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Protein

Transcription-repair-coupling factor

Gene

mfd

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site. Can also dissociate RNAP that is blocked by low concentration of nucleoside triphosphates or by physical obstruction, such as bound proteins. In addition, can rescue arrested complexes by promoting forward translocation. Has ATPase activity, which is required for removal of stalled RNAP, but seems to lack helicase activity. May act through a translocase activity that rewinds upstream DNA, leading either to translocation or to release of RNAP when the enzyme active site cannot continue elongation.UniRule annotation5 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi628 – 6358ATPUniRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • ATP-dependent helicase activity Source: EcoCyc
  • damaged DNA binding Source: InterPro
  • DNA binding Source: EcoCyc
  • DNA translocase activity Source: EcoCyc
  • RNA polymerase core enzyme binding Source: EcoCyc

GO - Biological processi

  • cellular response to DNA damage stimulus Source: EcoliWiki
  • DNA repair Source: EcoliWiki
  • regulation of transcription, DNA-templated Source: EcoliWiki
  • transcription-coupled nucleotide-excision repair, DNA damage recognition Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11619-MONOMER.
ECOL316407:JW1100-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription-repair-coupling factorUniRule annotation (EC:3.6.4.-UniRule annotation)
Short name:
TRCFUniRule annotation
Gene namesi
Name:mfdUniRule annotation
Ordered Locus Names:b1114, JW1100
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11619. mfd.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11481148Transcription-repair-coupling factorPRO_0000102166Add
BLAST

Proteomic databases

PaxDbiP30958.
PRIDEiP30958.

Interactioni

Subunit structurei

Monomer. Interacts with UvrA and RNAP.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
uvrAP0A6982EBI-554211,EBI-552091

GO - Molecular functioni

  • RNA polymerase core enzyme binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4260086. 165 interactions.
DIPiDIP-10199N.
IntActiP30958. 17 interactions.
MINTiMINT-1231460.
STRINGi511145.b1114.

Structurei

Secondary structure

1
1148
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi16 – 205Combined sources
Helixi26 – 3712Combined sources
Beta strandi38 – 403Combined sources
Beta strandi42 – 487Combined sources
Helixi49 – 6113Combined sources
Beta strandi67 – 693Combined sources
Helixi85 – 9713Combined sources
Helixi98 – 1003Combined sources
Beta strandi103 – 1097Combined sources
Helixi110 – 1145Combined sources
Helixi120 – 1256Combined sources
Beta strandi128 – 1314Combined sources
Helixi138 – 14710Combined sources
Beta strandi151 – 1555Combined sources
Beta strandi161 – 1655Combined sources
Beta strandi168 – 1714Combined sources
Beta strandi180 – 1856Combined sources
Beta strandi188 – 1969Combined sources
Turni197 – 2004Combined sources
Beta strandi201 – 21212Combined sources
Beta strandi214 – 2174Combined sources
Helixi221 – 23414Combined sources
Helixi244 – 2496Combined sources
Helixi257 – 2648Combined sources
Beta strandi265 – 2673Combined sources
Helixi272 – 2754Combined sources
Beta strandi281 – 2844Combined sources
Helixi288 – 30619Combined sources
Helixi317 – 3193Combined sources
Helixi324 – 3318Combined sources
Beta strandi336 – 3394Combined sources
Beta strandi350 – 3523Combined sources
Beta strandi366 – 3694Combined sources
Helixi372 – 3809Combined sources
Beta strandi385 – 3906Combined sources
Turni394 – 3985Combined sources
Helixi399 – 4024Combined sources
Helixi403 – 4053Combined sources
Helixi415 – 4173Combined sources
Beta strandi423 – 4286Combined sources
Beta strandi434 – 4363Combined sources
Turni437 – 4404Combined sources
Beta strandi441 – 4455Combined sources
Helixi446 – 4494Combined sources
Helixi461 – 4633Combined sources
Helixi467 – 4726Combined sources
Beta strandi482 – 4854Combined sources
Turni486 – 4883Combined sources
Beta strandi489 – 50315Combined sources
Beta strandi505 – 5128Combined sources
Helixi514 – 5163Combined sources
Beta strandi518 – 5225Combined sources
Helixi523 – 5286Combined sources
Beta strandi529 – 5313Combined sources
Beta strandi537 – 5393Combined sources
Helixi549 – 57628Combined sources
Helixi587 – 5959Combined sources
Helixi603 – 61715Combined sources
Beta strandi618 – 6203Combined sources
Beta strandi623 – 6275Combined sources
Turni632 – 6354Combined sources
Helixi636 – 64611Combined sources
Turni647 – 6493Combined sources
Beta strandi651 – 6555Combined sources
Helixi659 – 67214Combined sources
Turni674 – 6774Combined sources
Beta strandi680 – 6845Combined sources
Helixi689 – 70012Combined sources
Beta strandi705 – 7095Combined sources
Helixi712 – 7154Combined sources
Beta strandi721 – 73010Combined sources
Helixi731 – 7333Combined sources
Helixi736 – 74611Combined sources
Beta strandi749 – 7579Combined sources
Helixi761 – 7677Combined sources
Turni768 – 7703Combined sources
Beta strandi771 – 7755Combined sources
Beta strandi786 – 7927Combined sources
Helixi795 – 80612Combined sources
Turni807 – 8093Combined sources
Beta strandi811 – 8155Combined sources
Helixi822 – 83211Combined sources
Beta strandi838 – 8403Combined sources
Helixi847 – 85812Combined sources
Beta strandi864 – 8696Combined sources
Helixi872 – 8743Combined sources
Beta strandi880 – 8856Combined sources
Turni886 – 8894Combined sources
Helixi893 – 9008Combined sources
Beta strandi910 – 9167Combined sources
Helixi919 – 9213Combined sources
Helixi924 – 93310Combined sources
Beta strandi938 – 9403Combined sources
Helixi941 – 95919Combined sources
Helixi961 – 97010Combined sources
Helixi972 – 98817Combined sources
Helixi995 – 9973Combined sources
Turni1014 – 10163Combined sources
Helixi1020 – 103213Combined sources
Helixi1036 – 105015Combined sources
Helixi1055 – 107319Combined sources
Beta strandi1078 – 10803Combined sources
Beta strandi1082 – 10887Combined sources
Helixi1097 – 110610Combined sources
Helixi1108 – 11103Combined sources
Beta strandi1111 – 11144Combined sources
Turni1115 – 11173Combined sources
Beta strandi1118 – 11225Combined sources
Helixi1128 – 114316Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2B2NX-ray2.10A/B1-333[»]
2EYQX-ray3.20A/B1-1148[»]
3HJHX-ray1.95A1-470[»]
4DFCX-ray2.80A/C127-213[»]
ProteinModelPortaliP30958.
SMRiP30958. Positions 2-1147.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP30958.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini615 – 776162Helicase ATP-bindingUniRule annotationAdd
BLAST
Domaini798 – 951154Helicase C-terminalUniRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi729 – 7324DEEH box

