DBPA_ECOLI
ID DBPA_ECOLI Reviewed; 457 AA.
AC P21693;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 2.
DT 03-AUG-2022, entry version 167.
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};
GN OrderedLocusNames=b1343, JW1337;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2216714; DOI=10.1093/nar/18.18.5413;
RA Iggo R., Picksley S., Southgate J., McPheat J., Lane D.P.;
RT "Identification of a putative RNA helicase in E.coli.";
RL Nucleic Acids Res. 18:5413-5417(1990).
RN [2]
RP SEQUENCE REVISION TO N-TERMINUS, AND FUNCTION.
RX PubMed=8253085; DOI=10.1002/j.1460-2075.1993.tb06035.x;
RA Fuller-Pace F.V., Nicol S.M., Reid A.D., Lane D.P.;
RT "DbpA: a DEAD box protein specifically activated by 23s rRNA.";
RL EMBO J. 12:3619-3626(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP FUNCTION, AND RNA-BINDING.
RX PubMed=9016593; DOI=10.1093/nar/25.3.537;
RA Boeddecker N., Stade K., Franceschi F.;
RT "Characterization of DbpA, an Escherichia coli DEAD box protein with ATP
RT independent RNA unwinding activity.";
RL Nucleic Acids Res. 25:537-544(1997).
RN [7]
RP FUNCTION.
RX PubMed=9836593; DOI=10.1021/bi981837y;
RA Tsu C.A., Uhlenbeck O.C.;
RT "Kinetic analysis of the RNA-dependent adenosinetriphosphatase activity of
RT DbpA, an Escherichia coli DEAD protein specific for 23S ribosomal RNA.";
RL Biochemistry 37:16989-16996(1998).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, DOMAIN, AND RNA-BINDING.
RX PubMed=11574482; DOI=10.1093/emboj/20.19.5503;
RA Diges C.M., Uhlenbeck O.C.;
RT "Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S
RT rRNA.";
RL EMBO J. 20:5503-5512(2001).
RN [9]
RP FUNCTION, ACTIVITY REGULATION, DOMAIN, AND RNA-BINDING.
RX PubMed=11350034; DOI=10.1017/s1355838201010135;
RA Tsu C.A., Kossen K., Uhlenbeck O.C.;
RT "The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in
RT 23S rRNA.";
RL RNA 7:702-709(2001).
RN [10]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=15910005; DOI=10.1021/bi050033x;
RA Diges C.M., Uhlenbeck O.C.;
RT "Escherichia coli DbpA is a 3' --> 5' RNA helicase.";
RL Biochemistry 44:7903-7911(2005).
RN [11]
RP SUBUNIT.
RX PubMed=16325852; DOI=10.1016/j.jmb.2005.10.058;
RA Talavera M.A., Matthews E.E., Eliason W.K., Sagi I., Wang J., Henn A.,
RA De La Cruz E.M.;
RT "Hydrodynamic characterization of the DEAD-box RNA helicase DbpA.";
RL J. Mol. Biol. 355:697-707(2006).
RN [12]
RP FUNCTION, CATALYTIC ACTIVITY, AND ACTIVITY REGULATION.
RX PubMed=18237742; DOI=10.1016/j.jmb.2007.12.046;
RA Henn A., Cao W., Hackney D.D., De La Cruz E.M.;
RT "The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA.";
RL J. Mol. Biol. 377:193-205(2008).
RN [13]
RP FUNCTION, AND MUTAGENESIS OF LYS-53; GLU-154 AND ARG-331.
RX PubMed=19734347; DOI=10.1093/nar/gkp711;
RA Sharpe Elles L.M., Sykes M.T., Williamson J.R., Uhlenbeck O.C.;
RT "A dominant negative mutant of the E. coli RNA helicase DbpA blocks
RT assembly of the 50S ribosomal subunit.";
RL Nucleic Acids Res. 37:6503-6514(2009).
RN [14]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=20160110; DOI=10.1073/pnas.0913081107;
RA Henn A., Cao W., Licciardello N., Heitkamp S.E., Hackney D.D.,
RA De La Cruz E.M.;
RT "Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box
RT helicase, DbpA.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:4046-4050(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. Requires a single-stranded RNA loading site on the 3' side of
CC the substrate helix. {ECO:0000255|HAMAP-Rule:MF_00965,
CC ECO:0000269|PubMed:11350034, ECO:0000269|PubMed:11574482,
CC ECO:0000269|PubMed:15910005, ECO:0000269|PubMed:18237742,
CC ECO:0000269|PubMed:19734347, ECO:0000269|PubMed:20160110,
CC ECO:0000269|PubMed:8253085, ECO:0000269|PubMed:9016593,
CC ECO:0000269|PubMed:9836593}.
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:11574482, ECO:0000269|PubMed:15910005,
CC ECO:0000269|PubMed:18237742, ECO:0000269|PubMed:20160110};
CC -!- ACTIVITY REGULATION: Requires hairpin 92 of 23S rRNA for optimal
CC activity. ATPase activity is stimulated by interaction of the N-
CC terminal domain with RNA. {ECO:0000269|PubMed:11350034,
CC ECO:0000269|PubMed:11574482, ECO:0000269|PubMed:18237742}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:16325852}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
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. {ECO:0000255|HAMAP-Rule:MF_00965,
CC ECO:0000269|PubMed:11350034, ECO:0000269|PubMed:11574482}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DbpA subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00965}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA36872.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; X52647; CAA36872.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC74425.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA14946.1; -; Genomic_DNA.
DR PIR; B64884; B64884.
DR RefSeq; NP_415859.1; NC_000913.3.
DR RefSeq; WP_000123737.1; NZ_SSZK01000012.1.
