RegulonDB RegulonDB 11.1: Gene Form
   

ldcC gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ldcC accA yaeR terminator yaeRp3 yaeRp3 TSS_391 TSS_391 TSS_390 TSS_390 TSS_389 TSS_389 TSS_388 TSS_388

Gene      
Name: ldcC    Texpresso search in the literature
Synonym(s): ECK0185, G6094, b0186, ldc, ldcH
Genome position(nucleotides): 209679 --> 211820
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.89
External database links:  
ASAP:
 ABE-0000633
ECHOBASE:
 EB3010
ECOLIHUB:
 ldcC
OU-MICROARRAY:
 b0186
STRING:
 511145.b0186
COLOMBOS: ldcC


Product      
Name: lysine decarboxylase 2
Synonym(s): Ldc, LdcC, LdcH, lysine decarboxylase, constitutive
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 80.59
Isoelectric point: 5.308
Motif(s):
 
Type Positions Sequence Comment
14 -> 124 YKDEPIKELESALVAQGFQIIWPQNSVDLLKFIEHNPRICGVIFDWDEYSLDLCSDINQLNEYLPLYAFINTHSTMDVSVQDMRMALWFFEYALGQAEDIAIRMRQYTDEY
130 -> 545 PPFTKALFTYVKERKYTFCTPGHMGGTAYQKSPVGCLFYDFFGGNTLKADVSISVTELGSLLDHTGPHLEAEEYIARTFGAEQSYIVTNGTSTSNKIVGMYAAPSGSTLLIDRNCHKSLAHLLMMNDVVPVWLKPTRNALGILGGIPRREFTRDSIEEKVAATTQAQWPVHAVITNSTYDGLLYNTDWIKQTLDVPSIHFDSAWVPYTHFHPIYQGKSGMSGERVAGKVIFETQSTHKMLAALSQASLIHIKGEYDEEAFNEAFMMHTTTSPSYPIVASVETAAAMLRGNPGKRLINRSVERALHFRKEVQRLREESDGWFFDIWQPPQVDEAECWPVAPGEQWHGFNDADADHMFLDPVKVTILTPGMDEQGNMSEEGIPAALVAKFLDERGIVVEKTGPYNLLFLFSIGIDKTK
284 -> 284 S UniProt: In Ref. 2; AA sequence..
314 -> 314 N UniProt: In Ref. 2; AA sequence..
411 -> 411 T UniProt: In Ref. 2; AA sequence..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.1 - carbon compounds
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0016829 - lyase activity
GO:0016831 - carboxy-lyase activity
GO:0008923 - lysine decarboxylase activity
GO:0042802 - identical protein binding
biological_process GO:0006520 - cellular amino acid metabolic process
GO:0006554 - lysine catabolic process
Note(s): Note(s): ...[more].
Reference(s): [1] Negrete A., et al., 2015
External database links:  
ALPHAFOLD:
 P52095
DIP:
 DIP-10086N
ECOCYC:
 LDC2-MONOMER
ECOLIWIKI:
 b0186
INTERPRO:
 IPR015421
INTERPRO:
 IPR015424
INTERPRO:
 IPR036633
INTERPRO:
 IPR005308
INTERPRO:
 IPR000310
INTERPRO:
 IPR015422
INTERPRO:
 IPR008286
INTERPRO:
 IPR011193
MODBASE:
 P52095
PDB:
 5FKZ
PFAM:
 PF03711
PFAM:
 PF03709
PFAM:
 PF01276
PRIDE:
 P52095
PRODB:
 PRO_000023075
PROSITE:
 PS00703
REFSEQ:
 NP_414728
SMR:
 P52095
UNIPROT:
 P52095


Operon      
Name: ldcC         
Operon arrangement:
Transcription unit        Promoter
ldcC


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_388 208850 forward nd [RS-EPT-CBR] [2]
  promoter TSS_389 209002 forward nd [RS-EPT-CBR] [2]
  promoter TSS_390 209273 forward nd [RS-EPT-CBR] [2]
  promoter TSS_391 209658 forward nd [RS-EPT-CBR] [2]
  promoter yaeRp3 211858 forward nd [COMP-AINF] [3]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Negrete A., Shiloach J., 2015, Constitutive expression of the sRNA GadY decreases acetate production and improves E. coli growth., Microb Cell Fact 14:148

 [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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