mfd:Gene Product(s)

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

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)


edit table

<protect></protect>

Notes

Function

[back to top]


<protect> 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[5]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006355

regulation of transcription, DNA-dependent

PMID:8465200[6]

IDA: Inferred from Direct Assay

P

complete

GO:0006974

response to DNA damage stimulus

PMID:8465200[6]

IDA: Inferred from Direct Assay

P

complete

GO:0000716

transcription-coupled nucleotide-excision repair, DNA damage recognition

PMID:8465200[6]

IDA: Inferred from Direct Assay

P

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003684

damaged DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004576

F

Seeded from EcoCyc (v14.0)

complete

GO:0003684

damaged DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005118

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003711

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004576

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005118

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0347

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004576

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005118

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004576

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005118

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

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
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003711

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc (v14.0)

complete

GO:0008026

ATP-dependent helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

edit table

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[7]

Experiment(s):EBI-893742

Protein

yffB

PMID:15690043[7]

Experiment(s):EBI-893742

Protein

ihfA

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

rpsM

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

yeeT

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

rplB

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

stpA

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

nfrA

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

tdcC

PMID:19402753[9]

LCMS(ID Probability):99.0

Protein

yffB

PMID:19402753[9]

LCMS(ID Probability):99.0

edit table

</protect>

Notes

Mfd is involved in transcription-coupled repair[6][10]. Mfd is is an ATPase that can release stalled or paused RNA polymerases from DNA lesions, including thymine dimers and abasic sites[11]

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

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)

edit table


Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

602..766

PF00270 DEAD/DEAH box helicase

PMID:19920124[12]

Domain

832..907

PF00271 Helicase conserved C-terminal domain

PMID:19920124[12]

Domain

476..573

PF02559 CarD-like/TRCF domain

PMID:19920124[12]

Domain

1005..1105

PF03461 TRCF domain

PMID:19920124[12]

edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=mfd taxon=562,83333 </beststructure>

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129077

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945681

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003763

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P30958

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11619

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11619

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945681

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001567

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1576

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Selby, CP et al. (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 11574-8 PubMed
  6. ↑ 6.0 6.1 6.2 6.3 Selby, CP & Sancar, A (1993) Molecular mechanism of transcription-repair coupling. Science 260 53-8 PubMed
  7. ↑ 7.0 7.1 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  9. ↑ 9.0 9.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  10. ↑ Roberts, J & Park, JS (2004) Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination. Curr. Opin. Microbiol. 7 120-5 PubMed
  11. ↑ 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
  12. ↑ 12.0 12.1 12.2 12.3 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=mfd:Gene_Product(s)&oldid=1493079"