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DBPA_BACSU
ID   DBPA_BACSU              Reviewed;         479 AA.
AC   P42305;
DT   01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT   28-JUL-2009, sequence version 2.
DT   03-AUG-2022, entry version 156.
DE   RecName: Full=ATP-dependent RNA helicase DbpA {ECO:0000255|HAMAP-Rule:MF_00965};
DE            EC=3.6.4.13 {ECO:0000255|HAMAP-Rule:MF_00965};
GN   Name=dbpA {ECO:0000255|HAMAP-Rule:MF_00965}; Synonyms=deaD, yxiN;
GN   OrderedLocusNames=BSU39110; ORFNames=SS8E;
OS   Bacillus subtilis (strain 168).
OC   Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX   NCBI_TaxID=224308;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=168 / BGSC1A1;
RX   PubMed=8969509; DOI=10.1099/13500872-142-11-3113;
RA   Yoshida K., Shindo K., Sano H., Seki S., Fujimura M., Yanai N., Miwa Y.,
RA   Fujita Y.;
RT   "Sequencing of a 65 kb region of the Bacillus subtilis genome containing
RT   the lic and cel loci, and creation of a 177 kb contig covering the gnt-
RT   sacXY region.";
RL   Microbiology 142:3113-3123(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=168;
RX   PubMed=9384377; DOI=10.1038/36786;
RA   Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA   Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA   Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA   Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA   Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA   Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA   Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA   Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA   Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA   Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA   Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA   Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA   Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA   Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA   Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA   Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA   Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA   Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA   Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA   Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA   Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA   Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA   Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA   Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA   Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA   Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA   Yoshikawa H., Danchin A.;
RT   "The complete genome sequence of the Gram-positive bacterium Bacillus
RT   subtilis.";
RL   Nature 390:249-256(1997).
RN   [3]
RP   SEQUENCE REVISION TO 364.
RX   PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA   Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA   Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT   "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT   168 reference genome a decade later.";
RL   Microbiology 155:1758-1775(2009).
RN   [4]
RP   FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND DOMAIN.
RC   STRAIN=168;
RX   PubMed=10481020; DOI=10.1093/nar/27.19.3811;
RA   Kossen K., Uhlenbeck O.C.;
RT   "Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD
RT   protein specifically activated by 23S rRNA: delineation of a novel sub-
RT   family of bacterial DEAD proteins.";
RL   Nucleic Acids Res. 27:3811-3820(1999).
RN   [5]
RP   FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, DOMAIN, AND MUTAGENESIS
RP   OF LYS-52; SER-182; THR-184 AND GLY-303.
RX   PubMed=19474341; DOI=10.1093/nar/gkp397;
RA   Karow A.R., Klostermeier D.;
RT   "A conformational change in the helicase core is necessary but not
RT   sufficient for RNA unwinding by the DEAD box helicase YxiN.";
RL   Nucleic Acids Res. 37:4464-4471(2009).
RN   [6]
RP   SUBUNIT.
RC   STRAIN=168;
RX   PubMed=20572937; DOI=10.1111/j.1365-2958.2010.07264.x;
RA   Lehnik-Habrink M., Pfortner H., Rempeters L., Pietack N., Herzberg C.,
RA   Stulke J.;
RT   "The RNA degradosome in Bacillus subtilis: identification of CshA as the
RT   major RNA helicase in the multiprotein complex.";
RL   Mol. Microbiol. 77:958-971(2010).
RN   [7]
RP   FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=168;
RX   PubMed=23175651; DOI=10.1128/jb.01475-12;
RA   Lehnik-Habrink M., Rempeters L., Kovacs A.T., Wrede C., Baierlein C.,
RA   Krebber H., Kuipers O.P., Stulke J.;
RT   "DEAD-box RNA helicases in Bacillus subtilis have multiple functions and
RT   act independently from each other.";
RL   J. Bacteriol. 195:534-544(2013).
RN   [8]
RP   X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 207-368, AND DOMAIN.
RX   PubMed=17142894; DOI=10.1107/s1744309106044642;
RA   Caruthers J.M., Hu Y., McKay D.B.;
RT   "Structure of the second domain of the Bacillus subtilis DEAD-box RNA
RT   helicase YxiN.";
RL   Acta Crystallogr. F 62:1191-1195(2006).
RN   [9]
RP   X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 404-479, DOMAIN, AND RNA-BINDING.
RX   PubMed=16611943; DOI=10.1261/rna.5906;
RA   Wang S., Hu Y., Overgaard M.T., Karginov F.V., Uhlenbeck O.C., McKay D.B.;
RT   "The domain of the Bacillus subtilis DEAD-box helicase YxiN that is
RT   responsible for specific binding of 23S rRNA has an RNA recognition motif
RT   fold.";
RL   RNA 12:959-967(2006).
RN   [10]
RP   X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) OF 404-479, DOMAIN, AND RNA-BINDING.
RX   PubMed=20673833; DOI=10.1016/j.jmb.2010.07.040;
RA   Hardin J.W., Hu Y.X., McKay D.B.;
RT   "Structure of the RNA binding domain of a DEAD-box helicase bound to its
RT   ribosomal RNA target reveals a novel mode of recognition by an RNA
RT   recognition motif.";
RL   J. Mol. Biol. 402:412-427(2010).
