RegulonDB RegulonDB 10.10: Gene Form
   

ppiD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ppiD ybaV hupB CpxR CpxR CpxR Fis terminator anti-terminator anti-anti-terminator ybaVp3 ybaVp3 TSS_606 (cluster) TSS_606 (cluster) ppiDp1 ppiDp1 ppiDp2 ppiDp2 TSS_605 TSS_605 TSS_604 (cluster) TSS_604 (cluster) TSS_603 TSS_603 TSS_602 TSS_602 TSS_601 TSS_601 TSS_600 TSS_600

Gene      
Name: ppiD    Texpresso search in the literature
Synonym(s): ECK0435, G6242, b0441, ybaU
Genome position(nucleotides): 461915 --> 463786 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.35
External database links:  
ASAP:
 ABE-0001531
ECHOBASE:
 EB3038
ECOLIHUB:
 ppiD
OU-MICROARRAY:
 b0441
STRING:
 511145.b0441
COLOMBOS: ppiD


Product      
Name: periplasmic folding chaperone
Synonym(s): PpiD, YbaU
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 68.15
Isoelectric point: 4.685
Motif(s):
 
Type Positions Sequence
1 -> 165 MMDSLRTAANSLVLKIIFGIIIVSFILTGVSGYLIGGGNNYAAKVNDQEISRGQFENAFNSERNRMQQQLGDQYSELAANEGYMKTLRQQVLNRLIDEALLDQYARELKLGISDEQVKQAIFATPAFQVDGKFDNSRYNGILNQMGMTADQYAQALRNQLTTQQL
247 -> 369 VSDADIQSYYDQHQDQFTQPQRTRYSIIQTKTEDEAKAVLDELNKGGDFAALAKEKSADIISARNGGDMGWLEDATIPDELKNAGLKEKGQLSGVIKSSVGFLIVRLDDIQPAKVKSLDEVRD
312 -> 312 G
313 -> 313 G
264 -> 357 TQPQRTRYSIIQTKTEDEAKAVLDELNKGGDFAALAKEKSADIISARNGGDMGWLEDATIPDELKNAGLKEKGQLSGVIKSSVGFLIVRLDDIQ

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.4 - chaperoning, repair (refolding)
  5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes
  5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
GO:0071575 - integral component of external side of plasma membrane
molecular_function GO:0005515 - protein binding
GO:0016853 - isomerase activity
GO:0003755 - peptidyl-prolyl cis-trans isomerase activity
GO:0042802 - identical protein binding
biological_process GO:0061077 - chaperone-mediated protein folding
GO:0000413 - protein peptidyl-prolyl isomerization
Note(s): Note(s): ...[more].
Evidence: [APPHINH] Assay of protein purified to homogeneity from its native host
Reference(s): [1] Furst M., et al., 2018
[2] Jauss B., et al., 2019
[3] Jones AM., et al., 2021
[4] Matern Y., et al., 2010
[5] Sachelaru I., et al., 2014
External database links:  
DIP:
 DIP-39902N
ECOCYC:
 G6242-MONOMER
ECOLIWIKI:
 b0441
INTERPRO:
 IPR000297
INTERPRO:
 IPR023058
INTERPRO:
 IPR027304
MODBASE:
 P0ADY1
PDB:
 2KGJ
PFAM:
 PF13624
PFAM:
 PF13145
PRIDE:
 P0ADY1
PRODB:
 PRO_000023579
PROSITE:
 PS01096
PROSITE:
 PS50198
REFSEQ:
 NP_414975
SMR:
 P0ADY1
UNIPROT:
 P0ADY1


Operon      
Name: ppiD         
Operon arrangement:
Transcription unit        Promoter
ppiD
ppiD


Transcriptional Regulation      
Display Regulation             
Activated by: CpxR


RNA cis-regulatory element    
Attenuation: Transcriptional


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_600 461451 forward nd [RS-EPT-CBR] [6]
  promoter TSS_601 461455 forward nd [RS-EPT-CBR] [6]
  promoter TSS_602 461459 forward nd [RS-EPT-CBR] [6]
  promoter TSS_603 461478 forward nd [RS-EPT-CBR] [6]
  promoter TSS_604 (cluster) 461543 forward nd [RS-EPT-CBR] [6]
  promoter TSS_605 461552 forward nd [RS-EPT-CBR] [6]
  promoter TSS_606 (cluster) 461851 forward nd [RS-EPT-CBR] [6]
  promoter ybaVp3 463752 forward nd [ICWHO] [7]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Furst M., Zhou Y., Merfort J., Muller M., 2018, Involvement of PpiD in Sec-dependent protein translocation., Biochim Biophys Acta Mol Cell Res 1865(2):273-280

 [2] Jauss B., Petriman NA., Drepper F., Franz L., Sachelaru I., Welte T., Steinberg R., Warscheid B., Koch HG., 2019, Noncompetitive binding of PpiD and YidC to the SecYEG translocon expands the global view on the SecYEG interactome in Escherichia coli., J Biol Chem 294(50):19167-19183

 [3] Jones AM., Virtanen P., Hammarlof D., Allen WJ., Collinson I., Hayes CS., Low DA., Koskiniemi S., 2021, Genetic Evidence for SecY Translocon-Mediated Import of Two Contact-Dependent Growth Inhibition (CDI) Toxins., mBio 12(1)

 [4] Matern Y., Barion B., Behrens-Kneip S., 2010, PpiD is a player in the network of periplasmic chaperones in Escherichia coli., BMC Microbiol 10:251

 [5] Sachelaru I., Petriman NA., Kudva R., Koch HG., 2014, Dynamic interaction of the sec translocon with the chaperone PpiD., J Biol Chem 289(31):21706-15

 [6] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [7] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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