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Standard Name	rsuA
Gene Synonym(s)	ECK2177, b2183, JW2171, yejD^[1], yejD
Product Desc.	16S rRNA pseudouridine synthase^[2]^[3] 16S RNA U516 pseudouridine synthase^[4]
Product Synonyms(s)	16S rRNA pseudouridylate 516 synthase^[1], B2183^[2]^[1], YejD^[2]^[1], RsuA^[2]^[1] , ECK2177, JW2171, yejD, b2183
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rsuA^[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	rsuA
Mnemonic	rRNA, small pseudouridine
Synonyms	ECK2177, b2183, JW2171, yejD^[1], yejD
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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	49.09 minutes	MG1655: 2278505..2277810 <gbrowseImage> name=NC_000913:2277810..2278505 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2231671..2230976 <gbrowseImage> name=NC_012967:2230976..2231671 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2163615..2164310 <gbrowseImage> name=NC_012759:2163615..2164310 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2283817..2283122 <gbrowseImage> name=NC_007779:2283122..2283817 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2369493..2368798 <gbrowseImage> name=NC_010473:2368798..2369493 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	2277810	Edman degradation	PMID:7612632
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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
ΔrsuA (Keio:JW2171)	deletion	deletion		PMID:16738554	Shigen CGSC9759^[5]
rsuA::Tn5KAN-I-SceI (FB20674)	Insertion at nt 531 in Minus orientation			PMID:15262929	E. coli Genome Project:FB20674	contains pKD46
rsuA::Tn5KAN-I-SceI (FB20675)	Insertion at nt 531 in Minus orientation			PMID:15262929	E. coli Genome Project:FB20675	does not contain pKD46
rsuAD102N,T		D102N,T	Loss of activity			seeded from UniProt:P0AA43
ΔrsuA740::kan				PMID:16738554	CGSC:102832
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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
JW2171	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGACTTGATAAATTTATCGC Primer 2:CCGACGACGCTGGCAATTTCTTC
1F2	Kohara Phage	Genobase	PMID:3038334
20F6	Kohara Phage	Genobase	PMID:3038334
zbd-3104::Tn10	Linked marker	CAG12021 = CGSC7344^[5]	est. P1 cotransduction: % ^[6] Synonyms:zbc-3105::Tn10, zbd-3105::Tn10
napA722::Tn10	Linked marker	CAG12098 = CGSC7400^[5]	est. P1 cotransduction: 42% ^[6] Synonyms:zeg-722, zei-722::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:EG12044	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12044	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001960	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945378	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1978	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007223	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	RsuA
Synonyms	16S rRNA pseudouridylate 516 synthase^[1], B2183^[2]^[1], YejD^[2]^[1], RsuA^[2]^[1] , ECK2177, JW2171, yejD, b2183
Product description	16S rRNA pseudouridine synthase^[2]^[3] 16S RNA U516 pseudouridine synthase^[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:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000748	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002942	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006145	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018496	F	Seeded from EcoCyc (v14.0)	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:0003723	RNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0694	F	Seeded from EcoCyc (v14.0)	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	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020103	F	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	References	Evidence
Protein	rpsJ	PMID:15690043	Experiment(s):EBI-885843, EBI-892392
Protein	rpsB	PMID:15690043	Experiment(s):EBI-892392
Protein	rpsD	PMID:15690043	Experiment(s):EBI-892392
Protein	rpsI	PMID:15690043	Experiment(s):EBI-892392
Protein	rpsM	PMID:15690043	Experiment(s):EBI-892392
Protein	rpsP	PMID:15690043	Experiment(s):EBI-892392
Protein	ycjF	PMID:15690043	Experiment(s):EBI-892392
Protein	ygeY	PMID:16606699	Experiment(s):EBI-1142134
Protein	greB	PMID:16606699	Experiment(s):EBI-1142134
Protein	ycjF	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsP	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsM	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsJ	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):28.456898
Protein	rpsD	PMID:19402753	LCMS(ID Probability):99.6
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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
cytoplasm			From EcoCyc^[3]
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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 MRLDKFIAQQ LGVSRAIAGR EIRGNRVTVD GEIVRNAAFK LLPEHDVAYD GNPLAQQHGP RYFMLNKPQG YVCSTDDPDH PTVLYFLDEP VAWKLHAAGR LDIDTTGLVL MTDDGQWSHR ITSPRHHCEK TYLVTLESPV ADDTAEQFAK GVQLHNEKDL TKPAVLEVIT PTQVRLTISE GRYHQVKRMF AAVGNHVVEL HRERIGGITL DADLAPGEYR PLTEEEIASV V
Length	231
Mol. Wt	25.864 kDa
pI	6.1 (calculated)
Extinction coefficient	21,430 - 21,680 (calc based on 7 Y, 2 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	References
Domain	1..47	PF01479 S4 domain	PMID:19920124
Domain	61..192	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=rsuA taxon=562,83333 </beststructure>

Models

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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:16130121	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945378	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007223	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AA43	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12044	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12044	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945378	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001960	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1978	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	E. coli K-12 MC4100	5.71E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	28.718+/-0.202	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.054676259	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	2485	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	754	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	1487	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)
rsuA
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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_000913:2278485..2278525 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:b2183 (EcoliWiki Page)	NCBI GEO profiles for rsuA
microarray	GenExpDB:b2183 (EcoliWiki Page)	Summary of data for rsuA 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
	GFP Fusion	Intergenic region (2278415..2278677) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:F11^[7]
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Notes

Accessions Related to rsuA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12044	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1978	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2183
EcoGene	EcoGene:EG12044	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001960	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007223	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
Arabidopsis thaliana	AT2G39140 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0185286 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	RSUA	From SHIGELLACYC
E. coli O157	RSUA	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)	PF01479 S4 domain
Panther (EcoliWiki Page)	PTHR21600:SF6
Superfamily (EcoliWiki Page)	SUPERFAMILY:55120
Superfamily (EcoliWiki Page)	SUPERFAMILY:55174
Pfam (EcoliWiki Page)	PF00849 RNA pseudouridylate synthase
EcoCyc	EcoCyc:EG12044	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12044	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001960	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1978	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007223	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 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 ^3.2 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rsuA: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 rsuA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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