PPID_ECOLI
ID PPID_ECOLI Reviewed; 623 AA.
AC P0ADY1; P77241; Q2MBY5;
DT 06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=Periplasmic chaperone PpiD {ECO:0000303|PubMed:18439025};
DE AltName: Full=Periplasmic folding chaperone {ECO:0000305};
GN Name=ppiD {ECO:0000303|PubMed:9670013}; Synonyms=ybaU;
GN OrderedLocusNames=b0441, JW0431;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Hatada E., Ohmori H., Qiao Y., Tsuji M., Fukuda R.;
RL Submitted (OCT-1996) to the EMBL/GenBank/DDBJ databases.
RN [2]
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 [3]
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 [4]
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 [5]
RP PRELIMINARY FUNCTION AS A PPIASE, SUBCELLULAR LOCATION, TOPOLOGY,
RP INDUCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF GLY-312; GLY-313;
RP GLY-347 AND ILE-350.
RX PubMed=9670013; DOI=10.1093/emboj/17.14.3968;
RA Dartigalongue C., Raina S.;
RT "A new heat-shock gene, ppiD, encodes a peptidyl-prolyl isomerase required
RT for folding of outer membrane proteins in Escherichia coli.";
RL EMBO J. 17:3968-3980(1998).
RN [6]
RP SUBUNIT, AND 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 [7]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=16267292; DOI=10.1128/jb.187.22.7680-7686.2005;
RA Justice S.S., Hunstad D.A., Harper J.R., Duguay A.R., Pinkner J.S.,
RA Bann J., Frieden C., Silhavy T.J., Hultgren S.J.;
RT "Periplasmic peptidyl prolyl cis-trans isomerases are not essential for
RT viability, but SurA is required for pilus biogenesis in Escherichia coli.";
RL J. Bacteriol. 187:7680-7686(2005).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=18439025; DOI=10.1021/bi800233w;
RA Antonoaea R., Fuerst M., Nishiyama K., Mueller M.;
RT "The periplasmic chaperone PpiD interacts with secretory proteins exiting
RT from the SecYEG translocon.";
RL Biochemistry 47:5649-5656(2008).
RN [9]
RP INTERACTION WITH PEPTIDE SUBSTRATES AND MISFOLDED PROTEINS.
RX PubMed=18498364; DOI=10.1111/j.1742-4658.2008.06493.x;
RA Stymest K.H., Klappa P.;
RT "The periplasmic peptidyl prolyl cis-trans isomerases PpiD and SurA have
RT partially overlapping substrate specificities.";
RL FEBS J. 275:3470-3479(2008).
RN [10]
RP FUNCTION, OVEREXPRESSION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF GLY-347
RP AND ILE-350.
RX PubMed=20920237; DOI=10.1186/1471-2180-10-251;
RA Matern Y., Barion B., Behrens-Kneip S.;
RT "PpiD is a player in the network of periplasmic chaperones in Escherichia
RT coli.";
RL BMC Microbiol. 10:251-251(2010).
RN [11]
RP SUBCELLULAR LOCATION, TOPOLOGY, AND INTERACTION WITH YFGM.
RX PubMed=21210718; DOI=10.1021/pr101105c;
RA Maddalo G., Stenberg-Bruzell F., Gotzke H., Toddo S., Bjorkholm P.,
RA Eriksson H., Chovanec P., Genevaux P., Lehtio J., Ilag L.L., Daley D.O.;
RT "Systematic analysis of native membrane protein complexes in Escherichia
RT coli.";
RL J. Proteome Res. 10:1848-1859(2011).
RN [12]
RP INTERACTION WITH YFGM.
RX PubMed=24855643; DOI=10.1074/jbc.m113.541672;
RA Goetzke H., Palombo I., Muheim C., Perrody E., Genevaux P., Kudva R.,
RA Mueller M., Daley D.O.;
RT "YfgM is an ancillary subunit of the SecYEG translocon in Escherichia
RT coli.";
RL J. Biol. Chem. 289:19089-19097(2014).
