RegulonDB RegulonDB 11.1: Gene Form
   

pflA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pflB pflA ycaK terminator TSS_1150 TSS_1150 TSS_1149 TSS_1149 TSS_1148 TSS_1148 TSS_1147 TSS_1147 TSS_1146 TSS_1146 TSS_1145 TSS_1145 TSS_1144 (cluster) TSS_1144 (cluster) TSS_1143 TSS_1143 TSS_1142 (cluster) TSS_1142 (cluster) TSS_1141 TSS_1141 TSS_1140 TSS_1140 TSS_1139 TSS_1139 TSS_1138 (cluster) TSS_1138 (cluster) TSS_1137 TSS_1137 TSS_1136 TSS_1136 TSS_1135 TSS_1135 TSS_1134 TSS_1134 TSS_1133 TSS_1133 TSS_1132 (cluster) TSS_1132 (cluster) TSS_1131 TSS_1131 TSS_1130 TSS_1130 TSS_1129 TSS_1129 TSS_1128 TSS_1128 TSS_1127 TSS_1127 TSS_1126 TSS_1126 TSS_1125 TSS_1125 TSS_1124 (cluster) TSS_1124 (cluster) TSS_1123 TSS_1123 TSS_1122 TSS_1122 TSS_1121 TSS_1121 TSS_1120 TSS_1120 TSS_1119 TSS_1119 TSS_1118 TSS_1118 TSS_1117 (cluster) TSS_1117 (cluster) TSS_1116 (cluster) TSS_1116 (cluster) TSS_1115 (cluster) TSS_1115 (cluster) TSS_1114 TSS_1114 TSS_1113 TSS_1113 TSS_1112 TSS_1112 TSS_1111 (cluster) TSS_1111 (cluster) TSS_1110 TSS_1110 TSS_1109 TSS_1109 TSS_1108 TSS_1108 TSS_1107 TSS_1107 TSS_1106 TSS_1106 TSS_1105 (cluster) TSS_1105 (cluster) TSS_1104 TSS_1104 pflAp8 pflAp8 TSS_1103 TSS_1103 pflAp pflAp TSS_1102 TSS_1102 TSS_1101 TSS_1101 TSS_1100 TSS_1100 TSS_1099 TSS_1099

Gene      
Name: pflA    Texpresso search in the literature
Synonym(s): ECK0893, EG10028, act, b0902
Genome position(nucleotides): 950340 <-- 951080
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.34
External database links:  
ASAP:
 ABE-0003068
CGSC:
 35839
ECHOBASE:
 EB0027
ECOLIHUB:
 pflA
OU-MICROARRAY:
 b0902
STRING:
 511145.b0902
COLOMBOS: pflA


Product      
Name: pyruvate formate-lyase activating enzyme
Synonym(s): Act, PFL activase, PFL-AE, PflA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 28.204
Isoelectric point: 6.44
Motif(s):
 
Type Positions Sequence Comment
2 -> 246 SVIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELGKHKWVAMGEEYKLDGVKPPKKETMERVKGILEQYGHKVMF UniProt: Pyruvate formate-lyase 1-activating enzyme.
16 -> 146 VDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVS
24 -> 178 ITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNVKVWIRYVVVPGWSDDD
36 -> 38 YCH UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest.
130 -> 132 DLK UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration
  2 - information transfer --> 2.3 - protein related --> 2.3.3 - posttranslational modification
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.3 - inhibition / activation of enzymes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0051536 - iron-sulfur cluster binding
GO:0051539 - 4 iron, 4 sulfur cluster binding
GO:0043365 - [formate-C-acetyltransferase]-activating enzyme activity
GO:0030955 - potassium ion binding
biological_process GO:0018201 - peptidyl-glycine modification
GO:0005975 - carbohydrate metabolic process
GO:0006006 - glucose metabolic process
GO:0006974 - cellular response to DNA damage stimulus
GO:0051604 - protein maturation
Note(s): Note(s): ...[more].
Reference(s): [1] Aso Y., et al., 2019
[2] Byer AS., et al., 2018
[3] Hasan CM., et al., 2008
[4] Knappe J., et al., 1984
[5] Knappe J., et al., 1976
[6] Marzan LW., et al., 2017
[7] Marzan LW., et al., 2013
[8] Matsuoka Y., et al., 2014
[9] Mugabi R., et al., 2012
[10] Salamanca-Cardona L., et al., 2016
[11] Salamanca-Cardona L., et al., 2014
[12] Salamanca-Cardona L., et al., 2017
[13] Shisler KA., et al., 2017
[14] Zhu J., et al., 2005
External database links:  
ALPHAFOLD:
 P0A9N4
DIP:
 DIP-35915N
ECOCYC:
 PFLACTENZ-MONOMER
ECOLIWIKI:
 b0902
INTERPRO:
 IPR012839
INTERPRO:
 IPR012838
INTERPRO:
 IPR007197
INTERPRO:
 IPR034457
INTERPRO:
 IPR001989
INTERPRO:
 IPR034465
INTERPRO:
 IPR013785
PANTHER:
 PTHR30352
PDB:
 3C8F
PDB:
 3CB8
PFAM:
 PF04055
PFAM:
 PF13353
PRIDE:
 P0A9N4
PRODB:
 PRO_000023516
PROSITE:
 PS51918
PROSITE:
 PS01087
REFSEQ:
 NP_415422
SMR:
 P0A9N4
UNIPROT:
 P0A9N4


