RegulonDB RegulonDB 10.7: 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
OU-MICROARRAY:
b0441
PORTECO:
ppiD
REGULONDB:
b0441
STRING:
511145.b0441
M3D: ppiD
COLOMBOS: ppiD
PortEco: b0441


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: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] Matern Y., et al., 2010
External database links:  
DIP:
DIP-39902N
ECOCYC:
G6242-MONOMER
ECOLIWIKI:
b0441
INTERPRO:
IPR023058
INTERPRO:
IPR027304
INTERPRO:
IPR000297
MODBASE:
P0ADY1
PDB:
2KGJ
PFAM:
PF13145
PRIDE:
P0ADY1
PRODB:
PRO_000023579
PROSITE:
PS50198
PROSITE:
PS01096
PROTEINMODELPORTAL:
P0ADY1
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] [2]
  promoter TSS_601 461455 forward nd [RS-EPT-CBR] [2]
  promoter TSS_602 461459 forward nd [RS-EPT-CBR] [2]
  promoter TSS_603 461478 forward nd [RS-EPT-CBR] [2]
  promoter TSS_604 (cluster) 461543 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_605 461552 forward nd [RS-EPT-CBR] [2]
  promoter TSS_606 (cluster) 461851 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter ybaVp3 463752 forward Similarity to the consensus
Read more >
[ICWHO] [3]


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] 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

 [2] 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.

 [3] 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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