ID   MFD_HELPY               Reviewed;         999 AA.
AC   O26066;
DT   15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT   01-JAN-1998, sequence version 1.
DT   27-MAR-2024, entry version 141.
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=HP_1541;
OS   Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC   Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales;
OC   Helicobacteraceae; Helicobacter.
OX   NCBI_TaxID=85962;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700392 / 26695;
RX   PubMed=9252185; DOI=10.1038/41483;
RA   Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA   Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA   Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA   Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA   McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA   Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA   Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA   Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT   "The complete genome sequence of the gastric pathogen Helicobacter
RT   pylori.";
RL   Nature 388:539-547(1997).
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}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; AE000511; AAD08581.1; -; Genomic_DNA.
DR   PIR; E64712; E64712.
DR   RefSeq; NP_208332.1; NC_000915.1.
DR   RefSeq; WP_000616334.1; NC_018939.1.
DR   AlphaFoldDB; O26066; -.
DR   SMR; O26066; -.
DR   DIP; DIP-3189N; -.
DR   IntAct; O26066; 8.
DR   MINT; O26066; -.
DR   STRING; 85962.HP_1541; -.
DR   PaxDb; 85962-C694_07985; -.
DR   EnsemblBacteria; AAD08581; AAD08581; HP_1541.
DR   KEGG; hpy:HP_1541; -.
DR   PATRIC; fig|85962.47.peg.1657; -.
DR   eggNOG; COG1197; Bacteria.
DR   InParanoid; O26066; -.
DR   OrthoDB; 9804325at2; -.
DR   PhylomeDB; O26066; -.
DR   Proteomes; UP000000429; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0043138; F:3'-5' DNA helicase activity; IBA:GO_Central.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003684; F:damaged DNA binding; IEA:InterPro.
DR   GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR   GO; GO:0006310; P:DNA recombination; IBA:GO_Central.
DR   GO; GO:0006270; P:DNA replication initiation; IBA:GO_Central.
DR   GO; GO:0006268; P:DNA unwinding involved in DNA replication; IBA:GO_Central.
DR   GO; GO:0006302; P:double-strand break repair; IBA:GO_Central.
DR   GO; GO:0006355; P:regulation of DNA-templated transcription; IEA:UniProtKB-UniRule.
DR   GO; GO:0000716; P:transcription-coupled nucleotide-excision repair, DNA damage recognition; IEA:UniProtKB-UniRule.
DR   CDD; cd17991; DEXHc_TRCF; 1.
DR   CDD; cd18810; SF2_C_TRCF; 1.
DR   Gene3D; 2.40.10.170; -; 1.
DR   Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 2.
DR   Gene3D; 3.30.2060.10; Penicillin-binding protein 1b domain; 1.
DR   Gene3D; 3.90.1150.50; Transcription-repair-coupling factor, D7 domain; 1.
DR   HAMAP; MF_00969; TRCF; 1.
DR   InterPro; IPR003711; CarD-like/TRCF_RID.
DR   InterPro; IPR036101; CarD-like/TRCF_RID_sf.
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   NCBIfam; TIGR00580; mfd; 1.
DR   PANTHER; PTHR30580; PRIMOSOMAL PROTEIN N; 1.
DR   PANTHER; PTHR30580:SF0; PRIMOSOMAL PROTEIN N; 1.
DR   Pfam; PF02559; CarD_TRCF_RID; 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; CarD-like; 1.
DR   SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 3.
DR   SUPFAM; SSF143517; TRCF domain-like; 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; Reference proteome.
FT   CHAIN           1..999
FT                   /note="Transcription-repair-coupling factor"
FT                   /id="PRO_0000102168"
FT   DOMAIN          499..656
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00969"
FT   DOMAIN          677..833
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00969"
FT   MOTIF           609..612
FT                   /note="DEEH box"
FT   BINDING         512..519
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00969"
SQ   SEQUENCE   999 AA;  113090 MW;  EE550EFB2A2946E5 CRC64;
     MIQSSLYRAL NKGFDYQILA CKDFKESELA KEVISYFKPN TKAILFPEFR AKKNDDLRSF
     FEEFLQLLGG LREFYQALEN KQETIIIAPI SALLHPLPKK ELLESFKITL LEKYNLKDLK
     DKLFYYGYEI LDLVEVEGEA SFRGDIVDIY APNSKAYRLS FFDTECESIK EFDPITQMSL
     KEDLLEIEIP PTLFSLDESS YKDLKTKVEQ SPLNSFSKDL TSFGLWFLGE KAQDLLIVYK
     SIISPRALEE IQELASLNEL DCERFKFLKV LENAQGYEDL EIHAHALEGF IALHSNHKIT
     LLAPNKTILD NAISALDAGN MECVIAPFVL NFKTPDGIFI SLNSFERKKK RQKSKLALNE
     LNPGEWVVHD DYGVGVFSQL VQHSVLGSKR DFLEIAYLGE DKLLLPVENL HLIARYVAQS
     DSVPAKDRLG KGSFLKLKAK VRTKLLEIAS KIIELAAERN LILGKKMDVH LAELEVFKSH
     AGFEYTSDQE KAIAEISKDL SSHRVMDRLL SGDVGFGKTE VAMHAIFCAF LNGFQSALVV
     PTTLLAHQHF ETLRARFENF GVKVARLDRY ASEKNKLLKA VELGQVDALI GTHAILGAKF
     KNLGLVVVDE EHKFGVKQKE ALKELSKSVH FLSMSATPIP RTLNMALSQI KGISSLKTPP
     TDRKPSRTFL KEKNDELLKE IIYRELRRNG QIFYIHNHIA SILKVKTKLE DLIPKLKIAI
     LHSQINANES EEIMLEFAKG NYQVLLCTSI VESGIHLPNA NTIIIDNAQN FGLADLHQLR
     GRVGRGKKEG FCYFLIEDQK SLNEQALKRL LALEKNSYLG SGESVAYHDL EIRGGGNLLG
     QDQSGHIKNI GYALYTRMLE DAIYELSGGK KRLEKSVEIQ LGVSAFLNPE LIASDSLRLD
     LYRRLSLCEN TDEVGQIHEE IEDRFGKIDD LSAQFLQIIT LKILANQLGI IKLSNFNQNI
     TITYSDEKKE SLKAPSKDDN DILETLLKHL RAQISLKRR
//