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Protein

Transcription-repair-coupling factor

Gene

mfd

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Helicase, Hydrolase
Biological processDNA damage, DNA repair
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11619-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

GO - Cellular componenti

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

Protein-protein interaction databases

BioGridi4260086, 165 interactors
ComplexPortaliCPX-2155 TRCF-UvrA complex
DIPiDIP-10199N
IntActiP30958, 17 interactors
STRINGi316385.ECDH10B_1186

Structurei

Secondary structure

11148
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Phylogenomic databases

eggNOGiENOG4108JA2 Bacteria
COG1197 LUCA
HOGENOMiHOG000216592
InParanoidiP30958
KOiK03723
OMAiLDIPRVN
PhylomeDBiP30958

Family and domain databases

CDDicd00079 HELICc, 1 hit
Gene3Di3.90.1150.50, 1 hit
HAMAPiMF_00969 TRCF, 1 hit
InterProiView protein in InterPro
IPR036101 CarD-like/TRCF_dom_sf
IPR003711 CarD-like/TRCF_domain
IPR011545 DEAD/DEAH_box_helicase_dom
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR004576 Mfd
IPR027417 P-loop_NTPase
IPR037235 TRCF-like_C
IPR005118 TRCF_C
PfamiView protein in Pfam
PF02559 CarD_CdnL_TRCF, 1 hit
PF00270 DEAD, 1 hit
PF00271 Helicase_C, 1 hit
PF03461 TRCF, 1 hit
SMARTiView protein in SMART
SM01058 CarD_TRCF, 1 hit
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SM00982 TRCF, 1 hit
SUPFAMiSSF141259 SSF141259, 1 hit
SSF143517 SSF143517, 1 hit
SSF52540 SSF52540, 4 hits
TIGRFAMsiTIGR00580 mfd, 1 hit
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit

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
PATRICifig|511145.12.peg.1158

Similar proteinsi

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
ComplexPortaliCPX-2155 TRCF-UvrA complex
DIPiDIP-10199N
IntActiP30958, 17 interactors
STRINGi316385.ECDH10B_1186

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
PATRICifig|511145.12.peg.1158

Organism-specific databases

EchoBASEiEB1576
EcoGeneiEG11619 mfd

Phylogenomic databases

eggNOGiENOG4108JA2 Bacteria
COG1197 LUCA
HOGENOMiHOG000216592
InParanoidiP30958
KOiK03723
OMAiLDIPRVN
PhylomeDBiP30958

Enzyme and pathway databases

BioCyciEcoCyc:EG11619-MONOMER

Miscellaneous databases

EvolutionaryTraceiP30958
PROiPR:P30958

Family and domain databases

CDDicd00079 HELICc, 1 hit
Gene3Di3.90.1150.50, 1 hit
HAMAPiMF_00969 TRCF, 1 hit
InterProiView protein in InterPro
IPR036101 CarD-like/TRCF_dom_sf
IPR003711 CarD-like/TRCF_domain
IPR011545 DEAD/DEAH_box_helicase_dom
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR004576 Mfd
IPR027417 P-loop_NTPase
IPR037235 TRCF-like_C
IPR005118 TRCF_C
PfamiView protein in Pfam
PF02559 CarD_CdnL_TRCF, 1 hit
PF00270 DEAD, 1 hit
PF00271 Helicase_C, 1 hit
PF03461 TRCF, 1 hit
SMARTiView protein in SMART
SM01058 CarD_TRCF, 1 hit
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SM00982 TRCF, 1 hit
SUPFAMiSSF141259 SSF141259, 1 hit
SSF143517 SSF143517, 1 hit
SSF52540 SSF52540, 4 hits
TIGRFAMsiTIGR00580 mfd, 1 hit
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiMFD_ECOLI
AccessioniPrimary (citable) accession number: P30958
Secondary accession number(s): P77592
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: November 1, 1997
Last modified: October 10, 2018
This is version 157 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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