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 27-MAR-2024, entry version 104.
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; Pseudomonadota; 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 KEGG; pfl:PFL_1307; -.
DR PATRIC; fig|220664.5.peg.1339; -.
DR eggNOG; COG0553; Bacteria.
DR HOGENOM; CLU_011520_0_0_6; -.
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 DNA-templated transcription; IEA:UniProtKB-UniRule.
DR CDD; cd18011; DEXDc_RapA; 1.
DR CDD; cd18793; SF2_C_SNF; 1.
DR Gene3D; 2.30.30.140; -; 1.
DR Gene3D; 2.30.30.930; -; 1.
DR Gene3D; 3.30.360.80; -; 1.
DR Gene3D; 6.10.140.1500; -; 1.
DR Gene3D; 6.10.140.2230; -; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR Gene3D; 3.40.50.10810; Tandem AAA-ATPase domain; 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; IPR049730; SNF2/RAD54-like_C.
DR InterPro; IPR000330; SNF2_N.
DR InterPro; IPR040765; Tudor_1_RapA.
DR InterPro; IPR040766; Tudor_2_RapA.
DR PANTHER; PTHR45766; DNA ANNEALING HELICASE AND ENDONUCLEASE ZRANB3 FAMILY MEMBER; 1.
DR PANTHER; PTHR45766:SF3; SWI_SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY A-LIKE PROTEIN 1; 1.
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; P-loop containing nucleoside triphosphate hydrolases; 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..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
//
