{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	rluD
Gene Synonym(s)	ECK2592, b2594, JW2576, sfhB, yfiI, G7351^[1]^[2]
Product Desc.	23S rRNA pseudouridine synthase^[2]^[3] 23S rRNA pseudouridine synthase; specific to U1911, U1915, and U1917; mutation supresses ftsH(Ts) mutants; null mutants grow very poorly^[4]
Product Synonyms(s)	23S rRNA pseudouridine synthase^[1], B2594^[2]^[1], YfiI^[2]^[1], RluD^[2]^[1], SfhB^[2]^[1] , ECK2592, JW2576, sfhB, yfiI, b2594
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yfiH^[2]
Regulation/Activity
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

The very poor growth of rluD mutants can be suppressed by a point mutation in prfB and a role in translation termination for the 23S rRNA helix 69 pseudouridines has been demonstrated (Ejby, 2007).^[4]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

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

Standard name	rluD
Mnemonic	rRNA, large, uridine
Synonyms	ECK2592, b2594, JW2576, sfhB, yfiI, G7351^[1]^[2]
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<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	58.91 minutes	MG1655: 2734033..2733053 <gbrowseImage> name=NC_000913:2733053..2734033 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2657419..2656439 <gbrowseImage> name=NC_012967:2656439..2657419 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2618865..2619845 <gbrowseImage> name=NC_012759:2618865..2619845 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2734667..2733687 <gbrowseImage> name=NC_007779:2733687..2734667 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2825798..2824818 <gbrowseImage> name=NC_010473:2824818..2825798 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

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	2733056	Edman degradation	PMID:11087118
edit table

Notes

Alleles and Phenotypes

[back to top]

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
ΔrluD (Keio:JW2576)	deletion	deletion		PMID:16738554	Shigen CGSC10045^[5]
rluDD139N,T		D139N,T	Loss of activity			seeded from UniProt:P33643
ΔrluD759::kan				PMID:16738554	CGSC:102736
edit table

Notes

Genetic Interactions

[back to top]

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

</protect>

Notes

Genetic Resources

[back to top]

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

Resource	Resource Type	Source	Notes/Reference
JW2576	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCACAACGAGTACAGCTCAC Primer 2:CCTAACCAGTCCACTTCATCCTT
21D7	Kohara Phage	Genobase	PMID:3038334
nadB51::Tn10	Linked marker	CAG18480 = CGSC7419^[5]	est. P1 cotransduction: 42% ^[6]
pheA18::Tn10	Linked marker	CAG12158 = CGSC7421^[5]	est. P1 cotransduction: 87% ^[6]
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12098	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12098	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002003	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947087	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2022	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008532	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name	RluD
Synonyms	23S rRNA pseudouridine synthase^[1], B2594^[2]^[1], YfiI^[2]^[1], RluD^[2]^[1], SfhB^[2]^[1] , ECK2592, JW2576, sfhB, yfiI, b2594
Product description	23S rRNA pseudouridine synthase^[2]^[3] 23S rRNA pseudouridine synthase; specific to U1911, U1915, and U1917; mutation supresses ftsH(Ts) mutants; null mutants grow very poorly^[4]
EC number (for enzymes)	4.2.1.70^[1]
edit table

Notes

Function

[back to top]

<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: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:IPR006224	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006225	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:IPR006224	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009982	pseudouridine synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006225	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
edit table

