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Protein

ATP-dependent RNA helicase DbpA

Gene

dbpA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes (Probable).3 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.UniRule annotation2 Publications

Enzyme regulationi

ATPase activity is stimulated by interaction with RNA.2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi46 – 53ATPUniRule annotation8

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Ribosome biogenesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciBSUB:BSU39110-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DbpAUniRule annotation (EC:3.6.4.13UniRule annotation)
Gene namesi
Name:dbpAUniRule annotation
Synonyms:deaD, yxiN
Ordered Locus Names:BSU39110
ORF Names:SS8E
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

No visible effect at 37 or 16 degrees Celsius; no change in ribosome profiles. A quadruple disruption of all RNA helicases (cshA, cshB, deaD, yfmL) is not lethal at 37 degrees Celsius, although both 50S and 70S ribosomes are decreased, while growth stops at 16 degrees.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi52K → Q: Still adopts a closed conformation upon binding of ATP and RNA, but lacks ATPase and RNA unwinding activities. 1 Publication1
Mutagenesisi182S → A: Slows down the catalytic cycle, but does not affect formation of a closed conformer and global conformation; when associated with A-184. 1 Publication1
Mutagenesisi184T → A: Slows down the catalytic cycle, but does not affect formation of a closed conformer and global conformation; when associated with A-182. 1 Publication1
Mutagenesisi303G → A: Prevents a complete closure of the inter-domain cleft, affecting ATP binding, ATP hydrolysis and RNA unwinding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000550971 – 479ATP-dependent RNA helicase DbpAAdd BLAST479

Proteomic databases

PaxDbiP42305.
PRIDEiP42305.

Expressioni

Inductioni

In rich medium highest expression in exponential growth, expression decreases in stationary phase (at protein level).1 Publication

Interactioni

Subunit structurei

May interact with RNA helicases CshA and CshB.1 Publication

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100021111.

Structurei

Secondary structure

1479
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi215 – 221Combined sources7
Helixi224 – 226Combined sources3
Helixi227 – 238Combined sources12
Beta strandi241 – 246Combined sources6
Helixi250 – 262Combined sources13
Beta strandi267 – 270Combined sources4
Helixi276 – 287Combined sources12
Beta strandi292 – 296Combined sources5
Helixi298 – 300Combined sources3
Turni301 – 303Combined sources3
Beta strandi310 – 316Combined sources7
Helixi321 – 327Combined sources7
Turni328 – 330Combined sources3
Beta strandi338 – 344Combined sources7
Helixi346 – 348Combined sources3
Helixi349 – 359Combined sources11
Beta strandi405 – 409Combined sources5
Helixi412 – 414Combined sources3
Helixi419 – 426Combined sources8
Helixi433 – 435Combined sources3
Beta strandi436 – 441Combined sources6
Beta strandi446 – 450Combined sources5
Helixi455 – 462Combined sources8
Beta strandi467 – 469Combined sources3
Beta strandi474 – 476Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2G0CX-ray1.70A404-479[»]
2HJVX-ray1.95A/B207-368[»]
3MOJX-ray2.90B404-479[»]
ProteinModelPortaliP42305.
SMRiP42305.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP42305.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini33 – 203Helicase ATP-bindingUniRule annotationAdd BLAST171
Domaini214 – 374Helicase C-terminalUniRule annotationAdd BLAST161

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni404 – 479Involved in 23S rRNA bindingAdd BLAST76

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi2 – 30Q motifAdd BLAST29
Motifi151 – 154DEAD box4

Domaini

Contains an N-terminal domain that binds non-specifically to RNA and a C-terminal domain that binds specifically and tightly to hairpin 92 of 23S rRNA. Undergoes a conformation change in the helicase core upon binding of RNA and ATP.UniRule annotation5 Publications

