RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

pflA gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	pflA
Synonym(s):	ECK0893, EG10028, act, b0902
Genome position(nucleotides):	950340 <-- 951080 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	50.34
External database links:

ASAP:	ABE-0003068
CGSC:	35839
ECHOBASE:	EB0027
OU-MICROARRAY:	b0902
PortEco:	pflA
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
	2 -> 246	SVIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELGKHKWVAMGEEYKLDGVKPPKKETMERVKGILEQYGHKVMF
	130 -> 132	DLK
	16 -> 142	VDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNL
	36 -> 38	YCH
	24 -> 178	ITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNVKVWIRYVVVPGWSDDD

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:0005975 - carbohydrate metabolic process GO:0006006 - glucose metabolic process GO:0006974 - cellular response to DNA damage stimulus GO:0055114 - oxidation-reduction process GO:0018307 - enzyme active site formation

Note(s):

Note(s): ...[more].

Reference(s):

[1] Byer AS., et al., 2018
[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., 2013
[7] Mugabi R., et al., 2012
[8] Shisler KA., et al., 2017
[9] Zhu J., et al., 2005

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

PANTHER:

PDB:

PDB:

PFAM:

PRIDE:

PRODB:

PROSITE:

REFSEQ:

SMART:

SMR:

UNIPROT:

Operon

Name:

pflA

Operon arrangement:

Transcription unit	Promoter
pflA	pflAp

RNA cis-regulatory element

Attenuation:	Transcriptional

Regulation by small RNA
	Display Regulation
small RNA	ryhB

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_1099	950823	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1100	950832	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1101	950837	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1102	950916	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1103	951155	reverse	nd	[RS-EPT-CBR]	[10]
promoter	pflAp8	951228	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.413. P-value: 3.802e-6 Read more >	[ICWHO]	[11]
promoter	TSS_1104	951504	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1105 (cluster)	951515	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 951514 to 951515, where the highest frequency is at position 950738. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[10]
promoter	TSS_1106	951822	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1107	951845	forward	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1108	952063	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1109	952068	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1110	952083	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1111 (cluster)	952140	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 952139 to 952140, where the highest frequency is at position 951363. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[10]
promoter	TSS_1112	952158	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1113	952163	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1114	952167	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1115 (cluster)	952170	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 952169 to 952170, where the highest frequency is at position 951393. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[10]
promoter	TSS_1116 (cluster)	952183	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 952182 to 952183, where the highest frequency is at position 951406. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[10]
promoter	TSS_1117 (cluster)	952196	reverse	For this promoter, there is a cluster of 12 transcription start sites,in the interval 952185 to 952196, where the highest frequency is at position 951411. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[10]
promoter	TSS_1118	952199	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1119	952267	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1120	952271	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1121	952279	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1122	952397	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1123	952407	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1124 (cluster)	952421	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 952420 to 952421, where the highest frequency is at position 951643. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[10]
promoter	TSS_1125	952437	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1126	952443	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1127	952470	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1128	952479	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1129	952493	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1130	952584	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1131	952658	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1132 (cluster)	952666	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 952665 to 952666, where the highest frequency is at position 951888. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[10]
promoter	TSS_1133	952674	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1134	952677	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1135	953144	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1136	953146	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1137	953199	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1138 (cluster)	953225	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 953224 to 953225, where the highest frequency is at position 952447. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[10]
promoter	TSS_1139	953227	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1140	953229	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1141	953233	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1142 (cluster)	953251	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 953250 to 953251, where the highest frequency is at position 952473. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[10]
promoter	TSS_1143	953262	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1144 (cluster)	953311	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 953310 to 953311, where the highest frequency is at position 952534. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[10]
promoter	TSS_1145	953356	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1146	953449	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1147	953452	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1148	953454	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1149	953456	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_1150	953537	reverse	nd	[RS-EPT-CBR]	[10]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[ICWHO] Inferred computationally without human oversight

Reference(s)
[1] 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
[2] Byer AS., Yang H., McDaniel EC., Kathiresan V., Impano S., Pagnier A., Watts H., Denler C., Vagstad AL., Piel J., Duschene KS., Shepard EM., Shields TP., Scott LG., Lilla EA., Yokoyama K., Broderick WE., Hoffman BM., Broderick JB., 2018, Paradigm Shift for Radical S-Adenosyl-l-methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis., J Am Chem Soc 140(28):8634-8638
[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., 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
[7] 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)
[8] 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
[9] 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
[10] 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.
[11] 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

RegulonDB