ID Q2YBC5_NITMU Unreviewed; 1156 AA.
AC Q2YBC5;
DT 20-DEC-2005, integrated into UniProtKB/TrEMBL.
DT 20-DEC-2005, sequence version 1.
DT 27-MAR-2024, entry version 130.
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=Nmul_A0639 {ECO:0000313|EMBL:ABB73946.1};
GN ORFNames=SAMN05216403_10310 {ECO:0000313|EMBL:SEF53042.1};
OS Nitrosospira multiformis (strain ATCC 25196 / NCIMB 11849 / C 71).
OC Bacteria; Pseudomonadota; Betaproteobacteria; Nitrosomonadales;
OC Nitrosomonadaceae; Nitrosospira.
OX NCBI_TaxID=323848 {ECO:0000313|EMBL:ABB73946.1, ECO:0000313|Proteomes:UP000002718};
RN [1] {ECO:0000313|EMBL:ABB73946.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=ATCC 25196 {ECO:0000313|EMBL:ABB73946.1};
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Lykidis A., Richardson P.;
RT "Complete sequence of Chromosome 1 of Nitrosospira multiformis ATCC
RT 25196.";
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|Proteomes:UP000002718}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25196 / NCIMB 11849 / C 71
RC {ECO:0000313|Proteomes:UP000002718};
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Lykidis A., Richardson P.;
RT "Complete sequence of chromosome 1 of Nitrosospira multiformis ATCC
RT 25196.";
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:ABB73946.1, ECO:0000313|Proteomes:UP000002718}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25196 {ECO:0000313|EMBL:ABB73946.1}, and ATCC 25196 /
RC NCIMB 11849 / C 71 {ECO:0000313|Proteomes:UP000002718};
RX PubMed=18390676; DOI=10.1128/AEM.02722-07;
RA Norton J.M., Klotz M.G., Stein L.Y., Arp D.J., Bottomley P.J., Chain P.S.,
RA Hauser L.J., Land M.L., Larimer F.W., Shin M.W., Starkenburg S.R.;
RT "Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing
RT bacterium from the soil environment.";
RL Appl. Environ. Microbiol. 74:3559-3572(2008).
RN [4] {ECO:0000313|EMBL:SEF53042.1, ECO:0000313|Proteomes:UP000236751}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Nl13 {ECO:0000313|EMBL:SEF53042.1,
RC ECO:0000313|Proteomes:UP000236751};
RA de Groot N.N.;
RL Submitted (OCT-2016) 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 ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; CP000103; ABB73946.1; -; Genomic_DNA.
DR EMBL; FNVK01000003; SEF53042.1; -; Genomic_DNA.
DR RefSeq; WP_011379996.1; NZ_FNVK01000003.1.
DR AlphaFoldDB; Q2YBC5; -.
DR STRING; 323848.Nmul_A0639; -.
DR KEGG; nmu:Nmul_A0639; -.
DR eggNOG; COG1197; Bacteria.
DR HOGENOM; CLU_005122_0_2_4; -.
DR OrthoDB; 9804325at2; -.
DR Proteomes; UP000002718; Chromosome.
DR Proteomes; UP000236751; 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:UP000002718}.
FT DOMAIN 624..789
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000259|PROSITE:PS51192"
FT DOMAIN 810..964
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51194"
SQ SEQUENCE 1156 AA; 129151 MW; B08BB631ABECE6EC CRC64;
MAFKLTIPSS GSTIRYGHFD GSSDSLALAQ LALEAKKAKP VTIITASALA AQRLLEEIPF
FAPELRTRLL PDWETLPYDT FSPHQDLVSE RLATLYQLMN GACDILIVPV TTALYRMPPP
EYLAAHTFFL ARGETLDLNA LRSQMTLAGY SHVTQVLSPG EYSVRGGLID LFPMGSPLPY
RIDLLDNEIE TIRTFDVDTQ RSVYPVTEIR LLPAREFPLD EEGRTRFRGR FREKFEGDPS
RSLIYKDISK GGSPAGIEYY LPLFFEHTAT LFDYLPQTAL LCLHHELYQT VESFWHDTQA
RYQLLRGDSD RPLLKPADLF LTTEAFFGAL KPYPRIEIPP EERATKTGGA EVQGLSIPLP
PLQIDRRAVN PAEKLSAFIA EFESSGGGRT LLLAESLGRR ELIADHLKQY RLNPDICDNY
AQFRASTSPF VLGVGPLHNG FIYPEKGIAF VTESELYARH LHGRGERDSR KTSAVADAVL
RDLSEIKAGD PVVHEQHGIG RYLGLVSMDL GEGETEFLSL EYASGDKLYV PVSQLHLIGR
YSGASPESAP LHKLGSGQWD KAKRKAMQQV RDTAAELLNI YAQRAARVGH AFRLKEQDYE
AFVEGFGFEE TPDQATAIAA VIDDLTSARP MDRLICGDVG FGKTEVALRA AFVAVADGRQ
VAVLVPTTLL AEQHFQNFSD RFGLIAEEWP VKIAELSRFR SGKEQAQALA GLADGQIDIV
IGTHKLIQKG VRFKNLGLVI IDEEHRFGVR HKEQLKSLRS EVDVLTLTAT PIPRTLALSL
EGLRDFSVIA TAPQRRLAIK TFVNRFSEGI IREACLRELK RGGQIYFLHN EVSTIQTMHD
KLARLLPEAR IGIAHGQMRE RELEHVMKDF YQQRFNLLLC TTIIETGIDV PTANTIIIHR
ADKFGLAQLH QLRGRVGRSH HQAYAYLLVP EEEALGTQAR KRLEAVQSME ELGAGFYLAM
HDLEIRGAGE VLGESQSGEM QEIGFTLYAN MLEAAVRSLK EGKEPDMQHP LGVATEINLH
VPALLPEDYC SDIHERLILY KRMANCTSDE QLDEMQIELT DRFGLLPDPV KALLDCHRLR
IAAAPLGIIR VEASSESIQV QFTPNPPVDA ARIVALLQRS RDYQLSGPDR LKIKTCIPEA
GERVRRIMDL FTELGT
//
