ID   MFD_STAAB               Reviewed;        1168 AA.
AC   Q2YVY2;
DT   03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT   20-DEC-2005, sequence version 1.
DT   03-AUG-2022, entry version 110.
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=SAB0452;
OS   Staphylococcus aureus (strain bovine RF122 / ET3-1).
OC   Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC   Staphylococcus.
OX   NCBI_TaxID=273036;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=bovine RF122 / ET3-1;
RX   PubMed=17971880; DOI=10.1371/journal.pone.0001120;
RA   Herron-Olson L., Fitzgerald J.R., Musser J.M., Kapur V.;
RT   "Molecular correlates of host specialization in Staphylococcus aureus.";
RL   PLoS ONE 2:E1120-E1120(2007).
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; AJ938182; CAI80140.1; -; Genomic_DNA.
DR   RefSeq; WP_000154238.1; NC_007622.1.
DR   AlphaFoldDB; Q2YVY2; -.
DR   SMR; Q2YVY2; -.
DR   PRIDE; Q2YVY2; -.
DR   KEGG; sab:SAB0452; -.
DR   HOGENOM; CLU_005122_1_3_9; -.
DR   OMA; WAPPCRE; -.
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; 4.
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..1168
FT                   /note="Transcription-repair-coupling factor"
FT                   /id="PRO_0000282667"
FT   DOMAIN          633..794
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00969"
FT   DOMAIN          808..969
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00969"
FT   MOTIF           747..750
FT                   /note="DEEQ box"
FT   BINDING         646..653
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00969"
SQ   SEQUENCE   1168 AA;  134278 MW;  FF6E674A5EFB55A5 CRC64;
     MTILTTLIKE DNHFQDLNQV FGQANTLVTG LSPSAKVTMI AEKYAQSNQQ LLLITNNLYQ
     ADKLETDLLQ FIDAEELYKY PVQDIMTEEF STQSPQLMSE RIRTLTALAQ GKKGLFIVPL
     NGLKKWLTSV EMWQNHQMTL RVGEDIDVDQ FLNKLVNMGY KRESVVSHIG EFSLRGGIID
     IFPLIGEPIR IELFDTEIDS IRDFDVETQR SKDNIEEVDI TTASDYIITE EVIRHLKEEL
     KTAYENTRPK IDKSVRNDLK ETYESFKLFE STYFDHQILR RLVAFMYETP STIIDYFQKD
     AIIAVDEFNR IKETEESLTV ESDSFISNII ESGNGFIGQS FIKYDDFETL IEGYPVTYFS
     LFATTMPIKL NHIIKFSCKP VQQFYGQYDI MRSEFQRYVN QNYHIVVLVE TETKVERMQA
     MLSEMHIPSI TKLHRSMSSG QAVIIEGSLS EGFELPDMGL VVITERELFK SKQKKQRKRT
     KAISNAEKIK SYQDLNVGDY IVHVHHGVGR YLGVETLEVG QTHRDYIKLQ YKGTDQLFVP
     VDQMDQVQKY VASEDKTPKL NKLGGSEWKK TKAKVQQSVE DIAEELIDLY KEREMAEGYQ
     YGEDTAEQTT FELDFPYELT PDQAKSIDEI KDDMQKSRPM DRLLCGDVGY GKTEVAVRAA
     FKAVMEGKQV AFLVPTTILA QQHYETLIER MQDFPVEIQL MSRFRTPKEI KQTKEGLKTG
     FVDIVVGTHK LLSKDIQYKD LGLLIVDEEQ RFGVRHKERI KTLKHNVDVL TLTATPIPRT
     LHMSMLGVRD LSVIETPPEN RFPVQTYVLE QNMSFIKEAL ERELSRDGQV FYLYNKVQSI
     YEKREQLQML MPDANIAVAH GQMTERDLEE TMLSFINNEY DILVTTTIIE TGVDVPNANT
     LIIEDADRFG LSQLYQLRGR VGRSSRIGYA YFLHPANKVL TETAEDRLQA IKEFTELGSG
     FKIAMRDLNI RGAGNLLGKQ QHGFIDTVGF DLYSQMLEEA VNEKRGIKEP ESEVPEVEVD
     LNLDAYLPTE YIANEQAKIE IYKKLRKTET FDQIIDIKDE LIDRFNDYPV EVARLLDIVE
     IKVHALHSGI TLIKDKGKII DIHLSVKATE NIDGEVLFKA TQPLGRTMKV GVQNNAMTIT
     LTKQNQWLDS LKFLVKCIEE SMRISDEA