ID A0A1Y2ZWN3_9GAMM Unreviewed; 1140 AA.
AC A0A1Y2ZWN3;
DT 30-AUG-2017, integrated into UniProtKB/TrEMBL.
DT 30-AUG-2017, sequence version 1.
DT 24-JAN-2024, entry version 25.
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=BCS42_00050 {ECO:0000313|EMBL:OTE95830.1};
OS Crenothrix sp. D3.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Methylococcales;
OC Crenotrichaceae; Crenothrix.
OX NCBI_TaxID=1880899 {ECO:0000313|EMBL:OTE95830.1, ECO:0000313|Proteomes:UP000198219};
RN [1] {ECO:0000313|EMBL:OTE95830.1, ECO:0000313|Proteomes:UP000198219}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=D3 {ECO:0000313|EMBL:OTE95830.1};
RA Oswald K., Graf J.S., Littman S., Tienken D., Brand A., Wehrli B.,
RA Albertsen M., Daims H., Wagner M., Kuypers M.M., Schubert C.J., Milucka J.;
RT "Crenothrix are major methane consumers in stratified lakes.";
RL ISME J. 0:0-0(2017).
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:OTE95830.1}.
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DR EMBL; MBQZ01000054; OTE95830.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1Y2ZWN3; -.
DR STRING; 1880899.BCS42_00050; -.
DR Proteomes; UP000198219; 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}.
FT DOMAIN 611..772
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000259|PROSITE:PS51192"
FT DOMAIN 793..947
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51194"
SQ SEQUENCE 1140 AA; 127771 MW; D39F3BDFEA05A162 CRC64;
MTNLPVFPLH SPHSNKQTLI WTGLTGCADA LALANAIAQE NRLFVIVTPD NQTALQLIHE
LAFFLHNKHP ILHFPDWETL PYDVFSPLPE ITSERLKTLA LLPDVKQGAL VVSVNTLMHK
LAPREHVLAN SFAIKVGDVF NLELNRLKLE SVGYHCVSQV YAHAEFAIRG AIIDIFPMGS
NVPFRLELWD DEVDSIRTFD PETQLSLEKI DQIQLFPAQE FPFTDASIKH FRQAFRDQFP
NASAKNTLYV DVSKKISPNG IEYYLPLFVE QTATLFDYLP QNTVLVLSES FDDLALAFYS
EAEERYEQRK YDIERPLLKP EALFLSAAQL AQASKQFARI ILTSAVDDNP LPDLTINAKL
AEPAAALQHF VKDFQGKILF VAESAGRREA LADKLRSHKI AAKQVDNWQA FLNSVVSPCL
LVAPIDHGLL LDNPTLAIIT ESQLSGEKVE QRRRRRKSAA RELENIISNL NELGIGSPVV
HQEHGVGRYL GLQTLTVGGI ANEFLMLEYA NHDKLYVPVS ALQVISRYTG MNPEDAPLHK
LGNDAWQKLK KKAIARIYDV AAELLEIHAK RAIKQGHAFS IDDDEYQAFA DAFPFEETPD
QQAAIEAILQ DMASPQPMDR VICGDVGFGK TEVSMRAAFI AVQAGKQVAM LVPTTLLAQQ
HYQNYQDRFA DWAVRVEVLS RFVSPKQQKQ LAEQLAQGQI DIIIGTHALL SKELKYKALG
LVVIDEEHRF GVRQKEHFKK LRHELDMLTL TATPIPRTLN MAMAGLRDIS IIASPPPNRH
VIKTFITEWV DAQIKEACLR EIKRGGQVFF LHNDVKSMDK MARELGALIP EARIESAHGQ
MPERELERIM RDFYHQRFNL LLCSTIIESG IDIPSANTII INRADKLGLA QLHQLRGRVG
RSHHRAYAYF IVPPKSLLSK DAQKRLEAVE ASGELGAGFM LSSHDMEIRG AGELLGDEQS
GQIQEIGFSL YSELLERAVN ALKSGKQPEL DTPMDKGVEV DLQAAALIPE DYLADIHVRL
VLYKRISNTE TAADLHELQI EMIDRFGLLP EPVKTLFSIT VLKQQAEQLG IKKIEANAGG
GRIIFTPQPN INAEQLINLI QTQAQTYKFD GADKLRFTQN FTCVEQKVAF IGGLLKILSV
//
