GenomeNet

Database: UniProt
Entry: P42305
LinkDB: P42305
Original site: P42305 
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   16-OCT-2019, entry version 145.
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.,
RA   Miwa Y., Fujita Y.;
RT   "Sequencing of a 65 kb region of the Bacillus subtilis genome
RT   containing the lic and cel loci, and creation of a 177 kb contig
RT   covering the gnt-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.,
RA   Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S.,
RA   Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S.,
RA   Brouillet S., Bruschi C.V., Caldwell B., Capuano V., Carter N.M.,
RA   Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A.,
RA   Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T.,
RA   Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D.,
RA   Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N.,
RA   Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G.,
RA   Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A.,
RA   Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M.,
RA   Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M.,
RA   Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S.,
RA   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.,
RA   Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B.,
RA   Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R.,
RA   Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P.,
RA   Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H.,
RA   Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P.,
RA   Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F.,
RA   Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H.,
RA   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.,
RA   Sekowska A., Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT   "From a consortium sequence to a unified sequence: the Bacillus
RT   subtilis 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
RT   DEAD protein specifically activated by 23S rRNA: delineation of a
RT   novel sub-family of bacterial DEAD proteins.";
RL   Nucleic Acids Res. 27:3811-3820(1999).
RN   [5]
RP   FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, DOMAIN, AND
RP   MUTAGENESIS 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
RT   the 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
RT   and 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
RP   RNA-BINDING.
RX   PubMed=16611943; DOI=10.1261/rna.5906;
RA   Wang S., Hu Y., Overgaard M.T., Karginov F.V., Uhlenbeck O.C.,
RA   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
RT   motif fold.";
RL   RNA 12:959-967(2006).
RN   [10]
RP   X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) OF 404-479, DOMAIN, AND
RP   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
RT   its 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
CC       50S ribosomal subunit. Has an RNA-dependent ATPase activity, which
CC       is specific for 23S rRNA, and a 3' to 5' RNA helicase activity
CC       that uses the energy of ATP hydrolysis to destabilize and unwind
CC       short rRNA 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
CC       with RNA. {ECO:0000269|PubMed:10481020,
CC       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
CC       growth, expression decreases in stationary phase (at protein
CC       level). {ECO:0000269|PubMed:23175651}.
CC   -!- DOMAIN: Contains an N-terminal domain that binds non-specifically
CC       to RNA and a C-terminal domain that binds specifically and tightly
CC       to hairpin 92 of 23S rRNA. Undergoes a conformation change in the
CC       helicase core upon binding of RNA and ATP. {ECO:0000255|HAMAP-
CC       Rule:MF_00965, ECO:0000269|PubMed:10481020,
CC       ECO:0000269|PubMed:16611943, ECO:0000269|PubMed:17142894,
CC       ECO:0000269|PubMed:19474341, ECO:0000269|PubMed:20673833}.
CC   -!- DISRUPTION PHENOTYPE: No visible effect at 37 or 16 degrees
CC       Celsius; no change in ribosome profiles. A quadruple disruption of
CC       all RNA helicases (cshA, cshB, deaD, yfmL) is not lethal at 37
CC       degrees Celsius, although both 50S and 70S ribosomes are
CC       decreased, while growth stops at 16 degrees.
CC       {ECO:0000269|PubMed:23175651}.
CC   -!- SIMILARITY: Belongs to the DEAD box helicase family. DbpA
CC       subfamily. {ECO:0000255|HAMAP-Rule:MF_00965}.
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   SMR; P42305; -.
DR   STRING; 224308.BSU39110; -.
DR   PaxDb; P42305; -.
DR   PRIDE; P42305; -.
DR   EnsemblBacteria; CAB15947; CAB15947; BSU39110.
DR   GeneID; 937492; -.
DR   KEGG; bsu:BSU39110; -.
DR   PATRIC; fig|224308.179.peg.4235; -.
DR   eggNOG; ENOG4105C1J; Bacteria.
DR   eggNOG; COG0513; LUCA.
DR   HOGENOM; HOG000268809; -.
DR   InParanoid; P42305; -.
DR   KO; K05592; -.
DR   OMA; KAKNRSI; -.
