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Escherichia coli K-12 substr. MG1655 Polypeptide: SecD



Gene: secD Accession Numbers: EG10938 (EcoCyc), b0408, ECK0402

Regulation Summary Diagram: ?

Component of:
SecD-SecF-YajC-YidC Secretion Complex (extended summary available)
Sec Holo-Translocon (extended summary available)

Summary:
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)
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

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0015031 - protein transport Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Gardel87]
GO:0006605 - protein targeting Inferred by computational analysis [GOA06]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a]
GO:0006886 - intracellular protein transport Inferred by computational analysis [GOA01a]
GO:0043952 - protein transport by the Sec complex Inferred by computational analysis [GOA06]
GO:0065002 - intracellular protein transmembrane transport Inferred by computational analysis [GOA06]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0015450 - P-P-bond-hydrolysis-driven protein transmembrane transporter activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, DiazMejia09, Zhang07, Daley05]
GO:0005622 - intracellular Inferred by computational analysis [GOA06]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [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

Essentiality data for secD knockouts: ?

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

Subunit composition of SecD-SecF-YajC-YidC Secretion Complex = [YidC][YajC][SecF][SecD]
         inner-membrane protein insertion factor = YidC (extended summary available)

Component of: Sec Holo-Translocon (extended summary available)

Summary:
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 [Duong97b]. 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 [Danese98a].


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)

Summary:
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].

Reviews: [Lycklama12, duPlessis11, Driessen08, Driessen98, deKeyzer03, Manting00, Gold07a].
Comments: [Duong14]

Citations: [Ojemalm13]

Molecular Weight: 250.0 kD (experimental) [Schulze14]

GO Terms:

Biological Process: GO:0043952 - protein transport by the Sec complex Inferred from experiment [Schulze14]
GO:0065002 - intracellular protein transmembrane transport Inferred from experiment [Schulze14]
Molecular Function: GO:0009977 - proton motive force dependent protein transmembrane transporter activity Inferred from experiment [Schulze14]
GO:0015462 - protein-transmembrane transporting ATPase activity Inferred from experiment [Schulze14]
Cellular Component: GO:0031522 - cell envelope Sec protein transport complex Inferred from experiment [Schulze14]

Credits:
Last-Curated ? 06-Jul-2014 by Mackie A , Macquarie University


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 10 -> 29
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Sequence-Conflict 78
[Gardel90, UniProt10a]
Alternate sequence: F → S; UniProt: (in Ref. 1; CAA39634);
Sequence-Conflict 155
[Gardel90, UniProt10a]
Alternate sequence: R → A; UniProt: (in Ref. 1; CAA39634);
Protein-Segment 279 -> 426
[UniProt11a]
UniProt: Required for protein export; Sequence Annotation Type: region of interest.
Transmembrane-Region 456 -> 472
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Transmembrane-Region 502 -> 518
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Mutagenesis-Variant 519
[Tsukazaki11, UniProt11a]
Alternate sequence: D → N; UniProt: Abolishes protein translocation.
Transmembrane-Region 564 -> 580
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Transmembrane-Region 586 -> 605
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: probable;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0408 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10938; confirmed by SwissProt match.


References

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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

Danese98a: Danese PN, Silhavy TJ (1998). "Targeting and assembly of periplasmic and outer-membrane proteins in Escherichia coli." Annu Rev Genet 32;59-94. PMID: 9928475

deKeyzer03: de Keyzer J, van der Does C, Driessen AJ (2003). "The bacterial translocase: a dynamic protein channel complex." Cell Mol Life Sci 60(10);2034-52. PMID: 14618254

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

Driessen08: Driessen AJ, Nouwen N (2008). "Protein translocation across the bacterial cytoplasmic membrane." Annu Rev Biochem 77;643-67. PMID: 18078384

Driessen98: Driessen AJ, Fekkes P, van der Wolk JP (1998). "The Sec system." Curr Opin Microbiol 1(2);216-22. PMID: 10066476

Duong14: Duong F (2014). "Capturing the bacterial holo-complex." Proc Natl Acad Sci U S A 111(13);4739-40. PMID: 24707040

Duong97b: Duong F, Wickner W (1997). "The SecDFyajC domain of preprotein translocase controls preprotein movement by regulating SecA membrane cycling." EMBO J 16(16);4871-9. PMID: 9305629

duPlessis11: du Plessis DJ, Nouwen N, Driessen AJ (2011). "The Sec translocase." Biochim Biophys Acta 1808(3);851-65. PMID: 20801097

Gardel87: Gardel C, Benson S, Hunt J, Michaelis S, Beckwith J (1987). "secD, a new gene involved in protein export in Escherichia coli." J Bacteriol 169(3);1286-90. PMID: 3029032

Gardel90: Gardel C, Johnson K, Jacq A, Beckwith J (1990). "The secD locus of E.coli codes for two membrane proteins required for protein export." EMBO J 9(10);3209-16. PMID: 2170107

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Gold07a: Gold VA, Duong F, Collinson I (2007). "Structure and function of the bacterial Sec translocon." Mol Membr Biol 24(5-6);387-94. PMID: 17710643

Lycklama12: Lycklama A Nijeholt JA, Driessen AJ (2012). "The bacterial Sec-translocase: structure and mechanism." Philos Trans R Soc Lond B Biol Sci 367(1592);1016-28. PMID: 22411975

Manting00: Manting EH, Driessen AJ (2000). "Escherichia coli translocase: the unravelling of a molecular machine." Mol Microbiol 37(2);226-38. PMID: 10931320

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

Nouwen02: Nouwen N, Driessen AJ (2002). "SecDFyajC forms a heterotetrameric complex with YidC." Mol Microbiol 44(5);1397-405. PMID: 12068816

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

Pogliano94: Pogliano KJ, Beckwith J (1994). "Genetic and molecular characterization of the Escherichia coli secD operon and its products." J Bacteriol 176(3);804-14. PMID: 7507921

Pogliano94a: Pogliano JA, Beckwith J (1994). "SecD and SecF facilitate protein export in Escherichia coli." EMBO J 13(3);554-61. PMID: 8313900

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

Other References Related to Gene Regulation

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Nov 24, 2014, biocyc14.