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Gene |

Product(s) |

Expression|

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Standard Name	rluA
Gene Synonym(s)	ECK0059, b0058, JW0057, yabO^[1], yabO
Product Desc.	23S rRNA and tRNA pseudouridine synthase^[2]^[3] Dual specificity tRNA and rRNA pseudouridine synthase; specific to 23S rRNA U746 and tRNAphe U32; non-essential gene^[4]
Product Synonyms(s)	pseudouridine synthase for 23S rRNA (position 746) and tRNAphe(position 32)^[1], B0058^[2]^[1], YabO^[2]^[1], RluA^[2]^[1] , ECK0059, JW0057, yabO, b0058
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rluA^[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	rluA
Mnemonic	rRNA, large, uridine
Synonyms	ECK0059, b0058, JW0057, yabO^[1], yabO
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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	1.29 minutes	MG1655: 60346..59687 <gbrowseImage> name=NC_000913:59687..60346 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 63150..62491 <gbrowseImage> name=NC_012967:62491..63150 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 59687..60346 <gbrowseImage> name=NC_012759:59687..60346 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 60346..59687 <gbrowseImage> name=NC_007779:59687..60346 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 60346..59687 <gbrowseImage> name=NC_010473:59687..60346 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
Coding Start (SO:0000323)	MG1655	59690	Edman degradation	PMID:7493321
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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: Description	Reference	Availability	Comments
yabO::Tn5KAN-I-SceI (FB20005)	Insertion at nt 454 in Plus orientation			PMID:15262929	E. coli Genome Project:FB20005	contains pKD46
rluA(del) (Keio:JW0057)	deletion	deletion		PMID:16738554	Shigen CGSC8365^[5]
rluAK28M,R		K28M,R	Forms inclusion bodies, indicating precipitation even within the cell			seeded from UniProt:P0AA37
rluAP29G,L		P29G,L	Reduced structural stability and decrease in activity			seeded from UniProt:P0AA37
rluAC128A		C128A	No change in activity			seeded from UniProt:P0AA37
rluAC117A		C117A	No change in activity			seeded from UniProt:P0AA37
rluAD64N,T		D64N,T	Loss of activity			seeded from UniProt:P0AA37
rluA768(del)::kan				PMID:16738554	CGSC:102730
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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
JW0057	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGGGATGGAAAACTACAATCC Primer 2:CCAAAATCCGCTGGCGCTTTAAA
8D2	Kohara Phage	Genobase	PMID:3038334
carB96::Tn10	Linked marker	CAG12093 = CGSC7322^[5]	est. P1 cotransduction: 35% ^[6] Synonyms:car-96::Tn10
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 41% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
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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:EG12609	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12609	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946262	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002331	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2493	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000196	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	RluA
Synonyms	pseudouridine synthase for 23S rRNA (position 746) and tRNAphe(position 32)^[1], B0058^[2]^[1], YabO^[2]^[1], RluA^[2]^[1] , ECK0059, JW0057, yabO, b0058
Product description	23S rRNA and tRNA pseudouridine synthase^[2]^[3] Dual specificity tRNA and rRNA pseudouridine synthase; specific to 23S rRNA U746 and tRNAphe U32; non-essential gene^[4]
EC number (for enzymes)	4.2.1.70^[1]
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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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006145	F	Seeded from EcoCyc (v14.0)	complete
	GO:0031118	rRNA pseudouridine synthesis	PMID:10383384	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006224	F	Seeded from EcoCyc (v14.0)	complete
	GO:0031119	tRNA pseudouridine synthesis	PMID:10383384	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020103	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009451	RNA modification	PMID:10383384	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0009982	pseudouridine synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006145	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009982	pseudouridine synthase activity	PMID:10383384	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0009982	pseudouridine synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006224	F	Seeded from EcoCyc (v14.0)	complete
	GO:0001522	pseudouridine synthesis	PMID:10383384	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0009982	pseudouridine synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020103	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008033	tRNA processing	PMID:10383384	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0006364	rRNA processing	PMID:10383384	IMP: Inferred from Mutant Phenotype		P		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
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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 MGMENYNPPQ EPWLVILYQD DHIMVVNKPS GLLSVPGRLE EHKDSVMTRI QRDYPQAESV HRLDMATSGV IVVALTKAAE RELKRQFRER EPKKQYVARV WGHPSPAEGL VDLPLICDWP NRPKQKVCYE TGKPAQTEYE VVEYAADNTA RVVLKPITGR SHQLRVHMLA LGHPILGDRF YASPEARAMA PRLLLHAEML TITHPAYGNS MTFKAPADF
Length	219
Mol. Wt	24.86 kDa
pI	8.1 (calculated)
Extinction coefficient	29,910 - 30,160 (calc based on 9 Y, 3 W, and 2 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
Initiator Methionine	1	Removed	UniProt:P0AA37
Domain	22..170	PF00849 RNA pseudouridylate synthase		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=rluA 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:16128052	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946262	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000196	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AA37	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12609	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12609	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946262	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002331	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2493	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	Notes	Reference(s)
Protein	Ecoli K-12	5.437+/-0.073	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
Protein	E. coli K-12 MG1655	585	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	74	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	217	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)
rluA
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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_000913:60326..60366 source=MG1655 flip=1 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:b0058 (EcoliWiki Page)	NCBI GEO profiles for rluA
microarray	GenExpDB:b0058 (EcoliWiki Page)	Summary of data for rluA 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 rluA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12609	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2493	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0058
EcoGene	EcoGene:EG12609	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002331	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000196	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
Anopheles gambiae	ENSANGP00000013169 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G56345 (score: 1.000; bootstrap: 56%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000000204 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00038743 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000029009 (score: 1.000; bootstrap: 79%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000007760 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040801-238 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040801-252 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0216904 (score: 1.000; bootstrap: 91%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000008504 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000007264 (score: 1.000; bootstrap: 80%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000021069 (score: 1.000; bootstrap: 74%)	From Inparanoid:20070104
Mus musculus	MGI:1919186 (score: 1.000; bootstrap: 79%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000007605 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000015206 (score: 1.000; bootstrap: 78%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000133004 (score: 1.000; bootstrap: 87%)	From Inparanoid:20070104
Shigella flexneri	YABO	From SHIGELLACYC
E. coli O157	YABO	From ECOO157CYC
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Notes

Families

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:55120
Pfam (EcoliWiki Page)	PF00849 RNA pseudouridylate synthase
EcoCyc	EcoCyc:EG12609	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12609	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002331	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2493	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000196	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 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).

rluA:On One Page

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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 rluA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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