mfd:On One Page
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Quickview | Gene | Gene Product(s) | Expression | Evolution | On One Page |
Quickview | | Gene | | Product(s) | | Expression| | Evolution | | References | |
Quickview
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Standard Name |
mfd |
---|---|
Gene Synonym(s) |
ECK1100, b1114, JW1100[1], JW1100 |
Product Desc. |
transcription-repair coupling factor[2][3] Transcription repair coupling factor[4] |
Product Synonyms(s) |
transcription-repair coupling factor[1], B1114[2][1], Mfd[2][1], TRCF[3][1] , ECK1100, JW1100, b1114 |
Function from GO |
<GO_nr /> |
Knock-Out Phenotype | |
Regulation/Expression | |
Regulation/Activity | |
Quick Links | |
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Notes
Mfd dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. Arrested (backtracked) RNAP complexes are are also rescued by Mfd promoting forward translocation. Mfd structure resembles UvrB, including UvrA binding site, but no ATP-binding site.[4]
Gene
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
Standard name |
mfd |
---|---|
Mnemonic |
Mutation frequency decline |
Synonyms |
ECK1100, b1114, JW1100[1], JW1100 |
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Notes
Location(s) and DNA Sequence
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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.
Strain | Map location | Genome coordinates | Genome browsers | Sequence links |
---|---|---|---|---|
MG1655 |
25.21 minutes |
MG1655: 1173187..1169741 |
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NC_012967: 1188559..1185113 |
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NC_012759: 1073666..1077112 |
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W3110 |
|
W3110: 1175541..1172095 |
||
DH10B: 1228632..1225186 |
||||
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Notes
Sequence Features
See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.
Feature Type | Strain | Genomic Location | Evidence | Reference | Notes |
---|---|---|---|---|---|
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Notes
Alleles and Phenotypes
See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.
Allele | Nt change(s) | AA change(s) | Phenotype: Type | Phenotype: Description | Reference | Availability | Comments |
---|---|---|---|---|---|---|---|
Δmfd (Keio:JW1100) |
deletion |
deletion |
PMID:16738554 |
||||
mfd::Tn5KAN-2 (FB20256) |
Insertion at nt 291 in Plus orientation |
PMID:15262929 |
does not contain pKD46 | ||||
mfd-1 |
|||||||
Δmfd-739::kan |
PMID:16738554 |
||||||
mfd in MDS42 |
deletion |
Sensitivity to |
increases sensitivity to Bicyclomycin |
PMID:21183718 |
fig. 2 | ||
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Notes
Genetic Interactions
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Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
---|---|---|---|---|---|---|
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Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
Resource | Resource Type | Source | Notes/Reference |
---|---|---|---|
JW1100 |
Plasmid clone |
PMID:16769691 Status:Clone OK Primer 1:GCCCCTGAACAATATCGTTATAC Primer 2:CCAGCGATCGCGTTCTCTTCCAG | |
Kohara Phage |
PMID:3038334 | ||
Kohara Phage |
PMID:3038334 | ||
Linked marker |
est. P1 cotransduction: 60% [6] | ||
Linked marker |
est. P1 cotransduction: 17% [6] | ||
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Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
EcoCyc:EG11619 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG11619 |
Escherichia coli str. K-12 substr. MG1655 | |
RegulonDB:ECK120001567 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
EchoBASE:EB1576 |
Escherichia coli str. K-12 substr. MG1655 | |
ASAP:ABE-0003763 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
Name | URL | Comments |
---|---|---|
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Product(s)
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Nomenclature
See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.
Standard name |
Mfd |
---|---|
Synonyms |
transcription-repair coupling factor[1], B1114[2][1], Mfd[2][1], TRCF[3][1] , ECK1100, JW1100, b1114 |
Product description |
transcription-repair coupling factor[2][3] Transcription repair coupling factor[4] |
EC number (for enzymes) |
|
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Notes
Function
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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.
