MFD_RICTY
ID MFD_RICTY Reviewed; 1120 AA.
AC Q9AKD5;
DT 20-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=Transcription-repair-coupling factor {ECO:0000255|HAMAP-Rule:MF_00969};
DE Short=TRCF {ECO:0000255|HAMAP-Rule:MF_00969};
DE EC=3.6.4.- {ECO:0000255|HAMAP-Rule:MF_00969};
GN Name=mfd {ECO:0000255|HAMAP-Rule:MF_00969}; OrderedLocusNames=RT0586;
OS Rickettsia typhi (strain ATCC VR-144 / Wilmington).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales;
OC Rickettsiaceae; Rickettsieae; Rickettsia; typhus group.
OX NCBI_TaxID=257363;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC VR-144 / Wilmington;
RX PubMed=11319266; DOI=10.1093/oxfordjournals.molbev.a003864;
RA Andersson J.O., Andersson S.G.E.;
RT "Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes.";
RL Mol. Biol. Evol. 18:829-839(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC VR-144 / Wilmington;
RX PubMed=15317790; DOI=10.1128/jb.186.17.5842-5855.2004;
RA McLeod M.P., Qin X., Karpathy S.E., Gioia J., Highlander S.K., Fox G.E.,
RA McNeill T.Z., Jiang H., Muzny D., Jacob L.S., Hawes A.C., Sodergren E.,
RA Gill R., Hume J., Morgan M., Fan G., Amin A.G., Gibbs R.A., Hong C.,
RA Yu X.-J., Walker D.H., Weinstock G.M.;
RT "Complete genome sequence of Rickettsia typhi and comparison with sequences
RT of other Rickettsiae.";
RL J. Bacteriol. 186:5842-5855(2004).
CC -!- FUNCTION: Couples transcription and DNA repair by recognizing RNA
CC polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent
CC release of RNAP and its truncated transcript from the DNA, and
CC recruitment of nucleotide excision repair machinery to the damaged
CC site. {ECO:0000255|HAMAP-Rule:MF_00969}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00969}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the UvrB family.
CC {ECO:0000255|HAMAP-Rule:MF_00969}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the helicase family.
CC RecG subfamily. {ECO:0000255|HAMAP-Rule:MF_00969}.
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DR EMBL; AJ293313; CAC33732.1; -; Genomic_DNA.
DR EMBL; AE017197; AAU04051.1; -; Genomic_DNA.
DR RefSeq; WP_011191032.1; NC_006142.1.
DR AlphaFoldDB; Q9AKD5; -.
DR SMR; Q9AKD5; -.
DR STRING; 257363.RT0586; -.
DR EnsemblBacteria; AAU04051; AAU04051; RT0586.
DR KEGG; rty:RT0586; -.
DR eggNOG; COG1197; Bacteria.
DR HOGENOM; CLU_005122_3_2_5; -.
DR OMA; SHVVHIN; -.
DR OrthoDB; 234717at2; -.
DR Proteomes; UP000000604; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003684; F:damaged DNA binding; IEA:InterPro.
DR GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-UniRule.
DR GO; GO:0000716; P:transcription-coupled nucleotide-excision repair, DNA damage recognition; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.50.300; -; 2.
DR Gene3D; 3.90.1150.50; -; 1.
DR HAMAP; MF_00969; TRCF; 1.
DR InterPro; IPR036101; CarD-like/TRCF_dom_sf.
DR InterPro; IPR003711; CarD-like/TRCF_domain.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR004576; Mfd.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR037235; TRCF-like_C_D7.
DR InterPro; IPR005118; TRCF_C.
DR InterPro; IPR041471; UvrB_inter.
DR Pfam; PF02559; CarD_CdnL_TRCF; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF03461; TRCF; 1.
DR Pfam; PF17757; UvrB_inter; 1.
DR SMART; SM01058; CarD_TRCF; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00982; TRCF; 1.
DR SUPFAM; SSF141259; SSF141259; 1.
DR SUPFAM; SSF143517; SSF143517; 1.
DR SUPFAM; SSF52540; SSF52540; 3.
DR TIGRFAMs; TIGR00580; mfd; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 3: Inferred from homology;
KW ATP-binding; Cytoplasm; DNA damage; DNA repair; DNA-binding; Helicase;
KW Hydrolase; Nucleotide-binding.
FT CHAIN 1..1120
FT /note="Transcription-repair-coupling factor"
FT /id="PRO_0000281074"
FT DOMAIN 591..756
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00969"
FT DOMAIN 777..933
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00969"
FT MOTIF 709..712
FT /note="DEEQ box"
FT BINDING 604..611
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00969"
SQ SEQUENCE 1120 AA; 127960 MW; 7D69676C29A9CE28 CRC64;
MLQQKFPATA KCFFAIDNFT KHLNQDFILS VNNEEEALKL YKQAFFFSSN ENIYYFPSYD
TIPYDYTSPN TNIISRRAET LTKLITNNNS KLLITHAANL LNKLPPKDFF SKYFLKLYPK
IKFTIDELSM LLVENSFTRN ISSNDVGEFS VRGEIIDIIL PGPKAYRINF SWDYIESIKE
FDINTQISTK YCTELVISPV SEIVLNSKTI GNFKNNYLRN FGVNHTDNPL YEAVISGRKF
PGYEQLLPLF YDSCSSLVDY LNDPICIFDN LSKQEILEFE NSCNDFYLAR SNANKLKVNN
FYPALSPASL YFTASAITEL LEQKNNILIS YENSEQASLI GNISSTSFME KKTIFDKLFE
LIKANFHKKI IICSSVLSSF ERIKSIIQNY KYTFNEINKL DDAKASVINI GIIPLNQSFY
TKEYLFITSS ELLEEKTLYT NTNKKLKNIL LELDNLAEGE FVVHKDHGIG QFLKLEAFEI
QGKLHDFLKI LYSGNDKLYV PVENIEVIKK YGSNNVELDK LGSAAWHKSK AKLKDRIKEI
SLHLIQIAAK RKLNISTPIE FDLEEYDKFC ANFPFIETED QLTAINDIRK DLTNGMLMDR
LICGDVGFGK TEVAMRAVFM VAKSLNEYLP QVAVVVPTTI LCSQHFSRFI ERFKGFGLNI
KQLSSVVSSQ EANIIRLELA SGKINIIIGT HTLLHKNIKF FNLKLLIIDE EQHFGVSQKE
FLKSLKYSSH VLAMSATPIP RTLQMSLTGL KELSIIATPP LNRLEVRTSV MPFDTVIIRD
ALLREHFRGG RSFYVVPRIK DMEDIEKQLK QIVPELSYKI AHGKMTPSKI DEVMSEFYAG
KFDILISTTI IESGIDITEA NTMIIHNADT LGLSQLYQLR GRIGRGKIRG YAYLTVASNK
KLMQHSLRRL EIIQNSCALG SGFTIASHDA DLRGFGNLIG EEQSGQIREV GAELYQEMLE
EQIALLKDES IVSEQSFIPN INLGLSVFIP DHYVSDSALK IALYRRIGNL SNEIEVEKFK
DEMIDRFGLL PIEFNNLLDI VKIKLLCFKL NIENLDSGDD GFVIRFYKNA DMSDKILKFV
SRYSNQTKIK PNNKLVFIKK LVDKNIITEA NQLLWTLLEI
