RegulonDB RegulonDB 11.1: Gene Form
   

dppA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dppA dppB proK FNR IHF Cis-reg terminator dppAp dppAp TSS_4155 TSS_4155 TSS_4154 (cluster) TSS_4154 (cluster) TSS_4153 TSS_4153 TSS_4152 TSS_4152 TSS_4151 TSS_4151 TSS_4150 (cluster) TSS_4150 (cluster) TSS_4149 TSS_4149 TSS_4148 TSS_4148 TSS_4147 TSS_4147 TSS_4146 TSS_4146 TSS_4145 TSS_4145

Gene      
Name: dppA    Texpresso search in the literature
Synonym(s): ECK3531, EG10248, alu, b3544, dpp, fpp
Genome position(nucleotides): 3706098 <-- 3707705
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.55
External database links:  
ASAP:
 ABE-0011576
CGSC:
 35111
ECHOBASE:
 EB0244
ECOLIHUB:
 dppA
OU-MICROARRAY:
 b3544
STRING:
 511145.b3544
COLOMBOS: dppA


Product      
Name: dipeptide ABC transporter periplasmic binding protein
Synonym(s): Alu, Dpp, DppA, Fpp
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,periplasmic space
Molecular weight: 60.294
Isoelectric point: 6.62
Motif(s):
 
Type Positions Sequence Comment
1 -> 28 MRISLKKSGMLKLGLSLVAMTVAASVQA
29 -> 535 KTLVYCSEGSPEGFNPQLFTSGTTYDASSVPLYNRLVEFKIGTTEVIPGLAEKWEVSEDGKTYTFHLRKGVKWHDNKEFKPTRELNADDVVFSFDRQKNAQNPYHKVSGGSYEYFEGMGLPELISEVKKVDDNTVQFVLTRPEAPFLADLAMDFASILSKEYADAMMKAGTPEKLDLNPIGTGPFQLQQYQKDSRIRYKAFDGYWGTKPQIDTLVFSITPDASVRYAKLQKNECQVMPYPNPADIARMKQDKSINLMEMPGLNVGYLSYNVQKKPLDDVKVRQALTYAVNKDAIIKAVYQGAGVSAKNLIPPTMWGYNDDVQDYTYDPEKAKALLKEAGLEKGFSIDLWAMPVQRPYNPNARRMAEMIQADWAKVGVQAKIVTYEWGEYLKRAKDGEHQTVMMGWTGDNGDPDNFFATLFSCAASEQGSNYSKWCYKPFEDLIQPARATDDHNKRVELYKQAQVVMHDQAPALIIAHSTVFEPVRKEVKGYVVDPLGKHHFENVSIE UniProt: Dipeptide-binding protein.
48 -> 50 TSG UniProt: Dipeptide binding; Sequence Annotation Type: region of interest.
73 -> 453 EVIPGLAEKWEVSEDGKTYTFHLRKGVKWHDNKEFKPTRELNADDVVFSFDRQKNAQNPYHKVSGGSYEYFEGMGLPELISEVKKVDDNTVQFVLTRPEAPFLADLAMDFASILSKEYADAMMKAGTPEKLDLNPIGTGPFQLQQYQKDSRIRYKAFDGYWGTKPQIDTLVFSITPDASVRYAKLQKNECQVMPYPNPADIARMKQDKSINLMEMPGLNVGYLSYNVQKKPLDDVKVRQALTYAVNKDAIIKAVYQGAGVSAKNLIPPTMWGYNDDVQDYTYDPEKAKALLKEAGLEKGFSIDLWAMPVQRPYNPNARRMAEMIQADWAKVGVQAKIVTYEWGEYLKRAKDGEHQTVMMGWTGDNGDPDNFFATLFSCAAS
383 -> 385 RPY UniProt: Dipeptide binding; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.3 - amino acids
  2 - information transfer --> 2.3 - protein related --> 2.3.4 - chaperoning, repair (refolding)
  4 - transport --> 4.3 - Primary Active Transporters --> 4.3.A - Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters --> 4.3.A.1 - The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases --> 4.3.A.1.p - ABC superfamily, periplasmic binding component
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
GO:0043190 - ATP-binding cassette (ABC) transporter complex
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
molecular_function GO:0042277 - peptide binding
GO:0020037 - heme binding
GO:0071916 - dipeptide transmembrane transporter activity
GO:1904680 - peptide transmembrane transporter activity
biological_process GO:0035351 - heme transmembrane transport
GO:0015031 - protein transport
GO:0015833 - peptide transport
GO:0006935 - chemotaxis
GO:0015886 - heme transport
GO:0042938 - dipeptide transport
GO:0055085 - transmembrane transport
GO:0061077 - chaperone-mediated protein folding
GO:0050918 - positive chemotaxis
GO:0035442 - dipeptide transmembrane transport
Note(s): Note(s): ...[more].
Reference(s): [1] Gilvarg C., et al., 1965
[2] Kuenzl T., et al., 2018
[3] Tam R., et al., 1993
[4] Zainol MKM., et al., 2021
External database links:  
ALPHAFOLD:
 P23847
DIP:
 DIP-9467N
ECOCYC:
 DPPA-MONOMER
ECOLIWIKI:
 b3544
INTERPRO:
 IPR030678
INTERPRO:
 IPR039424
INTERPRO:
 IPR023765
INTERPRO:
 IPR000914
MODBASE:
 P23847
PANTHER:
 PTHR30290
PDB:
 1DPE
PDB:
 1DPP
PFAM:
 PF00496
PRIDE:
 P23847
PRODB:
 PRO_000022473
PROSITE:
 PS01040
REFSEQ:
 NP_418001
SMR:
 P23847
UNIPROT:
 P23847


Operon      
Name: dppABCDF         
Operon arrangement:
Transcription unit        Promoter
dppABCDF


Transcriptional Regulation      
Display Regulation             
Activated by: IHF
Repressed by: FNR


RNA cis-regulatory element    
   
Cis-reg RtT RNA
   
   


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_4145 3704861 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_4146 3704911 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_4147 3706267 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_4148 3706923 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_4149 3706927 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_4150 (cluster) 3707044 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_4151 3707053 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_4152 3707203 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_4153 3707508 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_4154 (cluster) 3707699 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_4155 3707727 reverse nd [RS-EPT-CBR] [5]


Evidence    

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


Reference(s)    

 [1] Gilvarg C., Katchalski E., 1965, Peptide utilization in Escherichia coli., J Biol Chem 240:3093-8

 [2] Kuenzl T., Li-Blatter X., Srivastava P., Herdewijn P., Sharpe T., Panke S., 2018, Mutant Variants of the Substrate-Binding Protein DppA from Escherichia coli Enhance Growth on Nonstandard γ-Glutamyl Amide-Containing Peptides., Appl Environ Microbiol 84(13)

 [3] Tam R., Saier MH., 1993, Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria., Microbiol Rev 57(2):320-46

 [4] Zainol MKM., Linforth RJC., Winzor DJ., Scott DJ., 2021, Thermodynamics of semi-specific ligand recognition: the binding of dipeptides to the E.coli dipeptide binding protein DppA., Eur Biophys J 50(8):1103-1110

 [5] 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.

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