CC   -!- FUNCTION: DEAD-box RNA helicase involved in the assembly of the 50S
CC       ribosomal subunit. Has an RNA-dependent ATPase activity, which is
CC       specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses
CC       the energy of ATP hydrolysis to destabilize and unwind short rRNA
CC       duplexes (Probable). {ECO:0000305|PubMed:10481020,
CC       ECO:0000305|PubMed:19474341, ECO:0000305|PubMed:23175651}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC         ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00965,
CC         ECO:0000269|PubMed:10481020, ECO:0000269|PubMed:19474341};
CC   -!- ACTIVITY REGULATION: ATPase activity is stimulated by interaction with
CC       RNA. {ECO:0000269|PubMed:10481020, ECO:0000269|PubMed:19474341}.
CC   -!- SUBUNIT: May interact with RNA helicases CshA and CshB.
CC       {ECO:0000269|PubMed:20572937}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC   -!- INDUCTION: In rich medium highest expression in exponential growth,
CC       expression decreases in stationary phase (at protein level).
CC       {ECO:0000269|PubMed:23175651}.
CC   -!- DOMAIN: Contains an N-terminal domain that binds non-specifically to
CC       RNA and a C-terminal domain that binds specifically and tightly to
CC       hairpin 92 of 23S rRNA. Undergoes a conformation change in the helicase
CC       core upon binding of RNA and ATP. {ECO:0000255|HAMAP-Rule:MF_00965,
CC       ECO:0000269|PubMed:10481020, ECO:0000269|PubMed:16611943,
CC       ECO:0000269|PubMed:17142894, ECO:0000269|PubMed:19474341,
CC       ECO:0000269|PubMed:20673833}.
CC   -!- DISRUPTION PHENOTYPE: No visible effect at 37 or 16 degrees Celsius; no
CC       change in ribosome profiles. A quadruple disruption of all RNA
CC       helicases (cshA, cshB, deaD, yfmL) is not lethal at 37 degrees Celsius,
CC       although both 50S and 70S ribosomes are decreased, while growth stops
CC       at 16 degrees. {ECO:0000269|PubMed:23175651}.
CC   -!- SIMILARITY: Belongs to the DEAD box helicase family. DbpA subfamily.
CC       {ECO:0000255|HAMAP-Rule:MF_00965}.
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DR   EMBL; D83026; BAA11693.1; -; Genomic_DNA.
DR   EMBL; AL009126; CAB15947.2; -; Genomic_DNA.
DR   PIR; E69613; E69613.
DR   RefSeq; NP_391790.2; NC_000964.3.
DR   RefSeq; WP_003243023.1; NZ_JNCM01000034.1.
DR   PDB; 2G0C; X-ray; 1.70 A; A=404-479.
DR   PDB; 2HJV; X-ray; 1.95 A; A/B=207-368.
DR   PDB; 3MOJ; X-ray; 2.90 A; B=404-479.
DR   PDBsum; 2G0C; -.
DR   PDBsum; 2HJV; -.
DR   PDBsum; 3MOJ; -.
DR   AlphaFoldDB; P42305; -.
DR   SMR; P42305; -.
DR   STRING; 224308.BSU39110; -.
DR   PaxDb; P42305; -.
DR   PRIDE; P42305; -.
DR   EnsemblBacteria; CAB15947; CAB15947; BSU_39110.
DR   GeneID; 937492; -.
DR   KEGG; bsu:BSU39110; -.
DR   PATRIC; fig|224308.179.peg.4235; -.
DR   eggNOG; COG0513; Bacteria.
DR   InParanoid; P42305; -.
DR   OMA; YDIELYQ; -.
DR   PhylomeDB; P42305; -.
DR   BioCyc; BSUB:BSU39110-MON; -.
DR   EvolutionaryTrace; P42305; -.
DR   Proteomes; UP000001570; Chromosome.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0034458; F:3'-5' RNA helicase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR   GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR   GO; GO:0003724; F:RNA helicase activity; IBA:GO_Central.
DR   GO; GO:0033592; F:RNA strand annealing activity; IBA:GO_Central.
DR   GO; GO:0000027; P:ribosomal large subunit assembly; IBA:GO_Central.
DR   Gene3D; 3.30.70.330; -; 1.
DR   Gene3D; 3.40.50.300; -; 2.
DR   HAMAP; MF_00965; DEAD_helicase_DbpA; 1.
DR   InterPro; IPR005580; DbpA/CsdA_RNA-bd_dom.
DR   InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR   InterPro; IPR028619; DEAD_helicase_DbpA.
DR   InterPro; IPR014001; Helicase_ATP-bd.
DR   InterPro; IPR001650; Helicase_C.
DR   InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR000629; RNA-helicase_DEAD-box_CS.
DR   InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
DR   Pfam; PF03880; DbpA; 1.
