P42305 (DBPA_BACSU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
ATP-dependent RNA helicase dbpA
EC=3.6.4.13

Gene names

Name:	dbpA
Synonyms:	deaD, yxiN
Ordered Locus Names:	BSU39110
ORF Names:	SS8E

Organism

Bacillus subtilis

Taxonomic identifier

1423 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	479 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Has a helix-destabilizing activity By similarity. Exhibits an RNA-dependent ATPase activity, specifically stimulated by bacterial 23S rRNA. May function in rRNA maturation and ribosome biogenesis.
Catalytic activity	ATP + H2O = ADP + phosphate.
Subcellular location	Cytoplasm Probable.
Sequence similarities	Belongs to the DEAD box helicase family. DbpA subfamily. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.

Ontologies

Keywords
Biological process	Ribosome biogenesis
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	ribosome biogenesis Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 479

479

ATP-dependent RNA helicase dbpA

PRO_0000055097

Regions

Domain

33 – 203

171

Helicase ATP-binding

Domain

214 – 374

161

Helicase C-terminal

Nucleotide binding

46 – 53

8

ATP By similarity

Region

404 – 479

76

Involved in 23S rRNA binding

Motif

2 – 30

29

Q motif

Motif

151 – 154

4

DEAD box

Experimental info

Sequence conflict

364

1

Q → P in BAA11693. Ref.1

Secondary structure

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479

Helix Strand Turn

Details...

Beta strand

215 – 221

7

Helix

224 – 226

3

Helix

227 – 238

12

Beta strand

241 – 246

6

Helix

250 – 262

13

Beta strand

267 – 270

4

Helix

276 – 287

12

Beta strand

292 – 296

5

Helix

298 – 300

3

Turn

301 – 303

3

Beta strand

310 – 316

7

Helix

321 – 327

7

Turn

328 – 330

3

Beta strand

338 – 344

7

Helix

346 – 348

3

Helix

349 – 359

11

Beta strand

405 – 409

5

Helix

419 – 426

8

Helix

433 – 435

3

Beta strand

436 – 441

6

Beta strand

446 – 450

5

Helix

455 – 462

8

Beta strand

474 – 476

3

Sequences

	Sequence		Length	Mass (Da)
	P42305 [UniParc]. Last modified July 28, 2009. Version 2. Checksum: 4E0BA582E523A414	FASTA	479	54,048
	10 20 30 40 50 60 MSHFKNYQIS HDILRALEGL GYTEPTKVQQ SVIPAALERK DLVVKSQTGS GKTASFGIPL 70 80 90 100 110 120 CELANWDENK PQALILTPTR ELAVQVKEDI TNIGRFKRIK ATAVFGKSSF DKQKAELKQK 130 140 150 160 170 180 SHIVVGTPGR VLDHIEKGTL PLDRLSYLVI DEADEMLNMG FIEQVEAIIK HLPTERTTML 190 200 210 220 230 240 FSATLPQDIE KLSRQYMQNP EHIEVKAAGL TTRNIEHAVI QVREENKFSL LKDVLMTENP 250 260 270 280 290 300 DSCIIFCRTK EHVNQLTDEL DDLGYPCDKI HGGMIQEDRF DVMNEFKRGE YRYLVATDVA 310 320 330 340 350 360 ARGIDIENIS LVINYDLPLE KESYVHRTGR TGRAGNKGKA ISFVTAFEKR FLADIEEYIG 370 380 390 400 410 420 FEIQKIEAPS QEEVARKKPE FLAKLNDRPE SKKDKSEELN KDIMKLYFNG GKKKKIRAVD 430 440 450 460 470 FVGTIAKIDG VSADDIGIIT IMDNASYVEI LNGKGPHVLK VMKNTTVKGK QLKVNKANK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequencing of a 65 kb region of the Bacillus subtilis genome containing the lic and cel loci, and creation of a 177 kb contig covering the gnt-sacXY region." Yoshida K., Shindo K., Sano H., Seki S., Fujimura M., Yanai N., Miwa Y., Fujita Y. Microbiology 142:3113-3123(1996) [PubMed: 8969509] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 168 / BGSC1A1.
[2]	"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis." Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A. Nature 390:249-256(1997) [PubMed: 9384377] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 168.
[3]	"From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later." Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I., Medigue C., Danchin A. Microbiology 155:1758-1775(2009) [PubMed: 19383706] [Abstract] Cited for: SEQUENCE REVISION TO 364.
[4]	"Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins." Kossen K., Uhlenbeck O.C. Nucleic Acids Res. 27:3811-3820(1999) [PubMed: 10481020] [Abstract] Cited for: CHARACTERIZATION. Strain: 168.
[5]	"The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold." Wang S., Hu Y., Overgaard M.T., Karginov F.V., Uhlenbeck O.C., McKay D.B. RNA 12:959-967(2006) [PubMed: 16611943] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 404-479, RNA-BINDING.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D83026 Genomic DNA. Translation: BAA11693.1.
AL009126 Genomic DNA. Translation: CAB15947.2.

PIR

E69613.

RefSeq

NP_391790.2. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2G0C	X-ray	1.70	A	404-479	[»]
2HJV	X-ray	1.95	A/B	207-368	[»]
3MOJ	X-ray	2.90	B	404-479	[»]

ProteinModelPortal

P42305.

SMR

P42305. Positions 2-478.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBBACT00000001637; EBBACP00000001637; EBBACG00000001635.

GeneID

937492.

GenomeReviews

Gene locus BSU39110 in contig AL009126_GR.

KEGG

bsu:BSU39110.

NMPDR

fig|224308.1.peg.3916.

PATRIC

18979884. VBIBacSub10457_4104.

Organism-specific databases

GenoList

BSU39110. [Micado]

Phylogenomic databases

GeneTree

EBGT00070000031896.

HOGENOM

HBG737336.

PhylomeDB

P42305.

ProtClustDB

CLSK883265.

Enzyme and pathway databases

BioCyc

BSUB:BSU39110-MONOMER.

Family and domain databases

InterPro

IPR005580. DbpA_RNA-bd.
IPR014001. DEAD-like_helicase.
IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR001650. Helicase_C.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]

Pfam

PF03880. DbpA. 1 hit.
PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]

SMART

SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]

PROSITE

PS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DBPA_BACSU

Accession

Primary (citable) accession number: P42305

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	July 28, 2009
Last modified:	January 25, 2012
This is version 97 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program