Qualifier | GO ID | GO term name | Reference | Evidence Code | with/from | Aspect | Notes | Status |
---|---|---|---|---|---|---|---|---|
GO:0006281 |
DNA repair |
PMID:1763073 |
IMP: Inferred from Mutant Phenotype |
P |
complete | |||
GO:0006355 |
regulation of transcription, DNA-dependent |
PMID:8465200 |
IDA: Inferred from Direct Assay |
P |
complete | |||
GO:0006974 |
response to DNA damage stimulus |
PMID:8465200 |
IDA: Inferred from Direct Assay |
P |
complete | |||
GO:0000716 |
transcription-coupled nucleotide-excision repair, DNA damage recognition |
PMID:8465200 |
IDA: Inferred from Direct Assay |
P |
complete | |||
GO:0000166 |
nucleotide binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0547 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0003676 |
nucleic acid binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001650 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0003676 |
nucleic acid binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR011545 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0003677 |
DNA binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0238 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0003684 |
damaged DNA binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR004576 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0003684 |
damaged DNA binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR005118 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0003700 |
transcription factor activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR003711 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0004386 |
helicase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001650 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0004386 |
helicase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR004576 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0004386 |
helicase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR005118 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0004386 |
helicase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0347 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0005524 |
ATP binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR001650 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0005524 |
ATP binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR004576 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0005524 |
ATP binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR005118 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0005524 |
ATP binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR011545 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0005524 |
ATP binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0067 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0006281 |
DNA repair |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR004576 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0006281 |
DNA repair |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR005118 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0006281 |
DNA repair |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0234 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0006355 |
regulation of transcription, DNA-dependent |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR003711 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0006974 |
response to DNA damage stimulus |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0227 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0008026 |
ATP-dependent helicase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR011545 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0016787 |
hydrolase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0378 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.
Partner Type | Partner | Notes | References | Evidence |
---|---|---|---|---|
Protein |
tdcC |
PMID:15690043 |
Experiment(s):EBI-893742 | |
Protein |
yffB |
PMID:15690043 |
Experiment(s):EBI-893742 | |
Protein |
ihfA |
PMID:16606699 |
Experiment(s):EBI-1138903 | |
Protein |
rpsM |
PMID:16606699 |
Experiment(s):EBI-1138903 | |
Protein |
yeeT |
PMID:16606699 |
Experiment(s):EBI-1138903 | |
Protein |
rplB |
PMID:16606699 |
Experiment(s):EBI-1138903 | |
Protein |
stpA |
PMID:16606699 |
Experiment(s):EBI-1138903 | |
Protein |
nfrA |
PMID:16606699 |
Experiment(s):EBI-1138903 | |
Protein |
tdcC |
PMID:19402753 |
LCMS(ID Probability):99.0 | |
Protein |
yffB |
PMID:19402753 |
LCMS(ID Probability):99.0 | |
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Notes
Mfd is involved in transcription-coupled repair[7][8]. Mfd is is an ATPase that can release stalled or paused RNA polymerases from DNA lesions, including thymine dimers and abasic sites[9]
Localization
See Help:Product_localization for how to add or edit information in this section of EcoliWiki.
Compartment | Description | Evidence | Reference/Source | Notes |
---|---|---|---|---|
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Notes
Structure and Physical Properties
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Physical Properties
See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
Name | |
---|---|
Sequence |
MPEQYRYTLP VKAGEQRLLG ELTGAACATL VAEIAERHAG PVVLIAPDMQ NALRLHDEIS QFTDQMVMNL ADWETLPYDS FSPHQDIISS RLSTLYQLPT MQRGVLIVPV NTLMQRVCPH SFLHGHALVM KKGQRLSRDA LRTQLDSAGY RHVDQVMEHG EYATRGALLD LFPMGSELPY RLDFFDDEID SLRVFDVDSQ RTLEEVEAIN LLPAHEFPTD KAAIELFRSQ WRDTFEVKRD PEHIYQQVSK GTLPAGIEYW QPLFFSEPLP PLFSYFPANT LLVNTGDLET SAERFQADTL ARFENRGVDP MRPLLPPQSL WLRVDELFSE LKNWPRVQLK TEHLPTKAAN ANLGFQKLPD LAVQAQQKAP LDALRKFLET FDGPVVFSVE SEGRREALGE LLARIKIAPQ RIMRLDEASD RGRYLMIGAA EHGFVDTVRN LALICESDLL GERVARRRQD SRRTINPDTL IRNLAELHIG QPVVHLEHGV GRYAGMTTLE AGGITGEYLM LTYANDAKLY VPVSSLHLIS RYAGGAEENA PLHKLGGDAW SRARQKAAEK VRDVAAELLD IYAQRAAKEG FAFKHDREQY QLFCDSFPFE TTPDQAQAIN AVLSDMCQPL AMDRLVCGDV GFGKTEVAMR AAFLAVDNHK QVAVLVPTTL LAQQHYDNFR DRFANWPVRI EMISRFRSAK EQTQILAEVA EGKIDILIGT HKLLQSDVKF KDLGLLIVDE EHRFGVRHKE RIKAMRANVD ILTLTATPIP RTLNMAMSGM RDLSIIATPP ARRLAVKTFV REYDSMVVRE AILREILRGG QVYYLYNDVE NIQKAAERLA ELVPEARIAI GHGQMREREL ERVMNDFHHQ RFNVLVCTTI IETGIDIPTA NTIIIERADH FGLAQLHQLR GRVGRSHHQA YAWLLTPHPK AMTTDAQKRL EAIASLEDLG AGFALATHDL EIRGAGELLG EEQSGSMETI GFSLYMELLE NAVDALKAGR EPSLEDLTSQ QTEVELRMPS LLPDDFIPDV NTRLSFYKRI ASAKTENELE EIKVELIDRF GLLPDPARTL LDIARLRQQA QKLGIRKLEG NEKGGVIEFA EKNHVNPAWL IGLLQKQPQH YRLDGPTRLK FIQDLSERKT RIEWVRQFMR ELEENAIA |
Length |
1,148 |
Mol. Wt |
129.985 kDa |
pI |
6.1 (calculated) |
Extinction coefficient |
95,230 - 96,105 (calc based on 27 Y, 10 W, and 7 C residues) |
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Domains/Motifs/Modification Sites
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
|
<motif_map/> |
Structure
| </protect>
Structure figures<protect> | ||||||
Notes
Gene Product Resources
See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.