DR   Pfam; PF00270; DEAD; 1.
DR   Pfam; PF00271; Helicase_C; 1.
DR   SMART; SM00487; DEXDc; 1.
DR   SMART; SM00490; HELICc; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   PROSITE; PS00039; DEAD_ATP_HELICASE; 1.
DR   PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR   PROSITE; PS51194; HELICASE_CTER; 1.
DR   PROSITE; PS51195; Q_MOTIF; 1.
PE   1: Evidence at protein level;
KW   3D-structure; ATP-binding; Cytoplasm; Helicase; Hydrolase;
KW   Nucleotide-binding; Reference proteome; Ribosome biogenesis; RNA-binding.
FT   CHAIN           1..479
FT                   /note="ATP-dependent RNA helicase DbpA"
FT                   /id="PRO_0000055097"
FT   DOMAIN          33..203
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00965"
FT   DOMAIN          214..374
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00965"
FT   REGION          404..479
FT                   /note="Involved in 23S rRNA binding"
FT   MOTIF           2..30
FT                   /note="Q motif"
FT   MOTIF           151..154
FT                   /note="DEAD box"
FT   BINDING         46..53
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00965"
FT   MUTAGEN         52
FT                   /note="K->Q: Still adopts a closed conformation upon
FT                   binding of ATP and RNA, but lacks ATPase and RNA unwinding
FT                   activities."
FT                   /evidence="ECO:0000269|PubMed:19474341"
FT   MUTAGEN         182
FT                   /note="S->A: Slows down the catalytic cycle, but does not
FT                   affect formation of a closed conformer and global
FT                   conformation; when associated with A-184."
FT                   /evidence="ECO:0000269|PubMed:19474341"
FT   MUTAGEN         184
FT                   /note="T->A: Slows down the catalytic cycle, but does not
FT                   affect formation of a closed conformer and global
FT                   conformation; when associated with A-182."
FT                   /evidence="ECO:0000269|PubMed:19474341"
FT   MUTAGEN         303
FT                   /note="G->A: Prevents a complete closure of the inter-
FT                   domain cleft, affecting ATP binding, ATP hydrolysis and RNA
FT                   unwinding."
FT                   /evidence="ECO:0000269|PubMed:19474341"
FT   CONFLICT        364
FT                   /note="Q -> P (in Ref. 1; BAA11693)"
FT                   /evidence="ECO:0000305"
FT   STRAND          215..221
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   HELIX           224..226
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   HELIX           227..238
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   STRAND          241..246
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   HELIX           250..262
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   STRAND          267..270
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   HELIX           276..287
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   STRAND          292..296
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   HELIX           298..300
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   TURN            301..303
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   STRAND          310..316
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   HELIX           321..327
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   TURN            328..330
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   STRAND          338..344
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   HELIX           346..348
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   HELIX           349..359
FT                   /evidence="ECO:0007829|PDB:2HJV"
FT   STRAND          405..409
FT                   /evidence="ECO:0007829|PDB:2G0C"
FT   HELIX           412..414
FT                   /evidence="ECO:0007829|PDB:3MOJ"
FT   HELIX           419..426
FT                   /evidence="ECO:0007829|PDB:2G0C"
FT   HELIX           433..435
FT                   /evidence="ECO:0007829|PDB:2G0C"
FT   STRAND          436..441
FT                   /evidence="ECO:0007829|PDB:2G0C"
FT   STRAND          446..450
FT                   /evidence="ECO:0007829|PDB:2G0C"
FT   HELIX           455..462
FT                   /evidence="ECO:0007829|PDB:2G0C"
FT   STRAND          467..469
FT                   /evidence="ECO:0007829|PDB:3MOJ"
FT   STRAND          474..476
FT                   /evidence="ECO:0007829|PDB:2G0C"
SQ   SEQUENCE   479 AA;  54048 MW;  4E0BA582E523A414 CRC64;
     MSHFKNYQIS HDILRALEGL GYTEPTKVQQ SVIPAALERK DLVVKSQTGS GKTASFGIPL
     CELANWDENK PQALILTPTR ELAVQVKEDI TNIGRFKRIK ATAVFGKSSF DKQKAELKQK
     SHIVVGTPGR VLDHIEKGTL PLDRLSYLVI DEADEMLNMG FIEQVEAIIK HLPTERTTML
     FSATLPQDIE KLSRQYMQNP EHIEVKAAGL TTRNIEHAVI QVREENKFSL LKDVLMTENP
     DSCIIFCRTK EHVNQLTDEL DDLGYPCDKI HGGMIQEDRF DVMNEFKRGE YRYLVATDVA
     ARGIDIENIS LVINYDLPLE KESYVHRTGR TGRAGNKGKA ISFVTAFEKR FLADIEEYIG
     FEIQKIEAPS QEEVARKKPE FLAKLNDRPE SKKDKSEELN KDIMKLYFNG GKKKKIRAVD
     FVGTIAKIDG VSADDIGIIT IMDNASYVEI LNGKGPHVLK VMKNTTVKGK QLKVNKANK
 
 
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