ID   RAPA_VIBVY              Reviewed;         969 AA.
AC   Q7MHE6;
DT   16-JAN-2004, integrated into UniProtKB/Swiss-Prot.
DT   15-DEC-2003, sequence version 1.
DT   03-AUG-2022, entry version 109.
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}; Synonyms=hepA;
GN   OrderedLocusNames=VV2925;
OS   Vibrio vulnificus (strain YJ016).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=196600;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=YJ016;
RX   PubMed=14656965; DOI=10.1101/gr.1295503;
RA   Chen C.-Y., Wu K.-M., Chang Y.-C., Chang C.-H., Tsai H.-C., Liao T.-L.,
RA   Liu Y.-M., Chen H.-J., Shen A.B.-T., Li J.-C., Su T.-L., Shao C.-P.,
RA   Lee C.-T., Hor L.-I., Tsai S.-F.;
RT   "Comparative genome analysis of Vibrio vulnificus, a marine pathogen.";
RL   Genome Res. 13:2577-2587(2003).
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; BA000037; BAC95689.1; -; Genomic_DNA.
DR   RefSeq; WP_011151234.1; NC_005139.1.
DR   AlphaFoldDB; Q7MHE6; -.
DR   SMR; Q7MHE6; -.
DR   STRING; 672.VV93_v1c26480; -.
DR   PRIDE; Q7MHE6; -.
DR   EnsemblBacteria; BAC95689; BAC95689; BAC95689.
DR   KEGG; vvy:VV2925; -.
DR   PATRIC; fig|196600.6.peg.2906; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   OrthoDB; 291634at2; -.
DR   Proteomes; UP000002675; 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; Reference proteome; Transcription;
KW   Transcription regulation.
FT   CHAIN           1..969
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_0000207191"
FT   DOMAIN          164..334
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          492..668
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;  109275 MW;  7C2B1FE2582F1BEF CRC64;
     MAFALGQRWI SDTESDLGLG TVVALDARTV TLMFAASEEN RVYASNDAPV TRVVFNVGDV
     VECQEGWSLK VEQVVEENGL YTYLGMREDT EETGVALREI FLSNQIRFNK PQDKMYAGQI
     DRMDNFVLRY RALKNQYEQH RSPMRGLCGM RAGLIPHQLY IAHEVGRRHA PRVLLADEVG
     LGKTIEAGMI IHQQVLLGRA ERILIVVPET LQHQWLVEMM RRFNLHFSIF DEERCIEAFA
     ESDNPFDTQQ YVLCSLDFLR KSRKRFEQAL EADWDLLVVD EAHHLEWSQD KPSRGYQVVE
     GLAERTPGVL LLTATPEQLG RESHFARLRL LDSDRFYDYA AFVEEEAQYA PVADAITALF
     SGVKLADEAK NQITELLSEQ DVEPLFRIIE SNADEESKAI ARQELIDNLM DRHGTGRVLF
     RNTRAAIKGF PVRNVHLLPM PIPTQYTTSM RVSGMIGGKL APEARAMKNL YPEEIFQEFE
     GEESSWWQFD CRVNWLLEKL KAQRSEKVLV IASRASTALQ LEQALREREG IRATVFHEGM
     SILERDKAAA YFAQEEGGAQ VLICSEIGSE GRNFQFANQL VMFDLPFNPD LLEQRIGRLD
     RIGQKRDIDI HVPYLQGTAQ EVLARWFNEG LNAFAETCPT GRTVYDQVSD QLIEMLASGS
     NEALNDVIAE SAKLNQALKA DLEQGRDRLL EMHSNGGEKA QQIVAEIAAK DGDTNLVSFA
     LSLFDTIGLN QDDKGENAIV VTPSEHMMVP SYPGLPYEGA TITFDRDTAL SREDMHFISW
     EHPMIQGGID LLMSEGVGTC AVSLLKNKAL PVGTLLLELI YAVDAQAPKR SGIGRFLPRT
     PIRLMMDARG NDLSAQVEFE SFNRQLSPVN RHLASKLVSS VQNDIHRLIE AGDQLVVENV
     EAIRQQAQQE MQQSLNSELE RLQALKAVNP NIRDEEIEAI DAQIKELNGY IAKAQFQLDS
     LRLIVVSHN