ID   RAPA_KLEP3              Reviewed;         968 AA.
AC   B5Y1Y4;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   25-NOV-2008, sequence version 1.
DT   03-AUG-2022, entry version 74.
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=KPK_4684;
OS   Klebsiella pneumoniae (strain 342).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
OX   NCBI_TaxID=507522;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=342;
RX   PubMed=18654632; DOI=10.1371/journal.pgen.1000141;
RA   Fouts D.E., Tyler H.L., DeBoy R.T., Daugherty S., Ren Q., Badger J.H.,
RA   Durkin A.S., Huot H., Shrivastava S., Kothari S., Dodson R.J., Mohamoud Y.,
RA   Khouri H., Roesch L.F.W., Krogfelt K.A., Struve C., Triplett E.W.,
RA   Methe B.A.;
RT   "Complete genome sequence of the N2-fixing broad host range endophyte
RT   Klebsiella pneumoniae 342 and virulence predictions verified in mice.";
RL   PLoS Genet. 4:E1000141-E1000141(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; CP000964; ACI10531.1; -; Genomic_DNA.
DR   AlphaFoldDB; B5Y1Y4; -.
DR   SMR; B5Y1Y4; -.
DR   EnsemblBacteria; ACI10531; ACI10531; KPK_4684.
DR   KEGG; kpe:KPK_4684; -.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   OrthoDB; 291634at2; -.
DR   Proteomes; UP000001734; 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_1000188179"
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;  109434 MW;  B75CF51AD1B0D328 CRC64;
     MPFTLGQRWI SDTESELGLG TVVALDARMV TLLFPAIGEN RLYSRNDSPI TRVMFNPGDT
     ITSHEGWQLH VDKVNEENGL LSYTGTRLDT QEANVTLREV LLDSKLVFSK PQDRLFAGQI
     DRMDRFALRY RARKFQSEQY RMPWSGLRGQ RTSLIPHQLN IAHDVGRRHA PRVLLADEVG
     LGKTIEAGMI LHQQLLSGAA ERVLIVVPET LQHQWLVEML RRFNLRFSLF DDERYAEAQH
     DAYNPFETEQ LVICSLDFVR RSKQRLEHLC DAEWDLMVVD EAHHLVWSEE APSREYQAIE
     QLAERVPGIL LLTATPEQLG MESHFARLRL LDPNRFHDFA QFVEEQQNYR PVADAVALLL
     AGNTLSDSEL NTLGDLIGEQ DIEPLLQAAN SDREDAQAAR QELVSMLMDR HGTSRVLFRN
     TRNGVKGFPK RELHTIRLPL PTQYQTAIKV SGIMGARKTA EERARDMLYP EQIYQEFEGD
     TGTWWNFDPR VEWLMGYLTS HRSQKVLVIC AKAATALQLE QVLREREGIR AAVFHEGMSI
     IERDRAAAWF AEEDTGAQVL LCSEIGSEGR NFQFASNLVM FDLPFNPDLL EQRIGRLDRI
     GQAHDIQIHV PYLEKTAQSV LVRWYHEGLD AFEHTCPTGR TVYDSVHDEL INYLAAPEST
     DGFDDLIKSC RQQHDALKAQ LEQGRDRLLE IHSNGGEKAQ ALAESIEEQD DDTSLIAFSM
     NLFDIVGINQ DDRGENLIVL TPSDHMLVPD FPGLPEDGCT ITFERDVALS REDAQFITWE
     HPLIRNGLDL ILSGDTGSST ISLLKNKALP VGTLLLELIY VVEAQAPKQL QLNRFLPATP
     VRLLLDKNGN NLAGQVEFES FNRQLSAVNR HTGSKLVNAV QQDVHAILQQ GEAQIAKAAL
     GLIDAARNEA DEKLTAELSR LEALKAVNPN IRDDELAAIE SNRQQVMDAL AQAGWRLDAL
     RLIVVTHQ