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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	dtd
Gene Synonym(s)	ECK3880, b3887, JW3858, yihZ^[1], yihZ
Product Desc.	D-Tyr-tRNA^Tyr deacylase^[2]^[3]; Component of [[:Category:Complex:D-Tyr-tRNA^Tyr deacylase\|D-Tyr-tRNA^Tyr deacylase]]^[3] D-tyrosine tRNA deacylase; also removes other, e.g. D-Trp and D-Asp, toxic D-amino acids from tRNA; dimer^[4]
Product Synonyms(s)	D-tyr-tRNA(Tyr) deacylase^[1], B3887^[2]^[1], Dtd^[2]^[1], YihZ^[2]^[1] , ECK3880, JW3858, yihZ, b3887
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yihX^[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	dtd
Mnemonic	D-tyrosine tRNA deacylase
Synonyms	ECK3880, b3887, JW3858, yihZ^[1], yihZ
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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	87.83 minutes	MG1655: 4075038..4075475 <gbrowseImage> name=NC_000913:4075038..4075475 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4055162..4055599 <gbrowseImage> name=NC_012967:4055162..4055599 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3964707..3965144 <gbrowseImage> name=NC_012759:3964707..3965144 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3559666..3559229 <gbrowseImage> name=NC_007779:3559229..3559666 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4174735..4175172 <gbrowseImage> name=NC_010473:4174735..4175172 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	4075038	Edman degradation	PMID:10383414
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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)	Reference	Availability
Δdtd (Keio:JW3858)	deletion	deletion	PMID:16738554	Shigen CGSC10786^[5]
Δdtd-749::kan			PMID:16738554	CGSC:100664
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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
JW3858	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATTGCATTAATTCAACGCGT Primer 2:CCTACCTGCAACCAGAATGTCAC
6H5	Kohara Phage	Genobase	PMID:3038334
6H9	Kohara Phage	Genobase	PMID:3038334
zih-35::Tn10	Linked marker	CAG18495 = CGSC7467^[5]	est. P1 cotransduction: 69% ^[6]
pflD501::Tn10	Linked marker	CAG18477 = CGSC7470^[5]	est. P1 cotransduction: 2% ^[6] Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).
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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:EG11852	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11852	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001783	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948378	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1798	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012690	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	Dtd
Synonyms	D-tyr-tRNA(Tyr) deacylase^[1], B3887^[2]^[1], Dtd^[2]^[1], YihZ^[2]^[1] , ECK3880, JW3858, yihZ, b3887
Product description	D-Tyr-tRNA^Tyr deacylase^[2]^[3]; Component of [[:Category:Complex:D-Tyr-tRNA^Tyr deacylase\|D-Tyr-tRNA^Tyr deacylase]]^[3] D-tyrosine tRNA deacylase; also removes other, e.g. D-Trp and D-Asp, toxic D-amino acids from tRNA; dimer^[4]
EC number (for enzymes)	3.1.-.-^[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	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00518	C	Seeded from EcoCyc (v14.0)	complete
	GO:0009451	RNA modification				P	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003732	C	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
	GO:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016788	hydrolase activity, acting on ester bonds	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00518	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016788	hydrolase activity, acting on ester bonds	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003732	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019478	D-amino acid catabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00518	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019478	D-amino acid catabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003732	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	Notes	References	Evidence
Protein	Subunits of [[:Category:Complex:D-Tyr-tRNA^Tyr deacylase\|D-Tyr-tRNA^Tyr deacylase]]	could be indirect
Protein	cca		PMID:15690043	Experiment(s):EBI-879990
Protein	rplC		PMID:15690043	Experiment(s):EBI-885002
Protein	rplV		PMID:15690043	Experiment(s):EBI-885002
Protein	yihI		PMID:15690043	Experiment(s):EBI-885002
Protein	stpA		PMID:16606699	Experiment(s):EBI-1146884
Protein	rplS		PMID:16606699	Experiment(s):EBI-1146884
Protein	rplN		PMID:16606699	Experiment(s):EBI-1146884
Protein	yihI		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
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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 MIALIQRVTR ASVTVEGEVT GEIGAGLLVL LGVEKDDDEQ KANRLCERVL GYRIFSDAEG KMNLNVQQAG GSVLVVSQFT LAADTERGMR PSFSKGASPD RAEALYDYFV ERCRQQEMNT QTGRFAADMQ VSLVNDGPVT FWLQV
Length	145
Mol. Wt	15.949 kDa
pI	4.6 (calculated)
Extinction coefficient	9,970 - 10,220 (calc based on 3 Y, 1 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
Domain	2..145	PF02580 D-Tyr-tRNA(Tyr) deacylase		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=dtd 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:16131727	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948378	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012690	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A6M4	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11852	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11852	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948378	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001783	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1798	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	8.308+/-0.07	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	1311	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	649	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	1026	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)
yihX
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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_000913:4075018..4075058 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:b3887 (EcoliWiki Page)	NCBI GEO profiles for dtd
microarray	GenExpDB:b3887 (EcoliWiki Page)	Summary of data for dtd 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 dtd Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11852	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1798	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3887
EcoGene	EcoGene:EG11852	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001783	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012690	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	ENSANGP00000017521 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT4G18460 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000011800 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00031064 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00004151 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000008022 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040801-175 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040801-186 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0183787 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0037898 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA15029-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000014301 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000262550 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000016916 (score: 1.000; bootstrap: 100%) ENSMMUP00000014074 (score: 0.753)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000007056 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1913294 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q5NA78 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000022793 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000012510 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YDL219W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC8C95 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000137672 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00026420001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000014195 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	YIHZ	From SHIGELLACYC
E. coli O157	YIHZ	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)	PF02580 D-Tyr-tRNA(Tyr) deacylase
Panther (EcoliWiki Page)	PTHR10472:SF4
Superfamily (EcoliWiki Page)	SUPERFAMILY:69500
EcoCyc	EcoCyc:EG11852	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11852	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001783	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1798	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012690	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 ^3.2 ^3.3 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).

dtd: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 dtd Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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