ID A0A1Y2QIY9_9BURK Unreviewed; 1160 AA.
AC A0A1Y2QIY9;
DT 30-AUG-2017, integrated into UniProtKB/TrEMBL.
DT 30-AUG-2017, sequence version 1.
DT 24-JAN-2024, entry version 27.
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=CAP38_03930 {ECO:0000313|EMBL:OSZ67904.1};
OS Hydrogenophaga sp. IBVHS2.
OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Hydrogenophaga.
OX NCBI_TaxID=1985170 {ECO:0000313|EMBL:OSZ67904.1, ECO:0000313|Proteomes:UP000243193};
RN [1] {ECO:0000313|EMBL:OSZ67904.1, ECO:0000313|Proteomes:UP000243193}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=IBVHS2 {ECO:0000313|EMBL:OSZ67904.1,
RC ECO:0000313|Proteomes:UP000243193};
RA Orr R.J.;
RT "Draft genome sequences of novel bacteria, isolated from environmental
RT samples.";
RL Submitted (MAY-2017) to the EMBL/GenBank/DDBJ databases.
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:OSZ67904.1}.
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DR EMBL; NFUT01000001; OSZ67904.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1Y2QIY9; -.
DR STRING; 1985170.CAP38_03930; -.
DR OrthoDB; 9804325at2; -.
DR Proteomes; UP000243193; 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 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}; Reference proteome {ECO:0000313|Proteomes:UP000243193}.
FT DOMAIN 624..785
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000259|PROSITE:PS51192"
FT DOMAIN 806..960
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51194"
SQ SEQUENCE 1160 AA; 129143 MW; 2A32ABF2FC1E68DB CRC64;
MDLPKLSPGK RHTLPHPGGS ADALLLAQLA LRERAASRLT AIVTADANDA QRLIDELAFF
APDLRVTLFP DWETLPYDTF SPHQDLISER LATLWRISQR DHEAGADVVL VPATTALYRL
APPSFLAGYT FEFKVRQKLD EARLKAQLTL AGYNHVTQVV SPGEYAVRGG LIDLFPMGSL
VPYRVDLFDD EIDSIRTFDP DSQRSLYPVP EVRLLPGREF PMDDAARALF RSRWRELLEG
DPTKSRIYKD IGNGVATAGI EYYLPLFFEE TATVFDYLGE QATVVLHGDL EPAFQRFWQD
TRDRHRLLHG DPDRPVLPPE SLFLQAEQFY TLANRHAQLA LRPGVGDVTH SAFVQTLPTL
SVVRGAEDPL AHLQAHLRAS PHRLLLLAES DGRRESLLDF IRASGLSPPV FDSLAEFQAS
DEKVGMATAA LNAGFAWIEG GIDFVTETEL FSAGPTTRRR RKQEQVSDVE ALIKDLSELN
VGDPVVHTQH GIGRYRGLVN LDMGEKNADG TPALQEFLHL EYADKAVLYV PVSQLQLIGR
YTGVSADEAP LHKLGSGQWE KARRKAAEQV RDAAAELLNI YARRAARQGH PFRYSPQDYE
TFANDFGFDE TADQRAAIHA VIQDMISPRP MDRLVCGDVG FGKTEVALRA AFVAVTGGKQ
VAFLAPTTLL AEQHYQTLVD RFSKWPVKVA EMSRFRTQKE ITAAMKGIAD GSVDIVVGTH
KLLSEKTQFK NLGLLIIDEE HRFGVRHKEA VKALRAEVDV LTLTATPIPR TLGMALEGLR
DLSVIATAPQ RRLAIKTFVR NEDKGVIREA VLRELKRGGQ VYFLHNEVET IENRRARLEG
LLPEARIGVA HGQMPERQLE AVMRDFVAQR TNLLLCSTII ETGIDVPSAN TIVISRADKF
GLAQLHQLRG RVGRSHHQAY AYLLVPEIES LTKQAQQRLD AIQQMEELGS GFYLAMHDLE
IRGAGEVLGE NQSGNMLEVG FQLYNEMLSE AVRSLKAGKE PDLLSPLSVT TDINLHAPAL
LPNDYCGDVH LRLSFYKKLA TAKSTDQVDA LLEEIVDRFG KLPPQAQTLI DVHRLRVLST
PYGVVKVDAA PGVTNITFRP NPPVEPMRII ELIQKNKHIK LAGNEKLRIE KALPEVKDRV
QLVRDVLRSL GQPVQSAETI
//