RN [13]
RP FUNCTION, INTERACTION WITH THE SECYEG TRANSLOCON, AND SUBCELLULAR LOCATION.
RX PubMed=24951590; DOI=10.1074/jbc.m114.577916;
RA Sachelaru I., Petriman N.A., Kudva R., Koch H.G.;
RT "Dynamic interaction of the sec translocon with the chaperone PpiD.";
RL J. Biol. Chem. 289:21706-21715(2014).
RN [14]
RP FUNCTION, AND INTERACTION WITH THE SECYEG TRANSLOCON.
RX PubMed=29097228; DOI=10.1016/j.bbamcr.2017.10.012;
RA Fuerst M., Zhou Y., Merfort J., Mueller M.;
RT "Involvement of PpiD in Sec-dependent protein translocation.";
RL Biochim. Biophys. Acta 1865:273-280(2018).
RN [15]
RP INTERACTION WITH THE SECYEG TRANSLOCON; YFGM AND YIDC.
RX PubMed=31699901; DOI=10.1074/jbc.ra119.010686;
RA Jauss B., Petriman N.A., Drepper F., Franz L., Sachelaru I., Welte T.,
RA Steinberg R., Warscheid B., Koch H.G.;
RT "Noncompetitive binding of PpiD and YidC to the SecYEG translocon expands
RT the global view on the SecYEG interactome in Escherichia coli.";
RL J. Biol. Chem. 294:19167-19183(2019).
RN [16]
RP FUNCTION (MICROBIAL INFECTION), INTERACTION WITH BACTERIOPHAGE T4
RP (MICROBIAL INFECTION), AND DISRUPTION PHENOTYPE (MICROBIAL INFECTION).
RX PubMed=33036312; DOI=10.3390/v12101135;
RA Wenzel S., Shneider M.M., Leiman P.G., Kuhn A., Kiefer D.;
RT "The central spike complex of bacteriophage T4 contacts PpiD in the
RT periplasm of Escherichia coli.";
RL Viruses 12:1135-1135(2020).
RN [17] {ECO:0007744|PDB:2KGJ}
RP STRUCTURE BY NMR OF 264-357, LACK OF PPIASE ACTIVITY, INTERACTION WITH
RP PEPTIDE SUBSTRATES, AND DOMAIN.
RX PubMed=19866485; DOI=10.1002/pro.277;
RA Weininger U., Jakob R.P., Kovermann M., Balbach J., Schmid F.X.;
RT "The prolyl isomerase domain of PpiD from Escherichia coli shows a parvulin
RT fold but is devoid of catalytic activity.";
RL Protein Sci. 19:6-18(2010).
CC -!- FUNCTION: Chaperone that functions as a gatekeeper on the periplasmic
CC side of the SecYEG translocon (PubMed:18439025, PubMed:20920237,
CC PubMed:29097228). Facilitates the translocation of precursor proteins
CC across SecYEG by interacting with the translocating substrate
CC (PubMed:29097228). Also plays a role in the release of newly
CC synthesized secreted proteins at the periplasmic exit site of the Sec
CC translocon (PubMed:18439025, PubMed:20920237, PubMed:29097228). May be
CC involved in the early periplasmic folding of many newly translocated
CC proteins (PubMed:18439025, PubMed:20920237). Acts as a transient
CC subunit of the Sec translocon that binds to the lateral gate of SecY
CC and is detached by nascent membrane proteins but not by SecA
CC (PubMed:24951590). {ECO:0000269|PubMed:18439025,
CC ECO:0000269|PubMed:20920237, ECO:0000269|PubMed:24951590,
CC ECO:0000269|PubMed:29097228}.
CC -!- FUNCTION: Does not have peptidyl-prolyl isomerase (PPIase) activity.
CC PPIase activity could not be generated by substitutions at the peptide
CC binding site of the isolated parvulin-like domain.
CC {ECO:0000269|PubMed:19866485}.
