SECD_ECOLI
ID SECD_ECOLI Reviewed; 615 AA.
AC P0AG90; P19673; P72348; P77531; Q2MC18;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Protein translocase subunit SecD;
DE AltName: Full=Sec translocon accessory complex subunit SecD;
GN Name=secD; OrderedLocusNames=b0408, JW0398;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=2170107; DOI=10.1002/j.1460-2075.1990.tb07519.x;
RA Gardel C., Johnson K., Jacq A., Beckwith J.;
RT "The secD locus of E.coli codes for two membrane proteins required for
RT protein export.";
RL EMBO J. 9:3209-3216(1990).
RN [2]
RP ERRATUM OF PUBMED:2170107.
RX PubMed=2249673; DOI=10.1002/j.1460-2075.1990.tb07645.x;
RA Gardel C., Johnson K., Jacq A., Beckwith J.;
RL EMBO J. 9:4205-4206(1990).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-76.
RX PubMed=7507921; DOI=10.1128/jb.176.3.804-814.1994;
RA Pogliano K.J., Beckwith J.;
RT "Genetic and molecular characterization of the Escherichia coli secD operon
RT and its products.";
RL J. Bacteriol. 176:804-814(1994).
RN [7]
RP SUBCELLULAR LOCATION.
RC STRAIN=BL21-DE3;
RX PubMed=16079137; DOI=10.1074/jbc.m506479200;
RA Stenberg F., Chovanec P., Maslen S.L., Robinson C.V., Ilag L.,
RA von Heijne G., Daley D.O.;
RT "Protein complexes of the Escherichia coli cell envelope.";
RL J. Biol. Chem. 280:34409-34419(2005).
RN [8]
RP SUBCELLULAR LOCATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=15919996; DOI=10.1126/science.1109730;
RA Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G.;
RT "Global topology analysis of the Escherichia coli inner membrane
RT proteome.";
RL Science 308:1321-1323(2005).
RN [9]
RP FUNCTION IN TRANSLOCATION, AND MUTAGENESIS OF ASP-519.
RX PubMed=21562494; DOI=10.1038/nature09980;
RA Tsukazaki T., Mori H., Echizen Y., Ishitani R., Fukai S., Tanaka T.,
RA Perederina A., Vassylyev D.G., Kohno T., Maturana A.D., Ito K., Nureki O.;
RT "Structure and function of a membrane component SecDF that enhances protein
RT export.";
RL Nature 474:235-238(2011).
RN [10]
RP FUNCTION, SUBUNIT, AND SUBCELLULAR LOCATION.
RC STRAIN=BL21-DE3;
RX PubMed=27435098; DOI=10.1042/bcj20160545;
RA Komar J., Alvira S., Schulze R.J., Martin R., Lycklama a Nijeholt J.A.,
RA Lee S.C., Dafforn T.R., Deckers-Hebestreit G., Berger I., Schaffitzel C.,
RA Collinson I.;
RT "Membrane protein insertion and assembly by the bacterial holo-translocon
RT SecYEG-SecDF-YajC-YidC.";
RL Biochem. J. 473:3341-3354(2016).
CC -!- FUNCTION: Part of the Sec protein translocase complex. Interacts with
CC the SecYEG preprotein conducting channel. SecDF uses the proton motive
CC force (PMF) to complete protein translocation after the ATP-dependent
CC function of SecA. The large periplasmic domain is thought to have a
CC base and head domain joined by a hinge; movement of the hinge may be
CC coupled to both proton transport and protein export, with the head
CC domain capturing substrate, and a conformational change preventing
CC backward movement and driving forward movement. Expression of
CC V.alginolyticus SecD and SecF in E.coli confers Na(+)-dependent protein
CC export, strongly suggesting SecDF functions via cation-coupled protein
CC translocation. {ECO:0000269|PubMed:21562494}.
