ID   RAPA_VIBPA              Reviewed;         969 AA.
AC   Q87LD0;
DT   16-JAN-2004, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2003, sequence version 1.
DT   03-AUG-2022, entry version 108.
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=VP2682;
OS   Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=223926;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=RIMD 2210633;
RX   PubMed=12620739; DOI=10.1016/s0140-6736(03)12659-1;
RA   Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K.,
RA   Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S.,
RA   Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.;
RT   "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism
RT   distinct from that of V. cholerae.";
RL   Lancet 361:743-749(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; BA000031; BAC60945.1; -; Genomic_DNA.
DR   RefSeq; NP_799061.1; NC_004603.1.
DR   RefSeq; WP_005461840.1; NC_004603.1.
DR   AlphaFoldDB; Q87LD0; -.
DR   SMR; Q87LD0; -.
DR   STRING; 223926.28807692; -.
DR   EnsemblBacteria; BAC60945; BAC60945; BAC60945.
DR   GeneID; 1190227; -.
DR   KEGG; vpa:VP2682; -.
DR   PATRIC; fig|223926.6.peg.2576; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   Proteomes; UP000002493; Chromosome 1.
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_0000207189"
FT   DOMAIN          164..334
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          492..686
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;  109805 MW;  A530BBE543B4062B CRC64;
     MTFALGQRWI SDTESDLGLG TVVAMDARTV TLMFAASEEN RVYARNDAPV TRVTFNVGDV
     IDCQEGWSLK VEEVLEDEGL YTYFGTREDT QETAVVLREI FLSNQIRFNK PQDKLYAGQI
     DRMDNFVLRY RALTNQFEQH KSPMRGLCGM RAGLIPHQLY IAHEVGRRHA PRVLLADEVG
     LGKTIEAGMI IHQQVLSGRA ERILIVVPET LQHQWLVEMM RRFNLHFSIF DEERCIEAFA
     DAENPFDTQQ YVLCSLDFLR KSRKRFEQAL EGEWDLLVVD EAHHLEWSQD KPSREYQVVE
     GLAERTPGVL LLTATPEQLG RESHFARLRL LDPDRFYDYE AFVEEEEQYA PVADAITSLF
     SGEKLPDEAK NQITELLSEQ DVEPLFRIIE SNSDEEAKAS ARQELIDNLM DRHGTGRVLF
     RNTRAAIKGF PTRNVHLMPM DIPQQYTTSM RVAGMIGGKM SSEARAMKNL YPEEIFQEFE
     GDDASWWQFD SRVNWLLEKV KEKRGEKILV IASRASTALQ LEQALREREG IRATVFHEGM
     SILERDKAAA YFAQEEGGAQ VLICSEIGSE GRNFQFANQL VMFDLPFNPD LLEQRIGRLD
     RIGQNRDIDI HVPYLKGTSQ AILARWFDEG LNAFAETCPT GRAVYDKYSD ALIEILASGD
     TSTLDEIIEE SAKLNKELKS QLEQGRDRLL EMHSNGGEKA QQIVEKIEST DGDTNLVTFA
     LSLFDTIGLN QDDKGENALV VTPSEHMMVP SYPGLPYEGA TITFDRDTAL SREDMHFISW
     EHPMIQGGID LLMSEGVGTS AVSLLKNKAL PVGTILLELI YAVDAQAPKR SGITRFLPKT
     PIRLMMDSRG NDLSAQVEFE GFNRQLSPVN RHLGSKLVTS VQKDVHRLIE AGDVLVEEKV
     EAVRKQAQQD MQQSLNTELE RLQALKAVNP NIRDEEIEAI EAQIKELTGY INQAQVQLDS
     LRLIVVSHN