MFD_HELPJ
ID MFD_HELPJ Reviewed; 1001 AA.
AC Q9ZJ57;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 132.
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=jhp_1458;
OS Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85963;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=J99 / ATCC 700824;
RX PubMed=9923682; DOI=10.1038/16495;
RA Alm R.A., Ling L.-S.L., Moir D.T., King B.L., Brown E.D., Doig P.C.,
RA Smith D.R., Noonan B., Guild B.C., deJonge B.L., Carmel G., Tummino P.J.,
RA Caruso A., Uria-Nickelsen M., Mills D.M., Ives C., Gibson R., Merberg D.,
RA Mills S.D., Jiang Q., Taylor D.E., Vovis G.F., Trust T.J.;
RT "Genomic sequence comparison of two unrelated isolates of the human gastric
RT pathogen Helicobacter pylori.";
RL Nature 397:176-180(1999).
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; AE001439; AAD07030.1; -; Genomic_DNA.
DR PIR; E71806; E71806.
DR RefSeq; WP_000616318.1; NZ_CP011330.1.
DR AlphaFoldDB; Q9ZJ57; -.
DR SMR; Q9ZJ57; -.
DR STRING; 85963.jhp_1458; -.
DR EnsemblBacteria; AAD07030; AAD07030; jhp_1458.
DR KEGG; hpj:jhp_1458; -.
DR PATRIC; fig|85963.30.peg.1085; -.
DR eggNOG; COG1197; Bacteria.
DR OMA; IIESGIH; -.
DR Proteomes; UP000000804; 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; 2.
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..1001
FT /note="Transcription-repair-coupling factor"
FT /id="PRO_0000102169"
FT DOMAIN 499..658
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00969"
FT DOMAIN 679..835
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00969"
FT MOTIF 611..614
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 1001 AA; 113437 MW; D5192A7AFF29631A CRC64;
MIQSSLYRAL NKGFDYQILA CKDFKESELA KEVISYFKPN IKAVLFPELR AKKNDDLRSF
FEEFLQLLGG LREFYQALEN KQETIIIAPI SALLHPLPKK ELLESFKITL LEKYNLKDLK
DKLFYYGYEI LDLVEVEGEA SFRGDIVDIY IPNSKAYRLS FFDAECESIK ELDPATQMSL
KEDLLEIEIP PTLFSLDEPS YKDLKTKVEQ SPLNSFSKDL TSFGLWFLGE KANDLLGVYQ
SIISPRALEE IQELASLNEL DDERFKFLKV LENAQGYEDL EIHVHALEGF IALHSNRKIT
LLAPNKTILD NSISVLDAGN MECVIAPFVL NFKTPDRIFI SLNSFERKKK RQKSKLALNE
LNAGEWVVHD DYGVGVFSQL IQHSVLGSKR DFLEIAYLGE DKLLLPVENL HLIARYVVQS
DSVPVKDRLG KGSFLKLKAK VRAKLLEIAG KIIELAAERN LILGKKMDTH LAELEIFKSH
AGFEYTSDQE KAIAEISRDL SSHRVMDRLL SGDVGFGKTE VAMHAIFCAF LNGFQSALVV
PTTLLAHQHF ETLKARFENF GVKVARLDRY IKTSEKSKLL KAVELGLVDV LIGTHAILGT
KFKNLGLMVV DEEHKFGVKQ KEALKELSKS VHFLSMSATP IPRTLNMALS QIKGISSLKT
PPTDRKPSRT FLKEKNDELL KEIIYRELRR NGQIFYIHNH IASISKVKTK LEDLIPKLKI
AILHSQINAN ESEEIMLEFA KGNYQVLLCT SIVESGIHLP NANTIIIDNA QNFGLADLHQ
LRGRVGRGKK EGFCYFLIED QKSLNEQALK RLLALEKNSY LGSGESIAYH DLEIRGGGNL
LGQDQSGHIK NIGYALYTRM LEDAIYELSG GKKRLEKSVE IQLGVSAFLN PELIASDSLR
LDLYRRLSLC ENVDEVGQIH EEIEDRFGKM DDLSAQFLQI ITLKILANQL GILKLSNFNQ
NITLTYSDEK KESLKAPSKD DNDILETLLK HLHAQISLKR R
