RegulonDB RegulonDB 10.9: Gene Form
   

mfd gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

mfd ycfT ldtC CpxR terminator mfdp1 mfdp1 TSS_1447 TSS_1447 mfdp2 mfdp2 TSS_1445 TSS_1445 TSS_1444 (cluster) TSS_1444 (cluster) TSS_1443 TSS_1443 ldtCp ldtCp

Gene      
Name: mfd    Texpresso search in the literature
Synonym(s): ECK1100, EG11619, b1114
Genome position(nucleotides): 1170518 <-- 1173964 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.77
External database links:  
ASAP:
ABE-0003763
CGSC:
35179
ECHOBASE:
EB1576
ECOLIHUB:
mfd
OU-MICROARRAY:
b1114
STRING:
511145.b1114
COLOMBOS: mfd


Product      
Name: transcription-repair coupling factor
Synonym(s): Mfd, TRCF
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 129.982
Isoelectric point: 6.084
Motif(s):
 
Type Positions Sequence
217 -> 340 FPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKNWPRVQLK
547 -> 780 GDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPP
724 -> 732 GLLIVDEEH
781 -> 990 ARRLAVKTFVREYDSMVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGSMETIGFSLYMELLENAVDALKAGR
948 -> 948 H

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0003684 - damaged DNA binding
GO:0043175 - RNA polymerase core enzyme binding
GO:0015616 - DNA translocase activity
biological_process GO:0006281 - DNA repair
GO:0006355 - regulation of transcription, DNA-templated
GO:0006974 - cellular response to DNA damage stimulus
GO:0000716 - transcription-coupled nucleotide-excision repair, DNA damage recognition
GO:0006283 - transcription-coupled nucleotide-excision repair
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[IMP] Inferred from mutant phenotype
Reference(s): [1] Brugger C., et al., 2020
[2] Ganesan A., et al., 2012
[3] Ganesan AK., et al., 2010
[4] Ho HN., et al., 2019
[5] Manelyte L., et al., 2010
[6] Monnet J., et al., 2013
[7] Murphy MN., et al., 2009
[8] Oller AR., et al., 1992
[9] Schalow BJ., et al., 2012
[10] Selby CP., et al., 1991
[11] Selby CP., et al., 1990
[12] Selby CP., et al., 1993
[13] Selby CP., et al., 1991
[14] Smith AJ., et al., 2005
[15] Smith AJ., et al., 2008
[16] Washburn RS., et al., 2003
External database links:  
DIP:
DIP-10199N
ECOCYC:
EG11619-MONOMER
ECOLIWIKI:
b1114
INTERPRO:
IPR011545
INTERPRO:
IPR041471
INTERPRO:
IPR037235
INTERPRO:
IPR036101
INTERPRO:
IPR027417
INTERPRO:
IPR014001
INTERPRO:
IPR005118
INTERPRO:
IPR004576
INTERPRO:
IPR003711
INTERPRO:
IPR001650
MODBASE:
P30958
PDB:
6XEO
PDB:
4DFC
PDB:
2EYQ
PDB:
2B2N
PDB:
3HJH
PFAM:
PF03461
PFAM:
PF00270
PFAM:
PF02559
PFAM:
PF17757
PFAM:
PF00271
PRIDE:
P30958
PRODB:
PRO_000023221
PROSITE:
PS51192
PROSITE:
PS51194
REFSEQ:
NP_415632
SMART:
SM01058
SMART:
SM00487
SMART:
SM00490
SMART:
SM00982
SMR:
P30958
SWISSMODEL:
P30958
UNIPROT:
P30958


Operon      
Name: mfd         
Operon arrangement:
Transcription unit        Promoter
mfd
mfd


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_1443 1171800 reverse nd [RS-EPT-CBR] [17]
  promoter TSS_1444 (cluster) 1173832 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [17]
  promoter TSS_1445 1173978 reverse nd [RS-EPT-CBR] [17]
  promoter TSS_1447 1174023 reverse nd [RS-EPT-CBR] [17]


Evidence    

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



Reference(s)    

 [1] Brugger C., Zhang C., Suhanovsky MM., Kim DD., Sinclair AN., Lyumkis D., Deaconescu AM., 2020, Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd., Nat Commun 11(1):3740

 [2] Ganesan A., Spivak G., Hanawalt PC., 2012, Transcription-coupled DNA repair in prokaryotes., Prog Mol Biol Transl Sci 110:25-40

 [3] Ganesan AK., Hanawalt PC., 2010, Transcription-coupled nucleotide excision repair of a gene transcribed by bacteriophage T7 RNA polymerase in Escherichia coli., DNA Repair (Amst) 9(9):958-63

 [4] Ho HN., Zalami D., Kohler J., van Oijen AM., Ghodke H., 2019, Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells., Biophys J 117(5):950-961

 [5] Manelyte L., Kim YI., Smith AJ., Smith RM., Savery NJ., 2010, Regulation and rate enhancement during transcription-coupled DNA repair., Mol Cell 40(5):714-24

 [6] Monnet J., Grange W., Strick TR., Joly N., 2013, Mfd as a central partner of transcription coupled repair., Transcription 4(3):109-13

 [7] Murphy MN., Gong P., Ralto K., Manelyte L., Savery NJ., Theis K., 2009, An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd., Nucleic Acids Res 37(18):6042-53

 [8] Oller AR., Fijalkowska IJ., Dunn RL., Schaaper RM., 1992, Transcription-repair coupling determines the strandedness of ultraviolet mutagenesis in Escherichia coli., Proc Natl Acad Sci U S A 89(22):11036-40

 [9] Schalow BJ., Courcelle CT., Courcelle J., 2012, Mfd is required for rapid recovery of transcription following UV-induced DNA damage but not oxidative DNA damage in Escherichia coli., J Bacteriol 194(10):2637-45

 [10] Selby CP., Sancar A., 1991, Gene- and strand-specific repair in vitro: partial purification of a transcription-repair coupling factor., Proc Natl Acad Sci U S A 88(18):8232-6

 [11] Selby CP., Sancar A., 1990, Transcription preferentially inhibits nucleotide excision repair of the template DNA strand in vitro., J Biol Chem 265(34):21330-6

 [12] Selby CP., Sancar A., 1993, Molecular mechanism of transcription-repair coupling., Science 260(5104):53-8

 [13] Selby CP., Witkin EM., Sancar A., 1991, Escherichia coli mfd mutant deficient in "mutation frequency decline" lacks strand-specific repair: in vitro complementation with purified coupling factor., Proc Natl Acad Sci U S A 88(24):11574-8

 [14] Smith AJ., Savery NJ., 2005, RNA polymerase mutants defective in the initiation of transcription-coupled DNA repair., Nucleic Acids Res 33(2):755-64

 [15] Smith AJ., Savery NJ., 2008, Effects of the bacterial transcription-repair coupling factor during transcription of DNA containing non-bulky lesions., DNA Repair (Amst) 7(10):1670-9

 [16] Washburn RS., Wang Y., Gottesman ME., 2003, Role of E.coli transcription-repair coupling factor Mfd in Nun-mediated transcription termination., J Mol Biol 329(4):655-62

 [17] 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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