CC -!- SUBUNIT: Forms a complex with SecF. Part of the essential Sec protein
CC translocation apparatus which comprises SecA, SecYEG and auxiliary
CC proteins SecDF-YajC and YidC. The SecDF-YidC-YajC translocase forms a
CC supercomplex with SecYEG, called the holo-translocon (HTL)
CC (PubMed:27435098). The stoichiometry of the super complex may be
CC SecYEG:YidC:SecDF 4:3:1, YajC is in the reconstituted complex (with
CC SecDF) but as no antibody is available it could not be quantified
CC (PubMed:27435098). {ECO:0000269|PubMed:27435098}.
CC -!- INTERACTION:
CC P0AG90; P07395: pheT; NbExp=4; IntAct=EBI-555724, EBI-555713;
CC -!- SUBCELLULAR LOCATION: Cell inner membrane {ECO:0000269|PubMed:15919996,
CC ECO:0000269|PubMed:16079137}; Multi-pass membrane protein
CC {ECO:0000269|PubMed:15919996, ECO:0000269|PubMed:16079137}.
CC -!- DISRUPTION PHENOTYPE: Disruption of both secD and SecF confers cold-
CC sensitive growth (strain secD1(Cs)). {ECO:0000269|PubMed:2170107}.
CC -!- SIMILARITY: Belongs to the SecD/SecF family. SecD subfamily.
CC {ECO:0000305}.
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DR EMBL; X56175; CAA39634.1; -; Genomic_DNA.
DR EMBL; U82664; AAB40164.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73511.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76188.1; -; Genomic_DNA.
DR EMBL; S68715; AAC60469.2; -; Genomic_DNA.
DR PIR; H64769; H64769.
DR RefSeq; NP_414942.1; NC_000913.3.
DR RefSeq; WP_000934822.1; NZ_STEB01000007.1.
DR PDB; 5MG3; EM; 14.00 A; D=2-615.
DR PDBsum; 5MG3; -.
DR AlphaFoldDB; P0AG90; -.
DR SMR; P0AG90; -.
DR BioGRID; 4263096; 309.
DR BioGRID; 853372; 1.
DR ComplexPortal; CPX-1095; Holo-translocon SecYEG-SecDF-YajC-YidC complex.
DR DIP; DIP-35837N; -.
DR IntAct; P0AG90; 10.
DR MINT; P0AG90; -.
DR STRING; 511145.b0408; -.
DR TCDB; 2.A.6.4.1; the resistance-nodulation-cell division (rnd) superfamily.
DR jPOST; P0AG90; -.
DR PaxDb; P0AG90; -.
DR PRIDE; P0AG90; -.
DR EnsemblBacteria; AAC73511; AAC73511; b0408.
DR EnsemblBacteria; BAE76188; BAE76188; BAE76188.
DR GeneID; 66671293; -.
DR GeneID; 949133; -.
DR KEGG; ecj:JW0398; -.
DR KEGG; eco:b0408; -.
DR PATRIC; fig|511145.12.peg.424; -.
DR EchoBASE; EB0931; -.
DR eggNOG; COG0342; Bacteria.
DR HOGENOM; CLU_007894_4_3_6; -.
DR InParanoid; P0AG90; -.
DR OMA; MVVYYRL; -.
DR PhylomeDB; P0AG90; -.
DR BioCyc; EcoCyc:SECD; -.
DR BioCyc; MetaCyc:SECD; -.
DR PRO; PR:P0AG90; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0031522; C:cell envelope Sec protein transport complex; IPI:ComplexPortal.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0016020; C:membrane; IC:ComplexPortal.
DR GO; GO:0005886; C:plasma membrane; IDA:EcoCyc.
DR GO; GO:0015450; F:protein-transporting ATPase activity; IEA:InterPro.
DR GO; GO:0065002; P:intracellular protein transmembrane transport; IEA:UniProtKB-UniRule.
DR GO; GO:0032978; P:protein insertion into membrane from inner side; IDA:ComplexPortal.
DR GO; GO:0006605; P:protein targeting; IEA:UniProtKB-UniRule.
