ID   RAPA_YERPN              Reviewed;         968 AA.
AC   Q1CMQ6; C4GNU4;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   11-JUL-2006, sequence version 1.
DT   03-AUG-2022, entry version 95.
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=YPN_0392;
GN   ORFNames=YP516_0400;
OS   Yersinia pestis bv. Antiqua (strain Nepal516).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Yersiniaceae; Yersinia.
OX   NCBI_TaxID=377628;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Nepal516;
RX   PubMed=16740952; DOI=10.1128/jb.00124-06;
RA   Chain P.S.G., Hu P., Malfatti S.A., Radnedge L., Larimer F., Vergez L.M.,
RA   Worsham P., Chu M.C., Andersen G.L.;
RT   "Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516:
RT   evidence of gene reduction in an emerging pathogen.";
RL   J. Bacteriol. 188:4453-4463(2006).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Nepal516;
RA   Plunkett G. III, Anderson B.D., Baumler D.J., Burland V., Cabot E.L.,
RA   Glasner J.D., Mau B., Neeno-Eckwall E., Perna N.T., Munk A.C., Tapia R.,
RA   Green L.D., Rogers Y.C., Detter J.C., Bruce D.C., Brettin T.S.;
RT   "Yersinia pestis Nepal516A whole genome shotgun sequencing project.";
RL   Submitted (APR-2009) to the EMBL/GenBank/DDBJ databases.
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; CP000305; ABG16724.1; -; Genomic_DNA.
DR   EMBL; ACNQ01000006; EEO78176.1; -; Genomic_DNA.
DR   RefSeq; WP_002220588.1; NZ_ACNQ01000006.1.
DR   AlphaFoldDB; Q1CMQ6; -.
DR   SMR; Q1CMQ6; -.
DR   EnsemblBacteria; ABG16724; ABG16724; YPN_0392.
DR   GeneID; 57974093; -.
DR   KEGG; ypn:YPN_0392; -.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   Proteomes; UP000008936; Chromosome.
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..968
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_1000088402"
FT   DOMAIN          164..334
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          490..644
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   968 AA;  110127 MW;  A0143C233E36F5B5 CRC64;
     MPFTLGQRWI SDTESELGLG TVVAIDVRMI TLLFPATGEN RLYARNDSPI TRVMFNPSDT
     ITHHEGWQLK VEEVTQENGL ITYIGTRLDT EETGVAMREV LLDSKLTFSK PQDRLFAGQI
     DRMDRFALRF RARKYQSEQF RLPWSGLRGI RASLIPHQLH IAYEVGQRHA PRVLLADEVG
     LGKTIEAGMI IHQQLLAGRA ERVLIVVPES LQHQWLVEML RRFNLRFSLF DDSRYSEALL
     DSSNPFDTEQ MVICSLDFVR RNKQRLEQLA DASWDLLVVD EAHHMAWSEE APSREYQVIE
     QLAEHIPGVL LLTATPEQLG QQSHFARLRL LDPDRFHDYE EFVNEQQKYR PIADAVTLLL
     GGERLTDDKL NLLGELIDEQ DIEPLLKAAN SQSEDSEAAR QELVTMLMDR HGTSRVLFRN
     TRNGVKGFPH RVLHQIKLPL PTQYQTAIKV SGIMGAKKTL DARAKDMLYP EQIYQEFEGE
     NATWWNFDPR VEWLLNYLVA NRGEKVLVIC AQAATALQLE QVLREREAIR AAVFHEGLSL
     IERDRAAAYF ASEEDGAQVL LCSEIGSEGR NFQFACQLVM FDLPFNPDLL EQRIGRLDRI
     GQNREIQIMV PYLEDTAQAI LVRWYHEGLD AFEHTCPTGR TIYDSSYQEL ISYLATPSEQ
     EGLDEFIHTC RQQHEGLKLQ LEQGRDRLLE MHSNGGEHGQ ELAQSIAEQD NDINLVSFAL
     NLFDIVGINQ EDRSDNLIVL TPSDHMLVPD FPGLPPDGCT VTFDREQALS REDAQFVSWE
     HPIIRNGLDL ILSGDTGSCA VSLLKNKALP VGTLLAELVY VVEAQAPKHL QLTRFLPPTP
     VRMLMDRNGT NLAAQVEFES FNRQLNAVNR HTSSKLVNAV QQEVHTMLQQ AEALVEAQAQ
     ALIETAKREA DDKLSTELAR LEALKAVNPN IRDDEIEALE HNRKMVLENL NQAGWRLDAI
     RLVVVTHQ