Resource type | Source | Notes/Reference |
---|---|---|
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Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
Escherichia coli str. K-12 substr. MG1655 | ||
Escherichia coli str. K-12 substr. MG1655 | ||
ASAP:ABE-0003763 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
EcoCyc:EG11619 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG11619 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
RegulonDB:ECK120001567 |
Escherichia coli str. K-12 substr. MG1655 | |
EchoBASE:EB1576 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
Name | URL | Comments |
---|---|---|
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Expression
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Overview
This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.
Cellular Levels
Molecule | Organism or Strain | Value | Units | Experimental Conditions | Assay used | Notes | Reference(s) |
---|---|---|---|---|---|---|---|
Protein |
E. coli K-12 MC4100 |
2.02E+02 |
molecules/cell |
|
emPAI |
PMID:18304323 | |
Protein |
Ecoli K-12 |
10.744+/-0.089 |
Molecules/cell |
|
Single Molecule Fluorescence |
PMID:20671182 | |
mRNA |
Ecoli K-12 |
0.028148578 |
Molecules/cell |
|
by RNA_Seq |
PMID:20671182 | |
Protein |
E. coli K-12 MG1655 |
588 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
Protein |
E. coli K-12 MG1655 |
353 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
Protein |
E. coli K-12 MG1655 |
525 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
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Notes
Transcription and Transcriptional Regulation
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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.
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Notes
This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.
Translation and Regulation of Translation
<protect><gbrowseImage>
name=NC_000913:1173167..1173207
source=MG1655
flip=1
type=Gene+DNA_+Protein
preset=Nterminus
</gbrowseImage>
This picture shows the sequence around the N-terminus.
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Notes
This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.
Turnover and Regulation of Turnover
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Notes
This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.
Experimental
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Mutations Affecting Expression
See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.
Allele Name | Mutation | Phenotype | Reference |
---|---|---|---|
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Expression Studies
See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.
Type | Reference | Notes |
---|---|---|
microarray |
NCBI GEO profiles for mfd | |
microarray |
Summary of data for mfd from multiple microarray studies | |
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Expression Resources
See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.
Resource Name | Resource Type | Description | Source | Notes |
---|---|---|---|---|
GFP Fusion |
Intergenic region (1173119..1173392) fused to gfpmut2. |
GFP fusion described in Zaslaver, et al. | ||
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Notes
Accessions Related to mfd Expression
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
EcoCyc:EG11619 |
Escherichia coli str. K-12 substr. MG1655 | |
EchoBASE:EB1576 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG11619 |
Escherichia coli str. K-12 substr. MG1655 | |
RegulonDB:ECK120001567 |
Escherichia coli str. K-12 substr. MG1655 | |
ASAP:ABE-0003763 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
Name | URL | Comments |
---|---|---|
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Evolution
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Homologs in Other Organisms
See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.
Organism | Homologs (Statistics) | Comments |
---|---|---|
Arabidopsis thaliana |
|
From Inparanoid:20070104 |
Shigella flexneri |
MFD |
From SHIGELLACYC |
E. coli O157 |
MFD |
From ECOO157CYC |
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Do-It-Yourself Web Tools
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Notes
Families
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
EcoCyc:EG11619 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG11619 |
Escherichia coli str. K-12 substr. MG1655 | |
RegulonDB:ECK120001567 |
Escherichia coli str. K-12 substr. MG1655 | |
EchoBASE:EB1576 |
Escherichia coli str. K-12 substr. MG1655 | |
ASAP:ABE-0003763 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
Name | URL | Comments |
---|---|---|
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References
See Help:References for how to manage references in EcoliWiki.
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
- ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
- ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
- ↑ Selby, CP & Sancar, A (1993) Molecular mechanism of transcription-repair coupling. Science 260 53-8 PubMed
- ↑ Roberts, J & Park, JS (2004) Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination. Curr. Opin. Microbiol. 7 120-5 PubMed
- ↑ 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 1670-9 PubMed
- ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed
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