dbpA:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

DbpA

Synonyms

ATP-dependent RNA helicase, specific for 23S rRNA[1], B1343[2][1], RhlC[2][1], DbpA[2][1] , ECK1340, JW1337, rhlC, b1343

Product description

DEAD box RNA helicase and RNA-dependent ATPase[2][3]

ATP-dependent 3'-5' RNA helicase, specific for 23S rRNA[4]

EC number (for enzymes)


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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0000027

ribosomal large subunit assembly

PMID:19734347[5]

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0003724

RNA helicase activity

PMID:9016593[6]

IDA: Inferred from Direct Assay

F

not coupled to ATPase activity

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000629

F

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

PMID:9016593[6]

IDA: Inferred from Direct Assay

F

stimulated by 23S rRNA

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0033677

DNA/RNA helicase activity

PMID:9016593[6]

IDA: Inferred from Direct Assay

F

not coupled to ATPase activity

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

prs

PMID:16606699[7]

Experiment(s):EBI-1139588

Protein

groL

PMID:16606699[7]

Experiment(s):EBI-1139588

Protein

purH

PMID:16606699[7]

Experiment(s):EBI-1139588

Protein

mqo

PMID:16606699[7]

Experiment(s):EBI-1139588

RNA

23S rRNA

stimulates ATPase activity PMID:9016593[6]

RNA

16S rRNA

PMID:9016593[6]

RNA

5S rRNA

PMID:9016593[6]

DNA

ATP

PMID:9016593[6]


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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

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
Length

457

Mol. Wt

49.188 kDa

pI

7.7 (calculated)

Extinction coefficient

26,470 - 27,595 (calc based on 3 Y, 4 W, and 9 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

27..194

PF00270 DEAD/DEAH box helicase

PMID:19920124[8]

Domain

259..336

PF00271 Helicase conserved C-terminal domain

PMID:19920124[8]

Domain

383..456

PF03880 DbpA RNA binding domain

PMID:19920124[8]

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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=dbpA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129304

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947153

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004511

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P21693

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10210

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10210

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947153

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000204

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0206

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Sharpe Elles, LM et al. (2009) A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. Nucleic Acids Res. 37 6503-14 PubMed
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 Böddeker, N et al. (1997) Characterization of DbpA, an Escherichia coli DEAD box protein with ATP independent RNA unwinding activity. Nucleic Acids Res. 25 537-45 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ 8.0 8.1 8.2 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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