DR PDB; 7BBB; NMR; -; A=209-457.
DR PDBsum; 7BBB; -.
DR AlphaFoldDB; P21693; -.
DR BMRB; P21693; -.
DR SMR; P21693; -.
DR BioGRID; 4262985; 99.
DR IntAct; P21693; 6.
DR STRING; 511145.b1343; -.
DR jPOST; P21693; -.
DR PaxDb; P21693; -.
DR PRIDE; P21693; -.
DR EnsemblBacteria; AAC74425; AAC74425; b1343.
DR EnsemblBacteria; BAA14946; BAA14946; BAA14946.
DR GeneID; 947153; -.
DR KEGG; ecj:JW1337; -.
DR KEGG; eco:b1343; -.
DR PATRIC; fig|1411691.4.peg.933; -.
DR EchoBASE; EB0206; -.
DR eggNOG; COG0513; Bacteria.
DR HOGENOM; CLU_003041_1_3_6; -.
DR InParanoid; P21693; -.
DR OMA; FGCQALV; -.
DR PhylomeDB; P21693; -.
DR BioCyc; EcoCyc:EG10210-MON; -.
DR BioCyc; MetaCyc:EG10210-MON; -.
DR BRENDA; 3.6.4.13; 2026.
DR PRO; PR:P21693; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0034458; F:3'-5' RNA helicase activity; IDA:EcoCyc.
DR GO; GO:0043531; F:ADP binding; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IDA:EcoCyc.
DR GO; GO:0016887; F:ATP hydrolysis activity; IDA:EcoliWiki.
DR GO; GO:0033677; F:DNA/RNA helicase activity; IDA:EcoliWiki.
DR GO; GO:0003724; F:RNA helicase activity; IDA:EcoliWiki.
DR GO; GO:0019843; F:rRNA binding; IDA:EcoCyc.
DR GO; GO:0000027; P:ribosomal large subunit assembly; IMP:EcoCyc.
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 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..457
FT /note="ATP-dependent RNA helicase DbpA"
FT /id="PRO_0000055096"
FT DOMAIN 34..205
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00965"
FT DOMAIN 230..376
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00965"
FT REGION 383..457
FT /note="Involved in 23S rRNA binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00965"
FT MOTIF 3..31
FT /note="Q motif"
FT MOTIF 153..156
FT /note="DEAD box"
FT BINDING 47..54
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00965"
FT MUTAGEN 53
FT /note="K->A: Shows accumulation of partially-assembled 45S
FT particles."
FT /evidence="ECO:0000269|PubMed:19734347"
FT MUTAGEN 154
FT /note="E->A: Shows accumulation of partially-assembled 45S
FT particles."
FT /evidence="ECO:0000269|PubMed:19734347"
FT MUTAGEN 331
FT /note="R->A: Shows accumulation of partially-assembled 45S
FT particles. Binds rRNA normally but is severely impaired in
FT ATPase and helicase activities. Overexpression confers a
FT dominant slow growth and cold-sensitive phenotype."
FT /evidence="ECO:0000269|PubMed:19734347"
FT TURN 209..212
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 215..221
FT /evidence="ECO:0007829|PDB:7BBB"
FT TURN 225..227
FT /evidence="ECO:0007829|PDB:7BBB"
FT HELIX 228..239
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 242..247
FT /evidence="ECO:0007829|PDB:7BBB"
FT HELIX 251..264
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 268..271
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:7BBB"
FT HELIX 277..288
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 293..297
FT /evidence="ECO:0007829|PDB:7BBB"
FT TURN 299..302
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 311..317
FT /evidence="ECO:0007829|PDB:7BBB"
FT HELIX 322..332
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 335..338
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 340..344
FT /evidence="ECO:0007829|PDB:7BBB"
FT HELIX 347..349
FT /evidence="ECO:0007829|PDB:7BBB"
FT HELIX 350..359
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 365..367
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 381..388
FT /evidence="ECO:0007829|PDB:7BBB"
FT HELIX 391..393
FT /evidence="ECO:0007829|PDB:7BBB"
FT HELIX 399..404
FT /evidence="ECO:0007829|PDB:7BBB"
FT TURN 405..408
FT /evidence="ECO:0007829|PDB:7BBB"
FT TURN 412..414
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 415..420
FT /evidence="ECO:0007829|PDB:7BBB"
FT STRAND 425..430
FT /evidence="ECO:0007829|PDB:7BBB"
FT HELIX 431..442
FT /evidence="ECO:0007829|PDB:7BBB"
SQ SEQUENCE 457 AA; 49188 MW; D9198B1FABA4D38A CRC64;
MTAFSTLNVL PPAQLTNLNE LGYLTMTPVQ AAALPAILAG KDVRVQAKTG SGKTAAFGLG
LLQQIDASLF QTQALVLCPT RELADQVAGE LRRLARFLPN TKILTLCGGQ PFGMQRDSLQ
HAPHIIVATP GRLLDHLQKG TVSLDALNTL VMDEADRMLD MGFSDAIDDV IRFAPASRQT
LLFSATWPEA IAAISGRVQR DPLAIEIDST DALPPIEQQF YETSSKGKIP LLQRLLSLHQ
PSSCVVFCNT KKDCQAVCDA LNEVGQSALS LHGDLEQRDR DQTLVRFANG SARVLVATDV
AARGLDIKSL ELVVNFELAW DPEVHVHRIG RTARAGNSGL AISFCAPEEA QRANIISDML
QIKLNWQTPP ANSSIATLEA EMATLCIDGG KKAKMRPGDV LGALTGDIGL DGADIGKIAV
HPAHVYVAVR QAVAHKAWKQ LQGGKIKGKT CRVRLLK