CC -!- FUNCTION: (Microbial infection) May play an important role in
CC bacteriophage T4 infection and be involved in the penetration of the
CC inner membrane by the bacteriophage injection machinery, resulting in a
CC DNA-conducting channel to translocate the phage DNA into the interior
CC of the cell. {ECO:0000269|PubMed:33036312}.
CC -!- SUBUNIT: Interacts with the SecYEG translocon (PubMed:24951590,
CC PubMed:29097228, PubMed:31699901). Binds to the lateral gate of SecY
CC (PubMed:24951590, PubMed:31699901). Forms a complex with YfgM
CC (PubMed:21210718, PubMed:24855643, PubMed:31699901). Also interacts
CC with YidC (PubMed:31699901). Interacts with peptide substrates and
CC misfolded proteins (PubMed:18498364, PubMed:19866485). Has been
CC isolated as a homodimer and homotrimer from inner membrane preparations
CC (PubMed:16079137). {ECO:0000269|PubMed:16079137,
CC ECO:0000269|PubMed:18498364, ECO:0000269|PubMed:19866485,
CC ECO:0000269|PubMed:21210718, ECO:0000269|PubMed:24855643,
CC ECO:0000269|PubMed:24951590, ECO:0000269|PubMed:29097228,
CC ECO:0000269|PubMed:31699901}.
CC -!- SUBUNIT: (Microbial infection) Interacts with the central spike complex
CC of bacteriophage T4. {ECO:0000269|PubMed:33036312}.
CC -!- INTERACTION:
CC P0ADY1; P0ADY1: ppiD; NbExp=2; IntAct=EBI-562001, EBI-562001;
CC -!- SUBCELLULAR LOCATION: Cell inner membrane {ECO:0000269|PubMed:16079137,
CC ECO:0000269|PubMed:21210718, ECO:0000269|PubMed:9670013}; Single-pass
CC type II membrane protein {ECO:0000269|PubMed:21210718,
CC ECO:0000269|PubMed:9670013}; Periplasmic side
CC {ECO:0000269|PubMed:21210718, ECO:0000269|PubMed:9670013}. Note=Located
CC at the lateral gate of SecY. {ECO:0000269|PubMed:24951590}.
CC -!- INDUCTION: By heat shock via the sigma factor RpoH (PubMed:9670013).
CC Member of the two-component system CpxA/CpxR regulon (PubMed:9670013).
CC {ECO:0000269|PubMed:9670013}.
CC -!- DOMAIN: Consists of an N-terminal helix that anchors PpiD in the inner
CC membrane, followed by three domains that face the periplasm. The first
CC or the third domain are probably chaperone domains. The second domain
CC is a parvulin-like domain, which is devoid of catalytic activity. It
CC shows a parvulin fold and resembles most closely the inactive first
CC parvulin domain of SurA, which is part of the chaperone unit of this
CC protein and presumably involved in substrate recognition.
CC {ECO:0000269|PubMed:19866485}.
CC -!- DISRUPTION PHENOTYPE: Deletion of the gene retards the release of a
CC translocating outer membrane protein into the periplasm
CC (PubMed:18439025). Null mutation leads to the induction of the
CC periplasmic stress response. Null mutants are hypersensitive to
CC hydrophobic antibiotics such as novobiocin and to detergents such as
CC SDS, and exhibit altered outer membrane proteins profile
CC (PubMed:9670013). In contrast, another study shows that inactivation of
CC the gene has no discernible effect on the levels of outer membrane
CC proteins (PubMed:16267292). Lack of the gene confers increased
CC temperature-sensitivity in a degP mutant (PubMed:20920237).
CC {ECO:0000269|PubMed:16267292, ECO:0000269|PubMed:18439025,
CC ECO:0000269|PubMed:20920237, ECO:0000269|PubMed:9670013}.
CC -!- DISRUPTION PHENOTYPE: (Microbial infection) Deletion of the gene leads
CC to partial reduction in the plating efficiency of bacteriophage T4.
CC {ECO:0000269|PubMed:33036312}.
