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On One Page

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Gene |

Product(s) |

Expression|

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References |

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Standard Name	truD
Gene Synonym(s)	ECK2740, b2745, JW2715, ygbO^[1], ygbO
Product Desc.	tRNA pseudouridine 13 synthase^[2]^[3] tRNA(Glu) U13 pseudouridine synthase^[4]
Product Synonyms(s)	pseudoruidine synthase^[1], B2745^[2]^[1], YgbO^[2]^[1], TruD^[2]^[1] , ECK2740, JW2715, ygbO, b2745
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s):
Regulation/Activity
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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	truD
Mnemonic	tRNA uridine
Synonyms	ECK2740, b2745, JW2715, ygbO^[1], ygbO
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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	61.82 minutes	MG1655: 2869326..2868277 <gbrowseImage> name=NC_000913:2868277..2869326 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2765116..2766165 <gbrowseImage> name=NC_012967:2765116..2766165 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2754089..2755138 <gbrowseImage> name=NC_012759:2754089..2755138 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2869960..2868911 <gbrowseImage> name=NC_007779:2868911..2869960 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2961868..2960819 <gbrowseImage> name=NC_010473:2960819..2961868 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	2868277	Edman degradation	PMID:12756329
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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
ΔtruD (Keio:JW2715)	deletion	deletion		PMID:16738554	Shigen CGSC10137^[5]
truDD80N,T		D80N,T	Loss of activity			seeded from UniProt:Q57261
ΔtruD750::kan				PMID:16738554	CGSC:103240
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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
JW2715	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATTGAGTTTGATAATCTCAC Primer 2:CCtTCAGCAATATGCGCATAATC
25D2	Kohara Phage	Genobase	PMID:3038334
1B5	Kohara Phage	Genobase	PMID:3038334
6C8	Kohara Phage	Genobase	PMID:3038334
srlD3131::Tn10	Linked marker	CAG18642 = CGSC7423^[5]	est. P1 cotransduction: 16% ^[6] Synonyms:zfh-3131::Tn10, zfi-3131::Tn10
cysI95::Tn10	Linked marker	CAG12173 = CGSC7425^[5]	est. P1 cotransduction: 53% ^[6] Synonyms:cysC95::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:G7422	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13109	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003987	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947214	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2912	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009011	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	TruD
Synonyms	pseudoruidine synthase^[1], B2745^[2]^[1], YgbO^[2]^[1], TruD^[2]^[1] , ECK2740, JW2715, ygbO, b2745
Product description	tRNA pseudouridine 13 synthase^[2]^[3] tRNA(Glu) U13 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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0001522	pseudouridine synthesis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001656	P	Seeded from EcoCyc (v14.0)	complete
	GO:0001522	pseudouridine synthesis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011760	P	Seeded from EcoCyc (v14.0)	complete
	GO:0001522	pseudouridine synthesis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020103	P	Seeded from EcoCyc (v14.0)	complete
	GO:0001522	pseudouridine synthesis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020119	P	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001656	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011760	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:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020119	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008033	tRNA processing	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0819	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009982	pseudouridine synthase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01082	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009982	pseudouridine synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001656	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009982	pseudouridine synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011760	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
	GO:0009982	pseudouridine synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020119	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016853	isomerase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0413	F	Seeded from EcoCyc (v14.0)	complete
	GO:0031119	tRNA pseudouridine synthesis	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01082	P	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	matC	PMID:16606699	Experiment(s):EBI-1143804
Protein	cysQ	PMID:16606699	Experiment(s):EBI-1143804
Protein	nohB	PMID:16606699	Experiment(s):EBI-1143804
Protein	rplB	PMID:16606699	Experiment(s):EBI-1143804
Protein	metG	PMID:16606699	Experiment(s):EBI-1143804
Protein	nohA	PMID:16606699	Experiment(s):EBI-1143804
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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 MIEFDNLTYL HGKPQGTGLL KANPEDFVVV EDLGFEPDGE GEHILVRILK NGCNTRFVAD ALAKFLKIHA REVSFAGQKD KHAVTEQWLC ARVPGKEMPD LSAFQLEGCQ VLEYARHKRK LRLGALKGNA FTLVLREVSN RDDVEQRLID ICVKGVPNYF GAQRFGIGGS NLQGAQRWAQ TNTPVRDRNK RSFWLSAARS ALFNQIVAER LKKADVNQVV DGDALQLAGR GSWFVATTEE LAELQRRVND KELMITAALP GSGEWGTQRE ALAFEQAAVA AETELQALLV REKVEAARRA MLLYPQQLSW NWWDDVTVEI RFWLPAGSFA TSVVRELINT TGDYAHIAE
Length	349
Mol. Wt	39.091 kDa
pI	6.5 (calculated)
Extinction coefficient	56,950 - 57,450 (calc based on 5 Y, 9 W, and 4 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	1..337	PF01142 tRNA pseudouridine synthase D (TruD)		PMID:19920124
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<motif_map/>

Structure
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Structures

<beststructure> gene=truD 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:16130652	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947214	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009011	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q57261	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7422	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13109	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947214	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003987	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2912	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	3.15E+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	9.883+/-0.078	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	1009	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	273	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	518	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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Transcription unit(s)
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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_000913:2869306..2869346 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:b2745 (EcoliWiki Page)	NCBI GEO profiles for truD
microarray	GenExpDB:b2745 (EcoliWiki Page)	Summary of data for truD 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 truD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7422	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2912	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2745
EcoGene	EcoGene:EG13109	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003987	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009011	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
Canis familiaris	ENSCAFP00000005989 (score: 1.000; bootstrap: 100%) ENSCAFP00000014286 (score: 0.139)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000013183 (score: 1.000; bootstrap: 100%) ENSGALP00000015590 (score: 0.095)	From Inparanoid:20070104
Mus musculus	MGI:1925947 (score: 1.000; bootstrap: 100%) MGI:1926145 (score: 0.143)	From Inparanoid:20070104
Oryza gramene	Q5ZBZ5 (score: 1.000; bootstrap: 100%) Q6L4W6 (score: 0.284)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000014063 (score: 1.000; bootstrap: 100%) ENSRNOP00000033040 (score: 0.079)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000050173 (score: 1.000; bootstrap: 100%) ENSXETP00000014881 (score: 0.140)	From Inparanoid:20070104
Shigella flexneri	YGBO	From SHIGELLACYC
E. coli O157	YGBO	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
Panther (EcoliWiki Page)	PTHR13326:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:55120
Pfam (EcoliWiki Page)	PF01142 tRNA pseudouridine synthase D (TruD)
EcoCyc	EcoCyc:G7422	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13109	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003987	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2912	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009011	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 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).

truD: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 truD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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