Domaini

Consists of a compact arrangement of structured domains linked by long, flexible linkers. The N-terminal region interacts with UvrA, the central region interacts with RNAP, and the C-terminal DNA translocase region possesses ATPase activity. Activity is regulated by a conformational switch from a dormant closed state to an active open state upon substrate binding.5 Publications

Sequence similaritiesi

In the N-terminal section; belongs to the UvrB family.UniRule annotation
In the C-terminal section; belongs to the helicase family. RecG subfamily.UniRule annotation
Contains 1 helicase ATP-binding domain.UniRule annotation
Contains 1 helicase C-terminal domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108JA2. Bacteria.
COG1197. LUCA.
HOGENOMiHOG000216592.
InParanoidiP30958.
KOiK03723.
OMAiGTHKLIQ.
PhylomeDBiP30958.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00969. TRCF. 1 hit.
InterProiIPR003711. CarD-like/TRCF_domain.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR004576. Mfd.
IPR027417. P-loop_NTPase.
IPR005118. TRCF_C.
[Graphical view]
PfamiPF02559. CarD_CdnL_TRCF. 1 hit.
PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
PF03461. TRCF. 1 hit.
[Graphical view]
SMARTiSM01058. CarD_TRCF. 1 hit.
SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SM00982. TRCF. 1 hit.
[Graphical view]
SUPFAMiSSF141259. SSF141259. 1 hit.
SSF52540. SSF52540. 4 hits.
TIGRFAMsiTIGR00580. mfd. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P30958-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPEQYRYTLP VKAGEQRLLG ELTGAACATL VAEIAERHAG PVVLIAPDMQ
60 70 80 90 100
NALRLHDEIS QFTDQMVMNL ADWETLPYDS FSPHQDIISS RLSTLYQLPT
110 120 130 140 150
MQRGVLIVPV NTLMQRVCPH SFLHGHALVM KKGQRLSRDA LRTQLDSAGY
160 170 180 190 200
RHVDQVMEHG EYATRGALLD LFPMGSELPY RLDFFDDEID SLRVFDVDSQ
210 220 230 240 250
RTLEEVEAIN LLPAHEFPTD KAAIELFRSQ WRDTFEVKRD PEHIYQQVSK
260 270 280 290 300
GTLPAGIEYW QPLFFSEPLP PLFSYFPANT LLVNTGDLET SAERFQADTL
310 320 330 340 350
ARFENRGVDP MRPLLPPQSL WLRVDELFSE LKNWPRVQLK TEHLPTKAAN
360 370 380 390 400
ANLGFQKLPD LAVQAQQKAP LDALRKFLET FDGPVVFSVE SEGRREALGE
410 420 430 440 450
LLARIKIAPQ RIMRLDEASD RGRYLMIGAA EHGFVDTVRN LALICESDLL
460 470 480 490 500
GERVARRRQD SRRTINPDTL IRNLAELHIG QPVVHLEHGV GRYAGMTTLE
510 520 530 540 550
AGGITGEYLM LTYANDAKLY VPVSSLHLIS RYAGGAEENA PLHKLGGDAW
560 570 580 590 600
SRARQKAAEK VRDVAAELLD IYAQRAAKEG FAFKHDREQY QLFCDSFPFE
610 620 630 640 650
TTPDQAQAIN AVLSDMCQPL AMDRLVCGDV GFGKTEVAMR AAFLAVDNHK
660 670 680 690 700
QVAVLVPTTL LAQQHYDNFR DRFANWPVRI EMISRFRSAK EQTQILAEVA
710 720 730 740 750
EGKIDILIGT HKLLQSDVKF KDLGLLIVDE EHRFGVRHKE RIKAMRANVD
760 770 780 790 800
ILTLTATPIP RTLNMAMSGM RDLSIIATPP ARRLAVKTFV REYDSMVVRE
810 820 830 840 850
AILREILRGG QVYYLYNDVE NIQKAAERLA ELVPEARIAI GHGQMREREL
860 870 880 890 900
ERVMNDFHHQ RFNVLVCTTI IETGIDIPTA NTIIIERADH FGLAQLHQLR
910 920 930 940 950
GRVGRSHHQA YAWLLTPHPK AMTTDAQKRL EAIASLEDLG AGFALATHDL
