ID D0LU01_HALO1 Unreviewed; 1257 AA.
AC D0LU01;
DT 15-DEC-2009, integrated into UniProtKB/TrEMBL.
DT 15-DEC-2009, sequence version 1.
DT 24-JAN-2024, entry version 86.
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 OrderedLocusNames=Hoch_4876 {ECO:0000313|EMBL:ACY17365.1};
OS Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2).
OC Bacteria; Myxococcota; Polyangia; Haliangiales; Kofleriaceae; Haliangium.
OX NCBI_TaxID=502025 {ECO:0000313|EMBL:ACY17365.1, ECO:0000313|Proteomes:UP000001880};
RN [1] {ECO:0000313|EMBL:ACY17365.1, ECO:0000313|Proteomes:UP000001880}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 14365 / CIP 107738 / JCM 11303 / AJ 13395 / SMP-2
RC {ECO:0000313|Proteomes:UP000001880};
RX PubMed=21304682; DOI=10.4056/sigs.69.1277;
RG US DOE Joint Genome Institute (JGI-PGF);
RA Ivanova N., Daum C., Lang E., Abt B., Kopitz M., Saunders E., Lapidus A.,
RA Lucas S., Glavina Del Rio T., Nolan M., Tice H., Copeland A., Cheng J.F.,
RA Chen F., Bruce D., Goodwin L., Pitluck S., Mavromatis K., Pati A.,
RA Mikhailova N., Chen A., Palaniappan K., Land M., Hauser L., Chang Y.J.,
RA Jeffries C.D., Detter J.C., Brettin T., Rohde M., Goker M., Bristow J.,
RA Markowitz V., Eisen J.A., Hugenholtz P., Kyrpides N.C., Klenk H.P.;
RT "Complete genome sequence of Haliangium ochraceum type strain (SMP-2).";
RL Stand. Genomic Sci. 2:96-106(2010).
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}.
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DR EMBL; CP001804; ACY17365.1; -; Genomic_DNA.
DR AlphaFoldDB; D0LU01; -.
DR STRING; 502025.Hoch_4876; -.
DR KEGG; hoh:Hoch_4876; -.
DR eggNOG; COG1197; Bacteria.
DR HOGENOM; CLU_005122_0_3_7; -.
DR OMA; NKKAFCY; -.
DR OrthoDB; 9804325at2; -.
DR Proteomes; UP000001880; 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 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; 3.40.50.11180; -; 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; 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 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; 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:UP000001880}.
FT DOMAIN 701..862
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000259|PROSITE:PS51192"
FT DOMAIN 908..1066
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51194"
FT REGION 390..418
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 910..929
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 394..412
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 914..929
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1257 AA; 137235 MW; B69DA0AB6E3916AD CRC64;
MSMASLDEAI RAVLSETDAP VIAHGLTRAS LALVAARLAE RADERAGPVV VVAPDESSAR
DLAQDVAFFL PHAQHAAAGT EPLAPPPALH LPALDTSPYA ELSPDRLALA QRMAGLVRLA
RGGALLGPVV VLSAPALLRR VMPREALLAR TAVLARDDEF DRDATAERLL RAGYTRAPVV
EDAGTFAVRG GVIDVFTPLY RYPARIELFG DMVESIRLFD PESQRTLRDL DQVYVHPVRE
TVVSEGAEVR RRILDAADAA HHPSAETRRV LERIDSGEEF VGIETLTPAF HTHLAPLASY
LVAGDAPPAC WVIVDPDAIG QAAEDEHDVA EDRYRERLDD GRLAFPPSDH YVSPDELRAT
LAEHAYRLEA RGLEMYQAAA DPLLSASDEM AAAPEAKSKP KAKSKPKPKP EQDGAQLMRF
GVDDNRLLRA SLERTRRQAA DELMKPLVEA ITAWRGDAYC IAVAAGTMAR ARQLAGLLSD
YECTAHVIEE RSVDVDALSP GAPPVIYPGE LSAGFALRTD KLVMLTADEI FGPRRRTSVR
QRAAARRARK ALAGGISDFS QLAPGDHVVH AMHGIGLYRG LAKLPVSATG PAVDFLHIEY
RGGQFYLPVY RLGEVSRYVG AEGHAPRLDK LGGVTWQKAR KKASAQVKAL AEELLKLYAQ
RAAQPGHAYP SSDHMFREFE ATFAFEETPD QQRAIDEVLA DMESERPMDR LVCGDVGYGK
TEVALRACFK AVAGGKQAAL LAPTTVLVEQ HYATVCERFA GWPVSVGRLS RFQSRAEQLD
TIKGLAAGTV DLVVGTHRVL SKDVRFKDLG LLVIDEEQRF GVTHKERLKR VRTQLDVLTL
TATPIPRTLH LAMSGLRDLS IIATPPADRR AVRTFVAQVD DGVLREGIRR ELGRGGQVFF
VCPRIGADPA PSKGKVKGKG KSQGETARRV RRGDISLDEW AEHLRALVPE ARVAVAHGQM
SAEALEKVMI DFVSGNLEIL VSTTIVESGL DIARANTMFV DRADSFGLAQ LYQLRGRIGR
SKQRAFCYLL VPPPEKLSSD ARRRLETLQR FSELGAGFQI ASHDLEIRGG GELLGAKQSG
AIAAVGFEAY AAMLEEAVAE LRSGDAGLVR PRDPELNVDV PGYIPDEYIP DTGQRLDLYK
RLSDAEDEDE LKILVEEITD RYGELPDEVE LLADLMVLKI HARTLRAQSL ELTQSRMSLA
LAEDTPLAPQ TLASLARKKA FRLTPDMRLV RNFTAEEGER PSASARACLL ELIACVT
//