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	ymdF	PMID:15690043	Experiment(s):EBI-889664
Protein	pepQ	PMID:15690043	Experiment(s):EBI-882193
Protein	ycaO	PMID:16606699	Experiment(s):EBI-1143426
Protein	galF	PMID:16606699	Experiment(s):EBI-1143426
Protein	talA	PMID:16606699	Experiment(s):EBI-1143426
Protein	prs	PMID:16606699	Experiment(s):EBI-1143426
Protein	rpsJ	PMID:16606699	Experiment(s):EBI-1143426
Protein	groL	PMID:16606699	Experiment(s):EBI-1143426
Protein	ycgL	PMID:16606699	Experiment(s):EBI-1143426
Protein	zwf	PMID:16606699	Experiment(s):EBI-1143426
Protein	thiD	PMID:16606699	Experiment(s):EBI-1143426
Protein	OrderedLocusNames=b4223,JW4182	PMID:16606699	Experiment(s):EBI-1143426
Protein	glpD	PMID:16606699	Experiment(s):EBI-1143426
Protein	rplB	PMID:16606699	Experiment(s):EBI-1143426
Protein	mlc	PMID:16606699	Experiment(s):EBI-1143426
Protein	ybgC	PMID:16606699	Experiment(s):EBI-1143426
Protein	pepQ	PMID:19402753	MALDI(Z-score):27.511193
edit table

</protect>

Notes

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
edit table

Notes

Structure and Physical Properties

[back to top]

<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 MAQRVQLTAT VSENQLGQRL DQALAEMFPD YSRSRIKEWI LDQRVLVNGK VCDKPKEKVL GGEQVAINAE IEEEARFEPQ DIPLDIVYED EDIIIINKPR DLVVHPGAGN PDGTVLNALL HYYPPIADVP RAGIVHRLDK DTTGLMVVAK TVPAQTRLVE SLQRREITRE YEAVAIGHMT AGGTVDEPIS RHPTKRTHMA VHPMGKPAVT HYRIMEHFRV HTRLRLRLET GRTHQIRVHM AHITHPLVGD PVYGGRPRPP KGASEAFIST LRKFDRQALH ATMLRLYHPI SGIEMEWHAP IPQDMVELIE VMRADFEEHK DEVDWL
Length	326
Mol. Wt	37.121 kDa
pI	6.8 (calculated)
Extinction coefficient	28,420 - 28,545 (calc based on 8 Y, 3 W, and 1 C residues)
edit table

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:P33643
Domain	18..65	PF01479 S4 domain		PMID:19920124
Domain	92..242	PF00849 RNA pseudouridylate synthase		PMID:19920124
edit table

<motif_map/>

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

Structures

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

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

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

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16130515	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947087	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008532	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P33643	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12098	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12098	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947087	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002003	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2022	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MC4100	1.76E+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	21.145+/-0.194	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	2383	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	716	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	1191	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

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

Transcription unit(s)
yfiH
edit table

Figure courtesy of RegulonDB

</protect>

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

[back to top]

<protect><gbrowseImage> name=NC_000913:2734013..2734053 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]

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

Allele Name	Mutation	Phenotype	Reference
edit table

Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b2594 (EcoliWiki Page)	NCBI GEO profiles for rluD
microarray	GenExpDB:b2594 (EcoliWiki Page)	Summary of data for rluD from multiple microarray studies
edit table

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 (2733956..2734194) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ09; Well:E6^[7]
edit table

Notes

Accessions Related to rluD Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12098	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2022	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2594
EcoGene	EcoGene:EG12098	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002003	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008532	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

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
Apis mellifera	ENSAPMP00000031590 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G76050 (score: 1.000; bootstrap: 98%)	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
Caenorhabditis elegans	WBGene00019498 (score: 1.000; bootstrap: 100%)	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	DDB0205216 (score: 1.000; bootstrap: 88%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000008504 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q5Z8P2 (score: 1.000; bootstrap: 99%) Q8SB33 (score: 0.485)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000007605 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YDL036C (score: 1.000; bootstrap: 100%) YOL066C (score: 1.000; bootstrap: 100%) YGR169C (score: 0.121)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000026859 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	SFHB	From SHIGELLACYC
E. coli O157	SFHB	From ECOO157CYC
edit table

Do-It-Yourself Web Tools

Notes

Families

[back to top]

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF01479 S4 domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:55120
Superfamily (EcoliWiki Page)	SUPERFAMILY:55174
Pfam (EcoliWiki Page)	PF00849 RNA pseudouridylate synthase
EcoCyc	EcoCyc:EG12098	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12098	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002003	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2022	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008532	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

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 ^1.12 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 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 ^4.2 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

rluD:On One Page

Quickview

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 rluD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search