ID   RAPA_ALIF1              Reviewed;         952 AA.
AC   Q5E881;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   15-MAR-2005, sequence version 1.
DT   03-AUG-2022, entry version 98.
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=VF_0270;
OS   Aliivibrio fischeri (strain ATCC 700601 / ES114) (Vibrio fischeri).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Aliivibrio.
OX   NCBI_TaxID=312309;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700601 / ES114;
RX   PubMed=15703294; DOI=10.1073/pnas.0409900102;
RA   Ruby E.G., Urbanowski M., Campbell J., Dunn A., Faini M., Gunsalus R.,
RA   Lostroh P., Lupp C., McCann J., Millikan D., Schaefer A., Stabb E.,
RA   Stevens A., Visick K., Whistler C., Greenberg E.P.;
RT   "Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with
RT   pathogenic congeners.";
RL   Proc. Natl. Acad. Sci. U.S.A. 102:3004-3009(2005).
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; CP000020; AAW84765.1; -; Genomic_DNA.
DR   RefSeq; WP_011261088.1; NC_006840.2.
DR   RefSeq; YP_203653.1; NC_006840.2.
DR   AlphaFoldDB; Q5E881; -.
DR   SMR; Q5E881; -.
DR   STRING; 312309.VF_0270; -.
DR   EnsemblBacteria; AAW84765; AAW84765; VF_0270.
DR   KEGG; vfi:VF_0270; -.
DR   PATRIC; fig|312309.11.peg.265; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   OrthoDB; 291634at2; -.
DR   Proteomes; UP000000537; 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..952
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_1000188195"
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   952 AA;  107559 MW;  2557B71BC64AF48A CRC64;
     MSFALGQRWI SDTESDLGLG TVVAVDDRTV SLLFAASEEN RLYAKHDAPV TRVMFNKGDT
     IESHEGWSLD VEDVIEEGGL LTYIGTRVDT DEANVVLRET LLSHQIRFNK PQDKLFAGQI
     DRMDRFALRF RALQNQYEQH KSPMRGLCGM RAGLIPHQLF IAHEVGRRYA PRVLLADEVG
     LGKTIEAGMI IHQQVLSGRA ERVLIVVPET LQHQWLVEMM RRFNLHFSIF DEERCVEAYA
     DSENPFDTAQ FVLCSLDFIR KSKRRFEQVV EADWDLLVVD EAHHLEWNQT KPSREYQVIE
     AIAEETPGVL LLTATPEQLG HESHFARLRL LDPDRFYDYD AFVEEERQYQ PVADAVTALM
     SGEKLSNDAK NRITELLSEQ DVEPLFRIIE SSAAEDEQAQ ARQELVDNLM DRHGTGRVLF
     RNTRAAIKGF PQRNLNLMPM PLPSQYATSM RVATMMGGRM TDEARAMKML YPEEIFQEFE
     GDSATWWQFD PRVNWLLELL KENRNEKVLI IASRASTALQ LEQALREREG IRGTVFHEGM
     SIIERDKAAA YFAQEEGGAQ VLICSEIGSE GRNFQFANQL VMFDLPFNPD LLEQRIGRLD
     RIGQKRDIEI HVPYLQGTSQ ELLARWFDEG LNAFGETCPT GRAVYDKFAD AIIAILATGK
     SDGLESLIEE SATLNKALKS QLEQGRDRLL EVHSNGGDKA KEIAEQIAAT DGDTNLVNFA
     LNLFDTIGLN QDDKGENAIV VTPAENMLVS SYPGLPYEGC TITFDRETAL SREDMNLISW
     EHPMIQGGID LVLTEGVGAT AVSLLKNKAL PAGTLLLELV YVVDAQAPKQ SGIARFLPKT
     PIRIMMDGKG NDLSAQVEFE SFNRQLSPVN RHMASKLVNS VQKEIHGLID KAEISMEERL
     ESVRTDAEKE MKAALNSELE RLQALKAVNP NIRDEELTQI GNSNERTIWL YW