DR GO; GO:0015031; P:protein transport; IMP:EcoliWiki.
DR GO; GO:0043952; P:protein transport by the Sec complex; IDA:ComplexPortal.
DR HAMAP; MF_01463_B; SecD_B; 1.
DR InterPro; IPR005791; SecD.
DR InterPro; IPR027398; SecD-TM.
DR InterPro; IPR022813; SecD/SecF_arch_bac.
DR InterPro; IPR022645; SecD/SecF_bac.
DR InterPro; IPR022646; SecD/SecF_CS.
DR PANTHER; PTHR30081; PTHR30081; 1.
DR Pfam; PF07549; Sec_GG; 1.
DR Pfam; PF13721; SecD-TM1; 1.
DR Pfam; PF02355; SecD_SecF; 1.
DR TIGRFAMs; TIGR00916; 2A0604s01; 1.
DR TIGRFAMs; TIGR01129; secD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell inner membrane; Cell membrane; Membrane;
KW Protein transport; Reference proteome; Translocation; Transmembrane;
KW Transmembrane helix; Transport.
FT CHAIN 1..615
FT /note="Protein translocase subunit SecD"
FT /id="PRO_0000095960"
FT TOPO_DOM 1..9
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 10..29
FT /note="Helical"
FT /evidence="ECO:0000305"
FT TOPO_DOM 30..455
FT /note="Periplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 456..472
FT /note="Helical"
FT /evidence="ECO:0000305"
FT TOPO_DOM 473..476
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT TOPO_DOM 498..501
FT /note="Periplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 502..518
FT /note="Helical"
FT /evidence="ECO:0000305"
FT TOPO_DOM 519..563
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 564..580
FT /note="Helical"
FT /evidence="ECO:0000305"
FT TOPO_DOM 581..585
FT /note="Periplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 586..605
FT /note="Helical"
FT /evidence="ECO:0000305"
FT TOPO_DOM 606..615
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT REGION 279..426
FT /note="Required for protein export"
FT MUTAGEN 519
FT /note="D->N: Abolishes protein translocation."
FT /evidence="ECO:0000269|PubMed:21562494"
FT CONFLICT 78
FT /note="F -> S (in Ref. 1; CAA39634)"
FT /evidence="ECO:0000305"
FT CONFLICT 155
FT /note="R -> A (in Ref. 1; CAA39634)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 615 AA; 66632 MW; 1099E6A9CC988EBE CRC64;
MLNRYPLWKY VMLIVVIVIG LLYALPNLFG EDPAVQITGA RGVAASEQTL IQVQKTLQEE
KITAKSVALE EGAILARFDS TDTQLRAREA LMGVMGDKYV VALNLAPATP RWLAAIHAEP
MKLGLDLRGG VHFLMEVDMD TALGKLQEQN IDSLRSDLRE KGIPYTTVRK ENNYGLSITF
RDAKARDEAI AYLSKRHPDL VISSQGSNQL RAVMSDARLS EAREYAVQQN INILRNRVNQ
LGVAEPVVQR QGADRIVVEL PGIQDTARAK EILGATATLE FRLVNTNVDQ AAAASGRVPG
DSEVKQTREG QPVVLYKRVI LTGDHITDST SSQDEYNQPQ VNISLDSAGG NIMSNFTKDN
IGKPMATLFV EYKDSGKKDA NGRAVLVKQE EVINIANIQS RLGNSFRITG INNPNEARQL
SLLLRAGALI APIQIVEERT IGPTLGMQNI EQGLEACLAG LLVSILFMII FYKKFGLIAT
SALIANLILI VGIMSLLPGA TLSMPGIAGI VLTLAVAVDA NVLINERIKE ELSNGRTVQQ
AIDEGYRGAF SSIFDANITT LIKVIILYAV GTGAIKGFAI TTGIGVATSM FTAIVGTRAI
VNLLYGGKRV KKLSI
