ID   RAPA_VIBCM              Reviewed;         969 AA.
AC   C3LR47;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   16-JUN-2009, sequence version 1.
DT   03-AUG-2022, entry version 69.
DE   RecName: Full=RNA polymerase-associated protein RapA {ECO:0000255|HAMAP-Rule:MF_01821};
DE            EC=3.6.4.- {ECO:0000255|HAMAP-Rule:MF_01821};
DE   AltName: Full=ATP-dependent helicase HepA {ECO:0000255|HAMAP-Rule:MF_01821};
GN   Name=rapA {ECO:0000255|HAMAP-Rule:MF_01821}; OrderedLocusNames=VCM66_2428;
OS   Vibrio cholerae serotype O1 (strain M66-2).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=579112;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=M66-2;
RX   PubMed=19115014; DOI=10.1371/journal.pone.0004053;
RA   Feng L., Reeves P.R., Lan R., Ren Y., Gao C., Zhou Z., Ren Y., Cheng J.,
RA   Wang W., Wang J., Qian W., Li D., Wang L.;
RT   "A recalibrated molecular clock and independent origins for the cholera
RT   pandemic clones.";
RL   PLoS ONE 3:E4053-E4053(2008).
CC   -!- FUNCTION: Transcription regulator that activates transcription by
CC       stimulating RNA polymerase (RNAP) recycling in case of stress
CC       conditions such as supercoiled DNA or high salt concentrations.
CC       Probably acts by releasing the RNAP, when it is trapped or immobilized
CC       on tightly supercoiled DNA. Does not activate transcription on linear
CC       DNA. Probably not involved in DNA repair. {ECO:0000255|HAMAP-
CC       Rule:MF_01821}.
CC   -!- SUBUNIT: Interacts with the RNAP. Has a higher affinity for the core
CC       RNAP than for the holoenzyme. Its ATPase activity is stimulated by
CC       binding to RNAP. {ECO:0000255|HAMAP-Rule:MF_01821}.
CC   -!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. RapA subfamily.
CC       {ECO:0000255|HAMAP-Rule:MF_01821}.
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DR   EMBL; CP001233; ACP06725.1; -; Genomic_DNA.
DR   RefSeq; WP_000006492.1; NC_012578.1.
DR   AlphaFoldDB; C3LR47; -.
DR   SMR; C3LR47; -.
DR   EnsemblBacteria; ACP06725; ACP06725; VCM66_2428.
DR   KEGG; vcm:VCM66_2428; -.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   Proteomes; UP000001217; Chromosome I.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0140658; F:ATP-dependent chromatin remodeler activity; IEA:InterPro.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0004386; F:helicase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0016817; F:hydrolase activity, acting on acid anhydrides; IEA:InterPro.
DR   GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-UniRule.
DR   Gene3D; 3.40.50.10810; -; 1.
DR   Gene3D; 3.40.50.300; -; 1.
DR   HAMAP; MF_01821; Helicase_RapA; 1.
DR   InterPro; IPR014001; Helicase_ATP-bd.
DR   InterPro; IPR001650; Helicase_C.
DR   InterPro; IPR023949; Helicase_RapA.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR022737; RapA_C.
DR   InterPro; IPR038718; SNF2-like_sf.
DR   InterPro; IPR000330; SNF2_N.
DR   InterPro; IPR040765; Tudor_1_RapA.
DR   InterPro; IPR040766; Tudor_2_RapA.
DR   Pfam; PF00271; Helicase_C; 1.
DR   Pfam; PF12137; RapA_C; 1.
DR   Pfam; PF00176; SNF2-rel_dom; 1.
DR   Pfam; PF18339; Tudor_1_RapA; 1.
DR   Pfam; PF18337; Tudor_RapA; 1.
DR   SMART; SM00487; DEXDc; 1.
DR   SMART; SM00490; HELICc; 1.
DR   SUPFAM; SSF52540; SSF52540; 2.
DR   PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR   PROSITE; PS51194; HELICASE_CTER; 1.
PE   3: Inferred from homology;
KW   Activator; ATP-binding; DNA-binding; Helicase; Hydrolase;
KW   Nucleotide-binding; Transcription; Transcription regulation.
FT   CHAIN           1..969
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_1000188194"
FT   DOMAIN          164..334
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          492..646
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   MOTIF           280..283
FT                   /note="DEAH box"
FT   BINDING         177..184
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
SQ   SEQUENCE   969 AA;  109440 MW;  DF22BEED6F4D7553 CRC64;
     MSFALGQRWI SDTESDLGLG TVVALDARTV TLMFAASEEN RVYARSDAPV TRVIFNVGDV
     VDSQQGWSLQ VEQVVEDQGV YTYLGTRVDT EESGVALREI FLSNQIRFNK PQDKLFAGQI
     DRMDNFVLRY RALTNQYQQH KSPMRGLCGM RAGLIPHQLY IAHEVGRRHA PRVLLADEVG
     LGKTIEAGMI IHQQVLTGRA ERILIVVPET LQHQWLVEMM RRFNLHFSIF DEERCVEAFS
     EADNPFETQQ YVLCSLDFLR KSRQRFEQAL EAEWDLLVVD EAHHLEWHPE KPSREYQVIE
     ALAEQTPGVL LLTATPEQLG RESHFARLRL LDADRFYDYE AFVKEEEQYA PVADAVTALF
     SGEKLSDEAK NKITELLSEQ DVEPLFKALE SHASEDEIAL ARQELIDNLM DRHGTGRVLF
     RNTRAAIKGF PVRNVHLLPL EIPSQYTTSM RVAGMLGGKL TPEARAMKML YPEEIFQEFE
     GEESSWWQFD SRVNWLLEKV KAKRSEKILV IASRASTALQ LEQALREREG IRATVFHEGM
     SIIERDKAAA YFAQEEGGAQ VLICSEIGSE GRNFQFANQL VMFDLPFNPD LLEQRIGRLD
     RIGQKRDIDV YVPYLTETSQ AILARWFQEG LNAFAETCPT GRAVYDAFAE RLIPILAAGG
     GEELEVIIEE SAKLNKTLKS QLEVGRDRLL EMHSNGGEKA QQIAEQIAKT DGDTNLVTFA
     LSLFDAIGLH QEDRGENALV VTPAEHMMVP SYPGLPYEGA TITFDRDTAL SREDMHFISW
     EHPMVQGGID LLMSEGVGTC AVSLLKNKAL PVGTILLELV YVVDAQAPKR SGISRFLPVS
     PIRILMDARG NDLSSQVEFE SFNRQLSPVN RHLASKLVSS VQHDVHRLIT ASETAVEPRV
     SAIREQAQRD MQQSLNSELE RLLALKAVNP NIRDEEIEVL DQQIKELTGY IAQAQYQLDS
     LRLIVVAHN