CC -!- MISCELLANEOUS: Overexpression restores viability of surA skp double
CC deletion mutant but it does not completely compensate for the growth
CC defect caused by the simultaneous lack of the SurA and Skp chaperones.
CC Suppression of surA skp lethality does not require the parvulin domain
CC but the membrane-localization of PpiD. In the absence of both SurA and
CC Skp, overproduction of PpiD can, at least in part, counteract the
CC defects in the biogenesis of OmpA and possibly of other OMPs.
CC {ECO:0000269|PubMed:20920237}.
CC -!- SIMILARITY: Belongs to the PpiD chaperone family. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to be a peptidyl-prolyl isomerase
CC (PPIase). It was shown later that even if PpiD shows sequence
CC similarity to PPIases, it is in fact devoid of PPIase activity
CC (PubMed:19866485). {ECO:0000269|PubMed:19866485,
CC ECO:0000305|PubMed:9670013}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; D82943; BAA11645.1; -; Genomic_DNA.
DR EMBL; U82664; AAB40197.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73544.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76221.1; -; Genomic_DNA.
DR PIR; A64774; A64774.
DR RefSeq; NP_414975.1; NC_000913.3.
DR RefSeq; WP_000969372.1; NZ_SSZK01000009.1.
DR PDB; 2KGJ; NMR; -; A=264-357.
DR PDBsum; 2KGJ; -.
DR AlphaFoldDB; P0ADY1; -.
DR BMRB; P0ADY1; -.
DR SMR; P0ADY1; -.
DR BioGRID; 4260732; 206.
DR DIP; DIP-39902N; -.
DR IntAct; P0ADY1; 8.
DR STRING; 511145.b0441; -.
DR TCDB; 3.A.5.1.1; the general secretory pathway (sec) family.
DR jPOST; P0ADY1; -.
DR PaxDb; P0ADY1; -.
DR PRIDE; P0ADY1; -.
DR EnsemblBacteria; AAC73544; AAC73544; b0441.
DR EnsemblBacteria; BAE76221; BAE76221; BAE76221.
DR GeneID; 946056; -.
DR KEGG; ecj:JW0431; -.
DR KEGG; eco:b0441; -.
DR PATRIC; fig|1411691.4.peg.1835; -.
DR EchoBASE; EB3038; -.
DR eggNOG; COG0760; Bacteria.
DR HOGENOM; CLU_023843_1_1_6; -.
DR InParanoid; P0ADY1; -.
DR OMA; DNSQGWI; -.
DR PhylomeDB; P0ADY1; -.
DR BioCyc; EcoCyc:G6242-MON; -.
DR EvolutionaryTrace; P0ADY1; -.
DR PRO; PR:P0ADY1; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0071575; C:integral component of external side of plasma membrane; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0003755; F:peptidyl-prolyl cis-trans isomerase activity; IEA:InterPro.
DR GO; GO:0061077; P:chaperone-mediated protein folding; IDA:EcoCyc.
DR Gene3D; 3.10.50.40; -; 1.
DR InterPro; IPR046357; PPIase_dom_sf.
DR InterPro; IPR000297; PPIase_PpiC.
DR InterPro; IPR023058; PPIase_PpiC_CS.
DR InterPro; IPR027304; Trigger_fact/SurA_dom_sf.
DR Pfam; PF13145; Rotamase_2; 1.
DR SUPFAM; SSF109998; SSF109998; 1.
DR PROSITE; PS01096; PPIC_PPIASE_1; 1.
DR PROSITE; PS50198; PPIC_PPIASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell inner membrane; Cell membrane; Chaperone; Membrane;
KW Reference proteome; Stress response; Transmembrane; Transmembrane helix.
FT CHAIN 1..623
FT /note="Periplasmic chaperone PpiD"
FT /id="PRO_0000193423"
FT TOPO_DOM 1..15
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:21210718,
FT ECO:0000305|PubMed:9670013"
FT TRANSMEM 16..36
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 37..623
FT /note="Periplasmic"
FT /evidence="ECO:0000269|PubMed:21210718,
FT ECO:0000305|PubMed:9670013"
FT DOMAIN 266..355
FT /note="PpiC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00278"
FT MUTAGEN 312
FT /note="G->A,R: Cannot complement a surA null mutant or
FT reduce the htrA-lacZ activity induced by periplasmic
FT stresses."
