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Protein

Transcription-repair-coupling factor

Gene

mfd

Organism
Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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.UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi605 – 6128ATPUniRule annotation

GO - Molecular functioni

GO - Biological processi

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

BioCyciRFEL315456:GKEK-380-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:RF_0367
OrganismiRickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)
Taxonomic identifieri315456 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiaspotted fever group
ProteomesiUP000008548 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11421142Transcription-repair-coupling factorPRO_0000281073Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi315456.RF_0367.

Structurei

3D structure databases

ProteinModelPortaliQ4UMJ0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini592 – 757166Helicase ATP-bindingUniRule annotationAdd
BLAST
Domaini778 – 932155Helicase C-terminalUniRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi710 – 7134DEEQ box

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

eggNOGiCOG1197.
HOGENOMiHOG000216592.
KOiK03723.
OMAiNSCALGS.
OrthoDBiEOG6FNHKW.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00969. TRCF.
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. 3 hits.
TIGRFAMsiTIGR00580. mfd. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q4UMJ0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLQQKFPATA KSFFATHNFT KNLKQDFILS SSNEDEALQL YKQALFFSSN
60 70 80 90 100
ENIYYFPSYD TIPYDHTSPN ANILSRRAEI LTKLTTNNSN GKLLITYAAN
110 120 130 140 150
LLNKLPPKDF FSKYFLKLSP KMKFTTDELA MFLVENSFTR NASSIDVGEF
160 170 180 190 200
AVRGEIIDII LPGPKAYRIN FSWDYIESIK EFDIDTQIST KSCSELVISP
210 220 230 240 250
ANEIVLNSET NGNFKNNYLR NFGVNHTDNP LYEAVISGRK FAGYEQLLPL
260 270 280 290 300
FYNSCSSLVD YLNDPIFIFD NLSKQAILEF EHSYNDFYSA RSEVNKLKFN
310 320 330 340 350
SFYPTLSPTD LYFTASEITE LLEQKNNIFI SYENSEQATL IENISSASFI
360 370 380 390 400
EKKTVFDKLF EIIKAHSSKK IVIGAASLSG LERIKSITQN YEYKYNEINK
410 420 430 440 450
LDEAKASVIN VGIIPLNQSF YTKEYLFITA SELLEEKSSS TNTNKKLKNI
460 470 480 490 500
LLELDNLAEG EFVVHKDHGI GQFLKLEALE IKGKLHDFLK ILYAGNDKLY
510 520 530 540 550
IPVENIEVIK KYGNDNAELD KLGSSSWQRS KAKLKNRIKE IALHLIQIAA
560 570 580 590 600
KRKLNSSASV EFDLEEYDKF CANFPFSETE DQLTAINDIK EDLRNGMLMD
610 620 630 640 650
RLICGDVGFG KTEVAMRAVF MVAKSLNEHL PQVAVVVPTT ILCSQHFSRF
660 670 680 690 700
IERFKGFGLN IKQLSSVISA KEAKIIRSEL ESGKINIIIG THSLLHKNTK
710 720 730 740 750
FFNLKLLIID EEQHFGVGQK EFLKSLKSSS HVLAMSATPI PRTLQMSMTG
760 770 780 790 800
LKELSIIATP PLNRLEVRTM VMPFDPVIIR DALLREHFRG GRSFYVVPRI
810 820 830 840 850
KDIEDIEKQL KQIVPELSYK IAHGKMTPSK IDEVMSEFYA GKFDILVSTT
860 870 880 890 900
IIESGIDIAE ANTMVIHKAD MLGLSQLYQL RGRIGRGKVR GYAYLTVASH
910 920 930 940 950
KKMTSHSLRR LEIIQNSCAL GSGFTIASHD MDLRGFGNLI GEEQSGQIKE
960 970 980 990 1000
VGTELYQEML EEQIAIFKDE PIVSEQLFIP TINLGLSVFI PDNYISDSAL
1010 1020 1030 1040 1050
KLGLYRRIGN LSNEIEVEKF KDEMIDRFGS LPIEFNNLLD IVKIKLLCFK
1060 1070 1080 1090 1100
LNIENLDSGD NGFVIKFYKN ADMTDKILKF VSTYSNQAKI KPDNKLVYIK
1110 1120 1130 1140
KLVDKNIIVE VNQLLWKLGG CRLDVIPNTS LRGAKRRGNL IK
Length:1,142
Mass (Da):129,663
Last modified:July 5, 2005 - v1
Checksum:iCC689B86E2253EC0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000053 Genomic DNA. Translation: AAY61218.1.
RefSeqiWP_011270706.1. NC_007109.1.
YP_246383.1. NC_007109.1.

Genome annotation databases

EnsemblBacteriaiAAY61218; AAY61218; RF_0367.
KEGGirfe:RF_0367.
PATRICi17891190. VBIRicFel64634_0429.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000053 Genomic DNA. Translation: AAY61218.1.
RefSeqiWP_011270706.1. NC_007109.1.
YP_246383.1. NC_007109.1.

3D structure databases

ProteinModelPortaliQ4UMJ0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi315456.RF_0367.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAY61218; AAY61218; RF_0367.
KEGGirfe:RF_0367.
PATRICi17891190. VBIRicFel64634_0429.

Phylogenomic databases

eggNOGiCOG1197.
HOGENOMiHOG000216592.
KOiK03723.
OMAiNSCALGS.
OrthoDBiEOG6FNHKW.

Enzyme and pathway databases

BioCyciRFEL315456:GKEK-380-MONOMER.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00969. TRCF.
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. 3 hits.
TIGRFAMsiTIGR00580. mfd. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite."
    Ogata H., Renesto P., Audic S., Robert C., Blanc G., Fournier P.-E., Parinello H., Claverie J.-M., Raoult D.
    PLoS Biol. 3:1-12(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC VR-1525 / URRWXCal2.

Entry informationi

Entry nameiMFD_RICFE
AccessioniPrimary (citable) accession number: Q4UMJ0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 2007
Last sequence update: July 5, 2005
Last modified: May 27, 2015
This is version 78 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. Rickettsia felis (Rickettsia azadi)
    Rickettsia felis (strain URRWXCal2): entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.