTL) is a large multisubunit complex that mediates the transport of nascent polypeptides across, or their integration into, the cytoplasmic membrane. The holo-translocon is a seven subunit complex containing an inner membrane heterotrimeric SecYEG complex that forms the protein conducting channel plus an ancillary complex, SecDFYajC and the Yid C membrane protein, both of which interact with SecYEG to enhance protein transport or integration. The energy for protein translocation is provided by the motor protein ATPase SecA and the proton motive force. The HTL complex is less effective in ATP-dependent SecA-driven protein secretion and more dependent on the PMF [Schulze14].
Simultaneous overexpression of all 7 subunits of the sec HTL facilitates purification and isolation of a complex that is competent for protein secretion and for membrane protein insertion in vitro. The complex contains one copy of SecYEG, one copy of SecDFYajC and one copy of YidC. The HTL associates preferentially with ribosomes displaying nascent peptide. Protein translocation in HTL containing proteoliposomes is stimulated by cardiolipin and by the PMF [Schulze14].
Two pathways of protein translocation converge at the Sec translocon. In the posttranslational pathway the newly synthesised polypeptide is bound by SecB, a cytosolic chaperone which aids targeting to the membrane and maintains a translocation competent conformation of the pre-protein, while in the co-translational pathway the SRP complex binds to the nascent protein as it emerges from the ribosome and the SRP/ribosome/protein complex is then targeted to the Sec translocase.
An experimental approach using alkaline phosphatase (PhoA) fusions to protein signal sequences has allowed discrimination between the major modes of transport, including the Sec protein translocase, across the inner membrane [Marrichi08].
Molecular Weight: 250.0 kD (experimental) [Schulze14]
|Biological Process:||GO:0043952 - protein transport by the Sec complex
GO:0065002 - intracellular protein transmembrane transport [Schulze14]
|Molecular Function:||GO:0009977 - proton motive force dependent protein transmembrane transporter activity
GO:0015462 - protein-transmembrane transporting ATPase activity [Schulze14]
|Cellular Component:||GO:0031522 - cell envelope Sec protein transport complex [Schulze14]|
|Transmembrane-Region||10 -> 29|
|Protein-Segment||279 -> 426|
|Transmembrane-Region||456 -> 472|
|Transmembrane-Region||502 -> 518|
|Transmembrane-Region||564 -> 580|
|Transmembrane-Region||586 -> 605|
10/20/97 Gene b0408 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10938; confirmed by SwissProt match.
Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554
Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043
DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114
Marrichi08: Marrichi MJ, Camacho L, Russell DG, Delisa MP (2008). "Genetic toggling of alkaline phosphatase folding reveals signal peptides for all major modes of transport across the inner membrane of bacteria." J Biol Chem 283(50):35223-35. PMID: 18819916
Ojemalm13: Ojemalm K, Botelho SC, Studle C, von Heijne G (2013). "Quantitative analysis of SecYEG-mediated insertion of transmembrane α-helices into the bacterial inner membrane." J Mol Biol 425(15);2813-22. PMID: 23659793
Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554
Samuelson00: Samuelson JC, Chen M, Jiang F, Moller I, Wiedmann M, Kuhn A, Phillips GJ, Dalbey RE (2000). "YidC mediates membrane protein insertion in bacteria." Nature 406(6796);637-41. PMID: 10949305
Schulze14: Schulze RJ, Komar J, Botte M, Allen WJ, Whitehouse S, Gold VA, Lycklama A Nijeholt JA, Huard K, Berger I, Schaffitzel C, Collinson I (2014). "Membrane protein insertion and proton-motive-force-dependent secretion through the bacterial holo-translocon SecYEG-SecDF-YajC-YidC." Proc Natl Acad Sci U S A 111(13);4844-9. PMID: 24550475
Tsukazaki11: Tsukazaki T, Mori H, Echizen Y, Ishitani R, Fukai S, Tanaka T, Perederina A, Vassylyev DG, Kohno T, Maturana AD, Ito K, Nureki O (2011). "Structure and function of a membrane component SecDF that enhances protein export." Nature 474(7350);235-8. PMID: 21562494
Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111
Reuter91: Reuter K, Slany R, Ullrich F, Kersten H (1991). "Structure and organization of Escherichia coli genes involved in biosynthesis of the deazaguanine derivative queuine, a nutrient factor for eukaryotes." J Bacteriol 173(7);2256-64. PMID: 1706703
Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220
©2014 SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493