FT /evidence="ECO:0000269|PubMed:9670013"
FT MUTAGEN 313
FT /note="G->A,R: Cannot complement a surA null mutant or
FT reduce the htrA-lacZ activity induced by periplasmic
FT stresses."
FT /evidence="ECO:0000269|PubMed:9670013"
FT MUTAGEN 347
FT /note="G->A: Can complement the growth defect of surA skp
FT double deletion mutant. Has originally been reported to
FT eliminate PPIase activity and to result in the loss of its
FT reported surA complementing function."
FT /evidence="ECO:0000269|PubMed:20920237,
FT ECO:0000269|PubMed:9670013"
FT MUTAGEN 350
FT /note="I->A: Can complement the growth defect of surA skp
FT double deletion mutant. Has originally been reported to
FT eliminate PPIase activity and to result in the loss of its
FT reported surA complementing function."
FT /evidence="ECO:0000269|PubMed:20920237,
FT ECO:0000269|PubMed:9670013"
FT MUTAGEN 350
FT /note="I->F: Cannot complement a surA null mutant or reduce
FT the htrA-lacZ activity induced by periplasmic stresses."
FT /evidence="ECO:0000269|PubMed:9670013"
FT STRAND 268..278
FT /evidence="ECO:0007829|PDB:2KGJ"
FT HELIX 279..291
FT /evidence="ECO:0007829|PDB:2KGJ"
FT HELIX 295..301
FT /evidence="ECO:0007829|PDB:2KGJ"
FT HELIX 306..309
FT /evidence="ECO:0007829|PDB:2KGJ"
FT TURN 310..312
FT /evidence="ECO:0007829|PDB:2KGJ"
FT STRAND 313..319
FT /evidence="ECO:0007829|PDB:2KGJ"
FT HELIX 325..328
FT /evidence="ECO:0007829|PDB:2KGJ"
FT STRAND 338..344
FT /evidence="ECO:0007829|PDB:2KGJ"
FT STRAND 347..357
FT /evidence="ECO:0007829|PDB:2KGJ"
SQ SEQUENCE 623 AA; 68150 MW; 0F646F687114A387 CRC64;
MMDSLRTAAN SLVLKIIFGI IIVSFILTGV SGYLIGGGNN YAAKVNDQEI SRGQFENAFN
SERNRMQQQL GDQYSELAAN EGYMKTLRQQ VLNRLIDEAL LDQYARELKL GISDEQVKQA
IFATPAFQVD GKFDNSRYNG ILNQMGMTAD QYAQALRNQL TTQQLINGVA GTDFMLKGET
DELAALVAQQ RVVREATIDV NALAAKQPVT EQEIASYYEQ NKNNFMTPEQ FRVSYIKLDA
ATMQQPVSDA DIQSYYDQHQ DQFTQPQRTR YSIIQTKTED EAKAVLDELN KGGDFAALAK
EKSADIISAR NGGDMGWLED ATIPDELKNA GLKEKGQLSG VIKSSVGFLI VRLDDIQPAK
VKSLDEVRDD IAAKVKHEKA LDAYYALQQK VSDAASNDTE SLAGAEQAAG VKATQTGWFS
KDNLPEELNF KPVADAIFNG GLVGENGAPG INSDIITVDG DRAFVLRISE HKPEAVKPLA
DVQEQVKALV QHNKAEQQAK VDAEKLLVDL KAGKGAEAMQ AAGLKFGEPK TLSRSGRDPI
SQAAFALPLP AKDKPSYGMA TDMQGNVVLL ALDEVKQGSM PEDQKKAMVQ GITQNNAQIV
FEALMSNLRK EAKIKIGDAL EQQ