960 970 980 990 1000
EIRGAGELLG EEQSGSMETI GFSLYMELLE NAVDALKAGR EPSLEDLTSQ
1010 1020 1030 1040 1050
QTEVELRMPS LLPDDFIPDV NTRLSFYKRI ASAKTENELE EIKVELIDRF
1060 1070 1080 1090 1100
GLLPDPARTL LDIARLRQQA QKLGIRKLEG NEKGGVIEFA EKNHVNPAWL
1110 1120 1130 1140
IGLLQKQPQH YRLDGPTRLK FIQDLSERKT RIEWVRQFMR ELEENAIA
Length:1,148
Mass (Da):129,983
Last modified:November 1, 1997 - v2
Checksum:i8E0D149306C8C31C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti365 – 3651A → R (PubMed:8465200).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74198.1.
AP009048 Genomic DNA. Translation: BAA35929.1.
PIRiG64855.
RefSeqiNP_415632.1. NC_000913.3.
WP_001115094.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74198; AAC74198; b1114.
BAA35929; BAA35929; BAA35929.
GeneIDi945681.
KEGGiecj:JW1100.
eco:b1114.
PATRICi32117471. VBIEscCol129921_1158.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74198.1.
AP009048 Genomic DNA. Translation: BAA35929.1.
PIRiG64855.
RefSeqiNP_415632.1. NC_000913.3.
WP_001115094.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2B2NX-ray2.10A/B1-333[»]
2EYQX-ray3.20A/B1-1148[»]
3HJHX-ray1.95A1-470[»]
4DFCX-ray2.80A/C127-213[»]
ProteinModelPortaliP30958.
SMRiP30958. Positions 2-1147.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260086. 165 interactions.
DIPiDIP-10199N.
IntActiP30958. 17 interactions.
MINTiMINT-1231460.
STRINGi511145.b1114.

Proteomic databases

PaxDbiP30958.
PRIDEiP30958.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74198; AAC74198; b1114.
BAA35929; BAA35929; BAA35929.
GeneIDi945681.
KEGGiecj:JW1100.
eco:b1114.
PATRICi32117471. VBIEscCol129921_1158.

Organism-specific databases

EchoBASEiEB1576.
EcoGeneiEG11619. mfd.

Phylogenomic databases

eggNOGiENOG4108JA2. Bacteria.
COG1197. LUCA.
HOGENOMiHOG000216592.
InParanoidiP30958.
KOiK03723.
OMAiGTHKLIQ.
PhylomeDBiP30958.

Enzyme and pathway databases

BioCyciEcoCyc:EG11619-MONOMER.
ECOL316407:JW1100-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP30958.
PROiP30958.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00969. TRCF. 1 hit.
InterProiIPR003711. CarD-like/TRCF_domain.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR004576. Mfd.
IPR027417. P-loop_NTPase.
IPR005118. TRCF_C.
[Graphical view]
PfamiPF02559. CarD_CdnL_TRCF. 1 hit.
PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
PF03461. TRCF. 1 hit.
[Graphical view]
SMARTiSM01058. CarD_TRCF. 1 hit.
SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SM00982. TRCF. 1 hit.
[Graphical view]
SUPFAMiSSF141259. SSF141259. 1 hit.
SSF52540. SSF52540. 4 hits.
TIGRFAMsiTIGR00580. mfd. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiMFD_ECOLI
AccessioniPrimary (citable) accession number: P30958
Secondary accession number(s): P77592
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: November 1, 1997
Last modified: September 7, 2016
This is version 144 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.