RegulonDB RegulonDB 11.1: Gene Form
   

pepD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pepD prfH gpt yafP ykfJ CsgD anti-terminator anti-anti-terminator TSS_453 TSS_453 gptp gptp TSS_452 TSS_452 pepDp1 pepDp1 TSS_450 TSS_450 pepDp2 pepDp2 TSS_448 (cluster) TSS_448 (cluster) TSS_447 TSS_447 pepDp3 pepDp3

Gene      
Name: pepD    Texpresso search in the literature
Synonym(s): ECK0238, EG10695, b0237, pepH
Genome position(nucleotides): 254259 <-- 255716
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.37
External database links:  
ASAP:
 ABE-0000809
CGSC:
 415
ECHOBASE:
 EB0689
ECOLIHUB:
 pepD
OU-MICROARRAY:
 b0237
STRING:
 511145.b0237
COLOMBOS: pepD


Product      
Name: peptidase D
Synonym(s): PepD, PepH
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 52.915
Isoelectric point: 5.054
Motif(s):
 
Type Positions Sequence Comment
2 -> 485 SELSQLSPQPLWDIFAKICSIPHPSYHEEQLAEYIVGWAKEKGFHVERDQVGNILIRKPATAGMENRKPVVLQAHLDMVPQKNNDTVHDFTKDPIQPYIDGEWVKARGTTLGADNGIGMASALAVLADENVVHGPLEVLLTMTEEAGMDGAFGLQGNWLQADILINTDSEEEGEIYMGCAGGIDFTSNLHLDREAVPAGFETFKLTLKGLKGGHSGGEIHVGLGNANKLLVRFLAGHAEELDLRLIDFNGGTLRNAIPREAFATIAVAADKVDVLKSLVNTYQEILKNELAEKEKNLALLLDSVANDKAALIAKSRDTFIRLLNATPNGVIRNSDVAKGVVETSLNVGVVTMTDNNVEIHCLIRSLIDSGKDYVVSMLDSLGKLAGAKTEAKGAYPGWQPDANSPVMHLVRETYQRLFNKTPNIQIIHAGLECGLFKKPYPEMDMVSIGPTITGPHSPDEQVHIESVGHYWTLLTELLKEIPAK UniProt: Cytosol non-specific dipeptidase.
73 -> 480 LQAHLDMVPQKNNDTVHDFTKDPIQPYIDGEWVKARGTTLGADNGIGMASALAVLADENVVHGPLEVLLTMTEEAGMDGAFGLQGNWLQADILINTDSEEEGEIYMGCAGGIDFTSNLHLDREAVPAGFETFKLTLKGLKGGHSGGEIHVGLGNANKLLVRFLAGHAEELDLRLIDFNGGTLRNAIPREAFATIAVAADKVDVLKSLVNTYQEILKNELAEKEKNLALLLDSVANDKAALIAKSRDTFIRLLNATPNGVIRNSDVAKGVVETSLNVGVVTMTDNNVEIHCLIRSLIDSGKDYVVSMLDSLGKLAGAKTEAKGAYPGWQPDANSPVMHLVRETYQRLFNKTPNIQIIHAGLECGLFKKPYPEMDMVSIGPTITGPHSPDEQVHIESVGHYWTLLTELLK
209 -> 293 KGLKGGHSGGEIHVGLGNANKLLVRFLAGHAEELDLRLIDFNGGTLRNAIPREAFATIAVAADKVDVLKSLVNTYQEILKNELAE

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.3 - proteins/peptides/glycopeptides
  2 - information transfer --> 2.3 - protein related --> 2.3.6 - turnover, degradation
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0103046 - alanylglutamate dipeptidase activity
GO:0005515 - protein binding
GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0008270 - zinc ion binding
GO:0008237 - metallopeptidase activity
GO:0016805 - dipeptidase activity
GO:0042803 - protein homodimerization activity
GO:0070573 - metallodipeptidase activity
biological_process GO:0006508 - proteolysis
GO:0043171 - peptide catabolic process
Note(s): Note(s): ...[more].
Reference(s): [1] Bartlow P., et al., 2012
[2] Henrich B., et al., 1991
[3] Henrich B., et al., 1989
External database links:  
ALPHAFOLD:
 P15288
DIP:
 DIP-10456N
ECOCYC:
 EG10695-MONOMER
ECOLIWIKI:
 b0237
INTERPRO:
 IPR002933
INTERPRO:
 IPR011650
INTERPRO:
 IPR001160
MODBASE:
 P15288
PANTHER:
 PTHR43501
PFAM:
 PF07687
PFAM:
 PF01546
PRIDE:
 P15288
PRINTS:
 PR00934
PRODB:
 PRO_000023509
REFSEQ:
 NP_414772
SMR:
 P15288
UNIPROT:
 P15288


Operon      
Name: pepD         
Operon arrangement:
Transcription unit        Promoter
pepD
pepD
pepD


Transcriptional Regulation      
Display Regulation             
Repressed by: CsgD


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_447 255756 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_448 (cluster) 255770 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_450 255807 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_452 255816 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_453 255918 forward nd [RS-EPT-CBR] [4]


Evidence    

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


Reference(s)    

 [1] Bartlow P., Tiwari N., Beitle RR., Ataai MM., 2012, Evaluation of Escherichia coli proteins that burden nonaffinity-based chromatography as a potential strategy for improved purification performance., Biotechnol Prog 28(1):137-45

 [2] Henrich B., Plapp R., 1991, Locations of the genes from pepD through proA on the physical map of the Escherichia coli chromosome., J Bacteriol 173(23):7407-8

 [3] Henrich B., Schroeder U., Frank RW., Plapp R., 1989, Accurate mapping of the Escherichia coli pepD gene by sequence analysis of its 5' flanking region., Mol Gen Genet 215(3):369-73

 [4] 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.

RegulonDB