mfd:Gene Product(s): Difference between revisions

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[[ihfA:Gene_Product(s)|ihfA]]<br />
[[ihfA:Gene_Product(s)|ihfA]]<br />
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|[[PMID:16606699]]<ref name=PMID:16606699/>
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Experiment(s):[http://www.ebi.ac.uk/iintact/search/do/search?searchString=EBI-1138903 EBI-1138903]<br />
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Protein
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[[rpsM:Gene_Product(s)|rpsM]]<br />
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Revision as of 03:33, 6 February 2009

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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]

Product description

transcription-repair coupling factor[2][3]

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. See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference(s) Evidence Code with/from Aspect Notes Status
GO:0005515

protein binding

PMID:16469698[4]

IPI: Inferred from Physical Interaction

UniProtKB:P0A8V2

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0000166

nucleotide binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0003676

nucleic acid binding

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650
InterPro:IPR011545

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0003677

DNA binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0003684

damaged DNA binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004576

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0003700

transcription factor activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003711

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0004386

helicase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR001650
SP_KW:KW-0347

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0005524

ATP binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR001650
InterPro:IPR004576
InterPro:IPR011545
SP_KW:KW-0067

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0006281

DNA repair

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR004576
SP_KW:KW-0234

P

Seeded from EcoCyc 12.5 [5]

complete

GO:0006355

regulation of transcription, DNA-dependent

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003711

P

Seeded from EcoCyc 12.5 [5]

complete

GO:0006974

response to DNA damage stimulus

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc 12.5 [5]

complete

GO:0008026

ATP-dependent helicase activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0016787

hydrolase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0006350

transcription

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

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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[6]

Experiment(s):EBI-893742

Protein

yffB

 PMID:15690043[6]

Experiment(s):EBI-893742

Protein

ihfA

 PMID:16606699[7]

Experiment(s):EBI-1138903

Protein

rpsM

 PMID:16606699[7]

Experiment(s):EBI-1138903

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See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Notes

Mfd is involved in transcription-coupled repair[8][9]. Mfd is is an ATPase that can release stalled or paused RNA polymerases from DNA lesions, including thymine dimers and abasic sites[10]

Localization

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

Compartment Description Evidence 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.

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
Mol. Wt

129.98 kDa (calc) [2]

pI
Extinction coefficient

95230 - 96105 (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.

Type Residues Description Notes

Domain

615 - 776

Helicase ATP-binding

UniProt:P30958

Domain

798 - 951

Helicase C-terminal

UniProt:P30958

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Structure

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Structures

<beststructure>mfd 562</beststructure>

Models

View models at:

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Notes

Gene Product Resources

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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

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

Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11619-MONOMER

SwissModel (EcoliWiki Page)

SwissModel:P30958

UniProt (EcoliWiki Page)

UniProt:P30958

PFAM (EcoliWiki Page)

PFAM:PF02559

RefSeq (EcoliWiki Page)

RefSeq:NP_415632

ModBase (EcoliWiki Page)

ModBase:P30958

PDB (EcoliWiki Page)

PDB:2B2N


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Notes

Links

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Name URL Comments
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References

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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 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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. ↑ Deaconescu, AM et al. (2006) Structural basis for bacterial transcription-coupled DNA repair. Cell 124 507-20 PubMed
  5. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 5.12 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  6. ↑ 6.0 6.1 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. ↑ 7.0 7.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ Selby, CP & Sancar, A (1993) Molecular mechanism of transcription-repair coupling. Science 260 53-8 PubMed
  9. ↑ Roberts, J & Park, JS (2004) Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination. Curr. Opin. Microbiol. 7 120-5 PubMed
  10. ↑ 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


Categories

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