ID   RAPA_PSEF5              Reviewed;         949 AA.
AC   Q4KH47;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   02-AUG-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=PFL_1307;
OS   Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
OX   NCBI_TaxID=220664;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-477 / NRRL B-23932 / Pf-5;
RX   PubMed=15980861; DOI=10.1038/nbt1110;
RA   Paulsen I.T., Press C.M., Ravel J., Kobayashi D.Y., Myers G.S.A.,
RA   Mavrodi D.V., DeBoy R.T., Seshadri R., Ren Q., Madupu R., Dodson R.J.,
RA   Durkin A.S., Brinkac L.M., Daugherty S.C., Sullivan S.A., Rosovitz M.J.,
RA   Gwinn M.L., Zhou L., Schneider D.J., Cartinhour S.W., Nelson W.C.,
RA   Weidman J., Watkins K., Tran K., Khouri H., Pierson E.A., Pierson L.S. III,
RA   Thomashow L.S., Loper J.E.;
RT   "Complete genome sequence of the plant commensal Pseudomonas fluorescens
RT   Pf-5.";
RL   Nat. Biotechnol. 23:873-878(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; CP000076; AAY90592.1; -; Genomic_DNA.
DR   RefSeq; WP_011059649.1; NC_004129.6.
DR   AlphaFoldDB; Q4KH47; -.
DR   SMR; Q4KH47; -.
DR   STRING; 220664.PFL_1307; -.
DR   EnsemblBacteria; AAY90592; AAY90592; PFL_1307.
DR   KEGG; pfl:PFL_1307; -.
DR   PATRIC; fig|220664.5.peg.1339; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   OrthoDB; 291634at2; -.
DR   Proteomes; UP000008540; 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; Reference proteome; Transcription;
KW   Transcription regulation.
FT   CHAIN           1..949
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_1000088366"
FT   DOMAIN          164..332
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          474..628
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   MOTIF           278..281
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   949 AA;  106293 MW;  F0939FD5C4C7C5AA CRC64;
     MAQQYQPGQR WISDSEAELG LGTVLAQDGR LLTVLYPATG DTRQYALRNA PLTRVRFSPG
     DSITHFEGWK MTVQEVDDVD GLLVYHGLNG QNEAVTLPET QLSNFIQFRL ASDRLFAGQI
     DPLAWFSLRY HTLEHTSRQL QSSLWGLGGV RAQPIAHQLH IAREVADRIA PRVLLADEVG
     LGKTIEAGLV IHRQLLSGRA SRVLILVPEN LQHQWLVEMR RRFNLQVALF DEERFIESDA
     SNPFEDTQLA LVALEWLVDD EKAQDALFAA GWDLMVVDEA HHLVWHEDQV SPEYALVEQL
     AETIPGVLLL TATPEQLGQD SHFARLRLLD PNRFHDLAAF RAESENYRPV AEAVQELMDK
     GRLSPEAHKT IHGFLGNEGE ALLAAVNDGD SEASARLVRE LLDRHGTGRV LFRNTRAAVQ
     GFPERKLHAY PLPCPDEYLE LPLGEHAELY PEVSFQAQPD VSDDEQRWWK FDPRVEWLID
     QLKMLKRTKV LVICAHAETA MDLEDALRVR SGIPATVFHE GMNILERDRA AAYFADEEFG
     AQVLICSEIG SEGRNFQFAH HLVLFDLPSH PDLLEQRIGR LDRIGQKHVI ELHVPYLETS
     PQERLFQWYH EALNAFLNTC PTGNALQHQF GPRLLPLLEN ADDGEWQALI DAARGERERL
     EAELHTGRDR LLELNSGGAG EGDALVEAIL EQDDQFALPI YMETLFDAFG IDSEDHSENA
     LILKPSEKML DASFPLGDDE GVTITYDRNQ ALSREDMQFI TWEHPMVQGG MDLVLSGSMG
     NTAVALIKNK ALKPGTVLLE LLYVSEVVAP RSLQLGRYLP PAALRCLLDA NGNDLSARVA
     FETLNDQLES VPKASANKFI QAQRDQLAPK INAGEAKVAP RHAERVAEAQ RRLAADTDEE
     LARLTALQAV NPTVRDSELV ALRQQREQGL AMLEKAALRL EAIRVLVAG