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Standard Name	dbpA
Gene Synonym(s)	ECK1340, b1343, JW1337, rhlC^[1], rhlC
Product Desc.	DEAD box RNA helicase and RNA-dependent ATPase^[2]^[3] ATP-dependent 3'-5' RNA helicase, specific for 23S rRNA^[4]
Product Synonyms(s)	ATP-dependent RNA helicase, specific for 23S rRNA^[1], B1343^[2]^[1], RhlC^[2]^[1], DbpA^[2]^[1] , ECK1340, JW1337, rhlC, b1343
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): C0343^[2]
Regulation/Activity
Quick Links
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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	dbpA
Mnemonic	DEAD Box Protein
Synonyms	ECK1340, b1343, JW1337, rhlC^[1], rhlC
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	30.34 minutes	MG1655: 1407535..1408908 <gbrowseImage> name=NC_000913:1407535..1408908 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1406681..1408054 <gbrowseImage> name=NC_012967:1406681..1408054 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1299594..1300967 <gbrowseImage> name=NC_012759:1299594..1300967 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1411225..1412598 <gbrowseImage> name=NC_007779:1411225..1412598 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1496931..1498304 <gbrowseImage> name=NC_010473:1496931..1498304 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔdbpA (Keio:JW1337)	deletion	deletion			PMID:16738554	Shigen CGSC9193^[5]	Nonessential
dbpA::Tn5KAN-2 (FB20298)	Insertion at nt 513 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20298	does not contain pKD46
ΔdbpA::kan	deletion		Biolog:respiration	unable to respire L-Aspartate	PMID:16095938
R331A		R331A	Growth Phenotype		PMID:17986459		ATPase defective. Dominant negative small colony phenotype.
ΔdbpA780::kan					PMID:16738554	CGSC:100532
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW1337	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACCGCTTTTTCTACCCTGAA Primer 2:CCTTTTAATAACCGCACCCGGCA
4A6	Kohara Phage	Genobase	PMID:3038334
zcj-233::Tn10	Linked marker	CAG12028 = CGSC7373^[5]	est. P1 cotransduction: 20% ^[6] Synonyms:zci-233::Tn10
recT3061::Tn10	Linked marker	CAG12081 = CGSC7375^[5]	est. P1 cotransduction: 91% ^[6] Synonyms:zcj-3061::Tn10, zda-3061::Tn10
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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
EcoCyc	EcoCyc:EG10210	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10210	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000204	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947153	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0206	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004511	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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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	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0003724	RNA helicase activity	PMID:9016593	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	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	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	Experiment(s):EBI-1139588
Protein	groL		PMID:16606699	Experiment(s):EBI-1139588
Protein	purH		PMID:16606699	Experiment(s):EBI-1139588
Protein	mqo		PMID:16606699	Experiment(s):EBI-1139588
RNA	23S rRNA	stimulates ATPase activity PMID:9016593
RNA	16S rRNA	PMID:9016593
RNA	5S rRNA	PMID:9016593
DNA	ATP	PMID:9016593
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Notes

Localization

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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	References
Domain	27..194	PF00270 DEAD/DEAH box helicase	PMID:19920124
Domain	259..336	PF00271 Helicase conserved C-terminal domain	PMID:19920124
Domain	383..456	PF03880 DbpA RNA binding domain	PMID:19920124
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<motif_map/>

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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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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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	258	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	60	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	92	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)
C0343
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:1407515..1407555 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b1343 (EcoliWiki Page)	NCBI GEO profiles for dbpA
microarray	GenExpDB:b1343 (EcoliWiki Page)	Summary of data for dbpA from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to dbpA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10210	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0206	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1343
EcoGene	EcoGene:EG10210	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000204	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004511	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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

Organism	Homologs (Statistics)	Comments
Shigella flexneri	DBPA	From SHIGELLACYC
E. coli O157	DBPA	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00271 Helicase conserved C-terminal domain
Pfam (EcoliWiki Page)	PF03880 DbpA RNA binding domain
Pfam (EcoliWiki Page)	PF00270 DEAD/DEAH box helicase
Superfamily (EcoliWiki Page)	SUPERFAMILY:52540
EcoCyc	EcoCyc:EG10210	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10210	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
ASAP	ASAP:ABE-0004511	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

dbpA:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to dbpA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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