Operon      
Name: pflA         
Operon arrangement:
Transcription unit        Promoter
pflA


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_1099 950823 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1100 950832 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1101 950837 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1102 950916 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1103 951155 reverse nd [RS-EPT-CBR] [15]
  promoter pflAp8 951228 reverse nd [COMP-AINF] [16]
  promoter TSS_1104 951504 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1105 (cluster) 951515 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1106 951822 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1107 951845 forward nd [RS-EPT-CBR] [15]
  promoter TSS_1108 952063 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1109 952068 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1110 952083 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1111 (cluster) 952140 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1112 952158 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1113 952163 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1114 952167 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1115 (cluster) 952170 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1116 (cluster) 952183 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1117 (cluster) 952196 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1118 952199 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1119 952267 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1120 952271 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1121 952279 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1122 952397 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1123 952407 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1124 (cluster) 952421 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1125 952437 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1126 952443 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1127 952470 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1128 952479 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1129 952493 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1130 952584 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1131 952658 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1132 (cluster) 952666 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1133 952674 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1134 952677 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1135 953144 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1136 953146 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1137 953199 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1138 (cluster) 953225 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1139 953227 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1140 953229 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1141 953233 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1142 (cluster) 953251 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1143 953262 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1144 (cluster) 953311 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1145 953356 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1146 953449 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1147 953452 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1148 953454 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1149 953456 reverse nd [RS-EPT-CBR] [15]
  promoter TSS_1150 953537 reverse nd [RS-EPT-CBR] [15]


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] Aso Y., Tsubaki M., Dang Long BH., Murakami R., Nagata K., Okano H., Phuong Dung NT., Ohara H., 2019, Continuous production of d-lactic acid from cellobiose in cell recycle fermentation using β-glucosidase-displaying Escherichia coli., J Biosci Bioeng 127(4):441-446

 [2] Byer AS., McDaniel EC., Impano S., Broderick WE., Broderick JB., 2018, Mechanistic Studies of Radical SAM Enzymes: Pyruvate Formate-Lyase Activating Enzyme and Lysine 2,3-Aminomutase Case Studies., Methods Enzymol 606:269-318

 [3] Hasan CM., Shimizu K., 2008, Effect of temperature up-shift on fermentation and metabolic characteristics in view of gene expressions in Escherichia coli., Microb Cell Fact 7:35

 [4] Knappe J., Neugebauer FA., Blaschkowski HP., Ganzler M., 1984, Post-translational activation introduces a free radical into pyruvate formate-lyase., Proc Natl Acad Sci U S A 81(5):1332-5

 [5] Knappe J., Schmitt T., 1976, A novel reaction of S-adenosyl-L-methionine correlated with the activation of pyruvate formate-lyase., Biochem Biophys Res Commun 71(4):1110-7

 [6] Marzan LW., Barua R., Akter Y., Arifuzzaman M., Islam MR., Shimizu K., 2017, A single metabolite production by Escherichia coli BW25113 and its pflA.cra mutant cultivated under microaerobic conditions using glycerol or glucose as a carbon source., J Genet Eng Biotechnol 15(1):161-168

 [7] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

 [8] Matsuoka Y., Shimizu K., 2014, Metabolic flux analysis for Escherichia coli by flux balance analysis., Methods Mol Biol 1191:237-60

 [9] Mugabi R., Sandgren D., Born M., Leith I., Horne SM., Pruβ BM., 2012, The role of activated acetate intermediates in the control of Escherichia coli biofilm amounts., Webmedcentral 3(7)

 [10] Salamanca-Cardona L., Scheel RA., Bergey NS., Stipanovic AJ., Matsumoto K., Taguchi S., Nomura CT., 2016, Consolidated bioprocessing of poly(lactate-co-3-hydroxybutyrate) from xylan as a sole feedstock by genetically-engineered Escherichia coli., J Biosci Bioeng 122(4):406-14

 [11] Salamanca-Cardona L., Scheel RA., Lundgren BR., Stipanovic AJ., Matsumoto K., Taguchi S., Nomura CT., 2014, Deletion of the pflA gene in Escherichia coli LS5218 and its effects on the production of polyhydroxyalkanoates using beechwood xylan as a feedstock., Bioengineered 5(5):284-7

 [12] Salamanca-Cardona L., Scheel RA., Mizuno K., Bergey NS., Stipanovic AJ., Matsumoto K., Taguchi S., Nomura CT., 2017, Effect of acetate as a co-feedstock on the production of poly(lactate-co-3-hydroxyalkanoate) by pflA-deficient Escherichia coli RSC10., J Biosci Bioeng 123(5):547-554

 [13] Shisler KA., Hutcheson RU., Horitani M., Duschene KS., Crain AV., Byer AS., Shepard EM., Rasmussen A., Yang J., Broderick WE., Vey JL., Drennan CL., Hoffman BM., Broderick JB., 2017, Monovalent Cation Activation of the Radical SAM Enzyme Pyruvate Formate-Lyase Activating Enzyme., J Am Chem Soc 139(34):11803-11813

 [14] Zhu J., Shimizu K., 2005, Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition., Metab Eng 7(2):104-15

 [15] 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.

 [16] 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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