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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)DescriptionActionsGraphical viewLength
Nucleotide bindingi628 – 635ATPUniRule annotation8

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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)DescriptionActionsGraphical viewLength
ChainiPRO_00001021661 – 1148Transcription-repair-coupling factorAdd BLAST1148

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 interactors.
DIPiDIP-10199N.
IntActiP30958. 17 interactors.
MINTiMINT-1231460.
STRINGi511145.b1114.

Structurei

Secondary structure

11148
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi16 – 20Combined sources5
Helixi26 – 37Combined sources12
Beta strandi38 – 40Combined sources3
Beta strandi42 – 48Combined sources7
Helixi49 – 61Combined sources13
Beta strandi67 – 69Combined sources3
Helixi85 – 97Combined sources13
Helixi98 – 100Combined sources3
Beta strandi103 – 109Combined sources7
Helixi110 – 114Combined sources5
Helixi120 – 125Combined sources6
Beta strandi128 – 131Combined sources4
Helixi138 – 147Combined sources10
Beta strandi151 – 155Combined sources5
Beta strandi161 – 165Combined sources5
Beta strandi168 – 171Combined sources4
Beta strandi180 – 185Combined sources6
Beta strandi188 – 196Combined sources9
Turni197 – 200Combined sources4
Beta strandi201 – 212Combined sources12
Beta strandi214 – 217Combined sources4
Helixi221 – 234Combined sources14
Helixi244 – 249Combined sources6
Helixi257 – 264Combined sources8
Beta strandi265 – 267Combined sources3
Helixi272 – 275Combined sources4
Beta strandi281 – 284Combined sources4
Helixi288 – 306Combined sources19
Helixi317 – 319Combined sources3
Helixi324 – 331Combined sources8
Beta strandi336 – 339Combined sources4
Beta strandi350 – 352Combined sources3
Beta strandi366 – 369Combined sources4
Helixi372 – 380Combined sources9
Beta strandi385 – 390Combined sources6
Turni394 – 398Combined sources5
Helixi399 – 402Combined sources4
Helixi403 – 405Combined sources3
Helixi415 – 417Combined sources3
Beta strandi423 – 428Combined sources6
Beta strandi434 – 436Combined sources3
Turni437 – 440Combined sources4
Beta strandi441 – 445Combined sources5
Helixi446 – 449Combined sources4
Helixi461 – 463Combined sources3
Helixi467 – 472Combined sources6
Beta strandi482 – 485Combined sources4
Turni486 – 488Combined sources3
Beta strandi489 – 503Combined sources15
Beta strandi505 – 512Combined sources8
Helixi514 – 516Combined sources3
Beta strandi518 – 522Combined sources5
Helixi523 – 528Combined sources6
Beta strandi529 – 531Combined sources3
Beta strandi537 – 539Combined sources3
Helixi549 – 576Combined sources28
Helixi587 – 595Combined sources9
Helixi603 – 617Combined sources15
Beta strandi618 – 620Combined sources3
Beta strandi623 – 627Combined sources5
Turni632 – 635Combined sources4
Helixi636 – 646Combined sources11
Turni647 – 649Combined sources3
Beta strandi651 – 655Combined sources5
Helixi659 – 672Combined sources14
Turni674 – 677Combined sources4
Beta strandi680 – 684Combined sources5
Helixi689 – 700Combined sources12
Beta strandi705 – 709Combined sources5
Helixi712 – 715Combined sources4
Beta strandi721 – 730Combined sources10
Helixi731 – 733Combined sources3
Helixi736 – 746Combined sources11
Beta strandi749 – 757Combined sources9
Helixi761 – 767Combined sources7
Turni768 – 770Combined sources3
Beta strandi771 – 775Combined sources5
Beta strandi786 – 792Combined sources7
Helixi795 – 806Combined sources12
Turni807 – 809Combined sources3
Beta strandi811 – 815Combined sources5
Helixi822 – 832Combined sources11
Beta strandi838 – 840Combined sources3
Helixi847 – 858Combined sources12
Beta strandi864 – 869Combined sources6
Helixi872 – 874Combined sources3
Beta strandi880 – 885Combined sources6
Turni886 – 889Combined sources4
Helixi893 – 900Combined sources8
Beta strandi910 – 916Combined sources7
Helixi919 – 921Combined sources3
Helixi924 – 933Combined sources10
Beta strandi938 – 940Combined sources3
Helixi941 – 959Combined sources19
Helixi961 – 970Combined sources10
Helixi972 – 988Combined sources17
Helixi995 – 997Combined sources3
Turni1014 – 1016Combined sources3
Helixi1020 – 1032Combined sources13
Helixi1036 – 1050Combined sources15
Helixi1055 – 1073Combined sources19
Beta strandi1078 – 1080Combined sources3
Beta strandi1082 – 1088Combined sources7
Helixi1097 – 1106Combined sources10
Helixi1108 – 1110Combined sources3
Beta strandi1111 – 1114Combined sources4
Turni1115 – 1117Combined sources3
Beta strandi1118 – 1122Combined sources5
Helixi1128 – 1143Combined sources16

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP30958.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini615 – 776Helicase ATP-bindingUniRule annotationAdd BLAST162
Domaini798 – 951Helicase C-terminalUniRule annotationAdd BLAST154

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi729 – 732DEEH box4

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)DescriptionActionsGraphical viewLength
Sequence conflicti365A → R (PubMed:8465200).Curated1

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2B2NX-ray2.10A/B1-333[»]
2EYQX-ray3.20A/B1-1148[»]
3HJHX-ray1.95A1-470[»]
4DFCX-ray2.80A/C127-213[»]
ProteinModelPortaliP30958.
SMRiP30958.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260086. 165 interactors.
DIPiDIP-10199N.
IntActiP30958. 17 interactors.
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: November 2, 2016
This is version 146 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.