ID J2QM79_9PSED Unreviewed; 1149 AA.
AC J2QM79;
DT 03-OCT-2012, integrated into UniProtKB/TrEMBL.
DT 03-OCT-2012, sequence version 1.
DT 24-JAN-2024, entry version 52.
DE RecName: Full=Transcription-repair-coupling factor {ECO:0000256|HAMAP-Rule:MF_00969};
DE Short=TRCF {ECO:0000256|HAMAP-Rule:MF_00969};
DE EC=3.6.4.- {ECO:0000256|HAMAP-Rule:MF_00969};
GN Name=mfd {ECO:0000256|HAMAP-Rule:MF_00969};
GN ORFNames=PMI26_02556 {ECO:0000313|EMBL:EJM43481.1};
OS Pseudomonas sp. GM33.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=1144329 {ECO:0000313|EMBL:EJM43481.1, ECO:0000313|Proteomes:UP000007274};
RN [1] {ECO:0000313|EMBL:EJM43481.1, ECO:0000313|Proteomes:UP000007274}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GM33 {ECO:0000313|EMBL:EJM43481.1,
RC ECO:0000313|Proteomes:UP000007274};
RX PubMed=23045501; DOI=10.1128/JB.01243-12;
RA Brown S.D., Utturkar S.M., Klingeman D.M., Johnson C.M., Martin S.L.,
RA Land M.L., Lu T.Y., Schadt C.W., Doktycz M.J., Pelletier D.A.;
RT "Twenty-one genome sequences from Pseudomonas species and 19 genome
RT sequences from diverse bacteria isolated from the rhizosphere and
RT endosphere of Populus deltoides.";
RL J. Bacteriol. 194:5991-5993(2012).
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:0000256|HAMAP-Rule:MF_00969}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00969}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the helicase family.
CC RecG subfamily. {ECO:0000256|HAMAP-Rule:MF_00969}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the UvrB family.
CC {ECO:0000256|HAMAP-Rule:MF_00969}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EJM43481.1}.
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DR EMBL; AKJO01000077; EJM43481.1; -; Genomic_DNA.
DR RefSeq; WP_007974032.1; NZ_AKJO01000077.1.
DR AlphaFoldDB; J2QM79; -.
DR PATRIC; fig|1144329.3.peg.2526; -.
DR Proteomes; UP000007274; Unassembled WGS sequence.
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 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; 3.40.50.11140; -; 1.
DR Gene3D; 3.40.50.11180; -; 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; IPR048635; MFD_D3.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR047112; RecG/Mfd.
DR InterPro; IPR037235; TRCF-like_C_D7.
DR InterPro; IPR005118; TRCF_C.
DR InterPro; IPR041471; UvrB_inter.
DR NCBIfam; TIGR00580; mfd; 1.
DR PANTHER; PTHR47964; ATP-DEPENDENT DNA HELICASE HOMOLOG RECG, CHLOROPLASTIC; 1.
DR PANTHER; PTHR47964:SF1; ATP-DEPENDENT DNA HELICASE HOMOLOG RECG, CHLOROPLASTIC; 1.
DR Pfam; PF02559; CarD_TRCF_RID; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF21132; MFD_D3; 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; 4.
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 {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_00969}; Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00969};
KW DNA damage {ECO:0000256|ARBA:ARBA00022763, ECO:0000256|HAMAP-
KW Rule:MF_00969};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204, ECO:0000256|HAMAP-
KW Rule:MF_00969};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|HAMAP-
KW Rule:MF_00969}; Helicase {ECO:0000256|ARBA:ARBA00022806};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_00969};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_00969}.
FT DOMAIN 617..778
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000259|PROSITE:PS51192"
FT DOMAIN 799..953
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51194"
SQ SEQUENCE 1149 AA; 128636 MW; 57965F7EB82BC90B CRC64;
MPVLRLPLLP AAAGKQHWGN LPGAALSLAI AEAASAAKRF TLLLTADSQS AERLEQELGF
FAPDLPVLHF PDWETLPYDL FSPHQDIISQ RIASLYRLPE LSHGVLVVPI TTALHRLAPT
KFLLGSSLVL DIGQKLDVEQ MRTRLEATGY RYVDTVYEHG EFTVRGSLID LFPMGSKLPY
RIDLFDDEIE TLRTFDPENQ RSIDKVDSVK LLPAKEFPLQ KEAVTRFKAR FRERFDVDFR
RCPIFQDLSS GITPAGIEYY LPLFFEETST LFDYLPQDTQ VFSLPGIEQA AENFWNDVRN
RYEERRVDPS RPLLPPDELF LPVEDCFARL KSWPRVVASQ QDVEPGVGRE RFPARELPNL
AIEAKATQPL AALAGFLDEF PGRVLFTAES AGRREVLLEL LERLKLRPKT VDSWPDFVAG
KDRLAITIAP LDEGLVLDDP ALALVAESPL FGQRVMQRRR REKRADANND AVIKNLTELR
EGAPVVHIDH GVGRYLGLAT LEIDNQTAEF LALEYAEGAK LYVPVANLHL IARYTGSDDA
LAPLHRLGSE TWQKAKRKAA EQVRDVAAEL LDIYARRAAR EGYAFADPKA DYATFSAGFP
FEETPDQQTT IEAVREDMLA PKPMDRLVCG DVGFGKTEVA MRAAFIAVHG GRQVAILVPT
TLLAQQHYNS FRDRFADWPV TVEVMSRFKS AKEVNAAVAD LAEGKIDIVI GTHKLLQDDV
KIKNLGLVII DEEHRFGVRQ KEQLKALRSE VDILTLTATP IPRTLNMAVS GMRDLSIIAT
PPARRLSVRT FVMEQNKSTV KEALLRELLR GGQVYYLHND VKTIEKCAAD LAELVPEARI
GIGHGQMRER ELEQVMSDFY HKRFNVLIAS TIIETGIDVP SANTIIIERA DKFGLAQLHQ
LRGRVGRSHH QAYAYLLTPP RQQITPDAEK RLEAIANTQD LGAGFVLATN DLEIRGAGEL
LGDGQSGQIQ AVGFTLYMEM LERAVKSIRK GEQPNLDQPL GGGPEVNLRV PALIPEDYLP
DVHARLILYK RIASATDEDG LKDLQVEMID RFGLLPEPTK NLIRITALKL QAEQLGIKKV
DGGPQGGRVE FAAQTPVDPL TLIKLIQSQP KRYKFEGATM FKFMVPMERP EERFNTVEAL
FERLVPKTA
//
