RegulonDB RegulonDB 11.0: Gene Form
   

potD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

potD potB potC ymfA ycfZ terminator TSS_1462 (cluster) TSS_1462 (cluster) TSS_1461 TSS_1461 TSS_1460 TSS_1460 TSS_1459 TSS_1459 TSS_1458 TSS_1458 potDp6 potDp6 potDp5 potDp5 TSS_1457 TSS_1457 TSS_1456 TSS_1456 ycfZp5 ycfZp5 ycfZp6 ycfZp6

Gene      
Name: potD    Texpresso search in the literature
Synonym(s): ECK1109, EG10752, b1123
Genome position(nucleotides): 1181783 <-- 1182829
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.81
External database links:  
ASAP:
ABE-0003789
CGSC:
31908
ECHOBASE:
EB0745
ECOLIHUB:
potD
OU-MICROARRAY:
b1123
STRING:
511145.b1123
COLOMBOS: potD


Product      
Name: spermidine preferential ABC transporter periplasmic binding protein
Synonym(s): PotD
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space,membrane
Molecular weight: 38.867
Isoelectric point: 5.003
Motif(s):
 
Type Positions Sequence Comment
1 -> 23 MKKWSRHLLAAGALALGMSAAHA
24 -> 348 DDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKTLYPDAETIKNGEWQNDVGAASSIYEEYYQKLKAGR UniProt: Spermidine/putrescine-binding periplasmic protein.
42 -> 313 LLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKT
46 -> 54 FTKETGIKV conserved between PotD and the maltose binding protein, MalE
168 -> 171 DARE UniProt: Spermidine-binding; Sequence Annotation Type: region of interest.

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.4 - amines
  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
molecular_function GO:0019809 - spermidine binding
GO:0019810 - putrescine binding
GO:0019808 - polyamine binding
biological_process GO:0015846 - polyamine transport
GO:0015848 - spermidine transport
GO:0015847 - putrescine transport
GO:1903711 - spermidine transmembrane transport
Note(s): Note(s): ...[more].
Reference(s): [1] Kashiwagi K., et al., 1996
[2] Pistocchi R., et al., 1993
[3] Scheib U., et al., 2014
[4] Zhang X., et al., 2013
External database links:  
ALPHAFOLD:
P0AFK9
ECOCYC:
POTD-MONOMER
ECOLIWIKI:
b1123
INTERPRO:
IPR001188
INTERPRO:
IPR006059
MODBASE:
P0AFK9
PDB:
1POY
PDB:
1POT
PFAM:
PF13416
PRIDE:
P0AFK9
PRINTS:
PR00909
PRODB:
PRO_000023570
REFSEQ:
NP_415641
SMR:
P0AFK9
SWISSMODEL:
P0AFK9
UNIPROT:
P0AFK9


Operon      
Name: potABCD         
Operon arrangement:
Transcription unit        Promoter
potABCD


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 ycfZp6 1181346 reverse nd [ICWHO] [5]
  promoter ycfZp5 1181380 reverse nd [ICWHO] [5]
  promoter TSS_1456 1182741 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_1457 1182847 reverse nd [RS-EPT-CBR] [6]
  promoter potDp5 1182848 reverse nd [ICWHO] [5]
  promoter potDp6 1182850 reverse nd [ICWHO] [5]
  promoter TSS_1458 1182851 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_1459 1182909 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_1460 1182913 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_1461 1182965 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_1462 (cluster) 1182969 reverse nd [RS-EPT-CBR] [6]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] Kashiwagi K., Pistocchi R., Shibuya S., Sugiyama S., Morikawa K., Igarashi K., 1996, Spermidine-preferential uptake system in Escherichia coli. Identification of amino acids involved in polyamine binding in PotD protein., J Biol Chem 271(21):12205-8

 [2] Pistocchi R., Kashiwagi K., Miyamoto S., Nukui E., Sadakata Y., Kobayashi H., Igarashi K., 1993, Characteristics of the operon for a putrescine transport system that maps at 19 minutes on the Escherichia coli chromosome., J Biol Chem 268(1):146-52

 [3] Scheib U., Shanmugaratnam S., Farias-Rico JA., Hocker B., 2014, Change in protein-ligand specificity through binding pocket grafting., J Struct Biol 185(2):186-92

 [4] Zhang X., Zhang Y., Liu J., Liu H., 2013, PotD protein stimulates biofilm formation by Escherichia coli., Biotechnol Lett 35(7):1099-106

 [5] 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

 [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.


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