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:0003723; F:RNA binding; 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   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; Complete proteome; Cytoplasm; Helicase;
KW   Hydrolase; Nucleotide-binding; Reference proteome;
KW   Ribosome biogenesis; RNA-binding.
FT   CHAIN         1    479       ATP-dependent RNA helicase DbpA.
FT                                /FTId=PRO_0000055097.
FT   DOMAIN       33    203       Helicase ATP-binding. {ECO:0000255|HAMAP-
FT                                Rule:MF_00965}.
FT   DOMAIN      214    374       Helicase C-terminal. {ECO:0000255|HAMAP-
FT                                Rule:MF_00965}.
FT   NP_BIND      46     53       ATP. {ECO:0000255|HAMAP-Rule:MF_00965}.
FT   REGION      404    479       Involved in 23S rRNA binding.
FT   MOTIF         2     30       Q motif.
FT   MOTIF       151    154       DEAD box.
FT   MUTAGEN      52     52       K->Q: Still adopts a closed conformation
FT                                upon binding of ATP and RNA, but lacks
FT                                ATPase and RNA unwinding activities.
FT                                {ECO:0000269|PubMed:19474341}.
FT   MUTAGEN     182    182       S->A: Slows down the catalytic cycle, but
FT                                does not affect formation of a closed
FT                                conformer and global conformation; when
FT                                associated with A-184.
FT                                {ECO:0000269|PubMed:19474341}.
FT   MUTAGEN     184    184       T->A: Slows down the catalytic cycle, but
FT                                does not affect formation of a closed
FT                                conformer and global conformation; when
FT                                associated with A-182.
FT                                {ECO:0000269|PubMed:19474341}.
FT   MUTAGEN     303    303       G->A: Prevents a complete closure of the
FT                                inter-domain cleft, affecting ATP
FT                                binding, ATP hydrolysis and RNA
FT                                unwinding. {ECO:0000269|PubMed:19474341}.
FT   CONFLICT    364    364       Q -> P (in Ref. 1; BAA11693).
FT                                {ECO:0000305}.
FT   STRAND      215    221       {ECO:0000244|PDB:2HJV}.
FT   HELIX       224    226       {ECO:0000244|PDB:2HJV}.
FT   HELIX       227    238       {ECO:0000244|PDB:2HJV}.
FT   STRAND      241    246       {ECO:0000244|PDB:2HJV}.
FT   HELIX       250    262       {ECO:0000244|PDB:2HJV}.
FT   STRAND      267    270       {ECO:0000244|PDB:2HJV}.
FT   HELIX       276    287       {ECO:0000244|PDB:2HJV}.
FT   STRAND      292    296       {ECO:0000244|PDB:2HJV}.
FT   HELIX       298    300       {ECO:0000244|PDB:2HJV}.
FT   TURN        301    303       {ECO:0000244|PDB:2HJV}.
FT   STRAND      310    316       {ECO:0000244|PDB:2HJV}.
FT   HELIX       321    327       {ECO:0000244|PDB:2HJV}.
FT   TURN        328    330       {ECO:0000244|PDB:2HJV}.
FT   STRAND      338    344       {ECO:0000244|PDB:2HJV}.
FT   HELIX       346    348       {ECO:0000244|PDB:2HJV}.
FT   HELIX       349    359       {ECO:0000244|PDB:2HJV}.
FT   STRAND      405    409       {ECO:0000244|PDB:2G0C}.
FT   HELIX       412    414       {ECO:0000244|PDB:3MOJ}.
FT   HELIX       419    426       {ECO:0000244|PDB:2G0C}.
FT   HELIX       433    435       {ECO:0000244|PDB:2G0C}.
FT   STRAND      436    441       {ECO:0000244|PDB:2G0C}.
FT   STRAND      446    450       {ECO:0000244|PDB:2G0C}.
FT   HELIX       455    462       {ECO:0000244|PDB:2G0C}.
FT   STRAND      467    469       {ECO:0000244|PDB:3MOJ}.
FT   STRAND      474    476       {ECO:0000244|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
//
DBGET integrated database retrieval system