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 27-MAR-2024, entry version 163.
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; Bacillota; 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; 224308-BSU39110; -.
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 OrthoDB; 9805696at2; -.
DR PhylomeDB; P42305; -.
DR BioCyc; BSUB:BSU39110-MONOMER; -.
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:0003724; F:RNA helicase activity; IBA:GO_Central.
DR GO; GO:0033592; F:RNA strand annealing activity; IBA:GO_Central.
DR GO; GO:0009409; P:response to cold; IBA:GO_Central.
DR GO; GO:0042254; P:ribosome biogenesis; IEA:UniProtKB-KW.
DR CDD; cd00268; DEADc; 1.
DR CDD; cd12500; RRM_BsYxiN_like; 1.
DR CDD; cd18787; SF2_C_DEAD; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 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 PANTHER; PTHR47963:SF2; ATP-DEPENDENT RNA HELICASE DBPA; 1.
DR PANTHER; PTHR47963; DEAD-BOX ATP-DEPENDENT RNA HELICASE 47, MITOCHONDRIAL; 1.
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; P-loop containing nucleoside triphosphate hydrolases; 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
//