Sequence similaritiesi

Belongs to the DEAD box helicase family. DbpA subfamily.UniRule annotation
Contains 1 helicase ATP-binding domain.UniRule annotation
Contains 1 helicase C-terminal domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C1J. Bacteria.
COG0513. LUCA.
HOGENOMiHOG000268809.
InParanoidiP42305.
OMAiQFRYLIA.
PhylomeDBiP42305.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00965. DEAD_helicase_DbpA. 1 hit.
InterProiIPR005580. DbpA_RNA-bd_dom.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR028619. DEAD_helicase_DbpA.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF03880. DbpA. 1 hit.
PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P42305-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSHFKNYQIS HDILRALEGL GYTEPTKVQQ SVIPAALERK DLVVKSQTGS
60 70 80 90 100
GKTASFGIPL CELANWDENK PQALILTPTR ELAVQVKEDI TNIGRFKRIK
110 120 130 140 150
ATAVFGKSSF DKQKAELKQK SHIVVGTPGR VLDHIEKGTL PLDRLSYLVI
160 170 180 190 200
DEADEMLNMG FIEQVEAIIK HLPTERTTML FSATLPQDIE KLSRQYMQNP
210 220 230 240 250
EHIEVKAAGL TTRNIEHAVI QVREENKFSL LKDVLMTENP DSCIIFCRTK
260 270 280 290 300
EHVNQLTDEL DDLGYPCDKI HGGMIQEDRF DVMNEFKRGE YRYLVATDVA
310 320 330 340 350
ARGIDIENIS LVINYDLPLE KESYVHRTGR TGRAGNKGKA ISFVTAFEKR
360 370 380 390 400
FLADIEEYIG FEIQKIEAPS QEEVARKKPE FLAKLNDRPE SKKDKSEELN
410 420 430 440 450
KDIMKLYFNG GKKKKIRAVD FVGTIAKIDG VSADDIGIIT IMDNASYVEI
460 470
LNGKGPHVLK VMKNTTVKGK QLKVNKANK
Length:479
Mass (Da):54,048
Last modified:July 28, 2009 - v2
Checksum:i4E0BA582E523A414
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti364Q → P in BAA11693 (PubMed:8969509).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D83026 Genomic DNA. Translation: BAA11693.1.
AL009126 Genomic DNA. Translation: CAB15947.2.
PIRiE69613.
RefSeqiNP_391790.2. NC_000964.3.
WP_003243023.1. NZ_JNCM01000034.1.

Genome annotation databases

EnsemblBacteriaiCAB15947; CAB15947; BSU39110.
GeneIDi937492.
KEGGibsu:BSU39110.
PATRICi18979884. VBIBacSub10457_4104.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D83026 Genomic DNA. Translation: BAA11693.1.
AL009126 Genomic DNA. Translation: CAB15947.2.
PIRiE69613.
RefSeqiNP_391790.2. NC_000964.3.
WP_003243023.1. NZ_JNCM01000034.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2G0CX-ray1.70A404-479[»]
2HJVX-ray1.95A/B207-368[»]
3MOJX-ray2.90B404-479[»]
ProteinModelPortaliP42305.
SMRiP42305.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100021111.

Proteomic databases

PaxDbiP42305.
PRIDEiP42305.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB15947; CAB15947; BSU39110.
GeneIDi937492.
KEGGibsu:BSU39110.
PATRICi18979884. VBIBacSub10457_4104.

Phylogenomic databases

eggNOGiENOG4105C1J. Bacteria.
COG0513. LUCA.
HOGENOMiHOG000268809.
InParanoidiP42305.
OMAiQFRYLIA.
PhylomeDBiP42305.

Enzyme and pathway databases

BioCyciBSUB:BSU39110-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP42305.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00965. DEAD_helicase_DbpA. 1 hit.
InterProiIPR005580. DbpA_RNA-bd_dom.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR028619. DEAD_helicase_DbpA.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF03880. DbpA. 1 hit.
PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDBPA_BACSU
AccessioniPrimary (citable) accession number: P42305
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: July 28, 2009
Last modified: November 2, 2016
This is version 129 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.