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Gene |

Product(s) |

Expression|

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Standard Name	tyrB
Gene Synonym(s)	ECK4046, b4054, JW4014^[1], JW4014
Product Desc.	TyrB^[2]^[3]; Component of TYRB-DIMER^[2]; tyrosine aminotransferase^[3] Tyrosine aminotransferase; aromatic amino acid aminotransferase; phenylalanine aminotransferase; dicarboxylic amino acid aminotransferase; homodimeric^[4]
Product Synonyms(s)	tyrosine aminotransferase, tyrosine-repressible, PLP-dependent^[1], B4054^[2]^[1], TyrB^[2]^[1] , ECK4046, JW4014, b4054
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): tyrB^[2], OP00123
Regulation/Activity
Quick Links
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Notes

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tyrB is in the TyrR regulon.^[4]

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	tyrB
Mnemonic	Tyrosine
Synonyms	ECK4046, b4054, JW4014^[1], JW4014
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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	91.93 minutes, 91.93 minutes	MG1655: 4265137..4266330 <gbrowseImage> name=NC_000913:4265137..4266330 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4246046..4247239 <gbrowseImage> name=NC_012967:4246046..4247239 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4203982..4205175 <gbrowseImage> name=NC_012759:4203982..4205175 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4270704..4271897 <gbrowseImage> name=NC_007779:4270704..4271897 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4364833..4366026 <gbrowseImage> name=NC_010473:4364833..4366026 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	4265137	Edman degradation	PMID:3907634 PMID:8218300
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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
tyrB(del) (Keio:JW4014)	deletion	deletion	PMID:16738554	Shigen CGSC10886^[5]
tyrB507				CGSC:7474
tyrB747(del)::kan			PMID:16738554	CGSC:103262
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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
JW4014	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTTCAAAAAGTTGACGCCTA Primer 2:CCCATCACCGCAGCAAACGCCTT
1E4	Kohara Phage	Genobase	PMID:3038334
12D1	Kohara Phage	Genobase	PMID:3038334
malF3089::Tn10	Linked marker	CAG12164 = CGSC7476^[5]	est. P1 cotransduction: 40% ^[6]
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[5]	est. P1 cotransduction: 18% ^[6]
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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:EG11040	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11040	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001029	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948563	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1033	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013278	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	TyrB
Synonyms	tyrosine aminotransferase, tyrosine-repressible, PLP-dependent^[1], B4054^[2]^[1], TyrB^[2]^[1] , ECK4046, JW4014, b4054
Product description	TyrB^[2]^[3]; Component of TYRB-DIMER^[2]; tyrosine aminotransferase^[3] Tyrosine aminotransferase; aromatic amino acid aminotransferase; phenylalanine aminotransferase; dicarboxylic amino acid aminotransferase; homodimeric^[4]
EC number (for enzymes)	2.6.1.57^[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: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:0008793	aromatic-amino-acid:2-oxoglutarate aminotransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.6.1.57	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004838	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004839	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004838	L-tyrosine:2-oxoglutarate aminotransferase activity	PMID:15983	IMP: Inferred from Mutant Phenotype		F	Table 4	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006532	aspartate biosynthetic process	PMID:15983	IGI: Inferred from Genetic Interaction	EcoliWiki:aspC\|EcoliWiki:ilvE	P	Table 5.	complete
	GO:0042803	protein homodimerization activity	PMID:352693	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	PMID:352693	IDA: Inferred from Direct Assay		F		complete
	GO:0005515	protein binding	PMID:352693	IDA: Inferred from Direct Assay		F		complete
	GO:0005737	cytoplasm	PMID:352693	IDA: Inferred from Direct Assay		C		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	TyrB is a dimer.	^[7]
Protein	groL		PMID:16606699	Experiment(s):EBI-1147350
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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 MFQKVDAYAG DPILTLMERF KEDPRSDKVN LSIGLYYNED GIIPQLQAVA EAEARLNAQP HGASLYLPME GLNCYRHAIA PLLFGADHPV LKQQRVATIQ TLGGSGALKV GADFLKRYFP ESGVWVSDPT WENHVAIFAG AGFEVSTYPW YDEATNGVRF NDLLATLKTL PARSIVLLHP CCHNPTGADL TNDQWDAVIE ILKARELIPF LDIAYQGFGA GMEEDAYAIR AIASAGLPAL VSNSFSKIFS LYGERVGGLS VMCEDAEAAG RVLGQLKATV RRNYSSPPNF GAQVVAAVLN DEALKASWLA EVEEMRTRIL AMRQELVKVL STEMPERNFD YLLNQRGMFS YTGLSAAQVD RLREEFGVYL IASGRMCVAG LNTANVQRVA KAFAAVM
Length	397
Mol. Wt	43.538 kDa
pI	5.3 (calculated)
Extinction coefficient	49,850 - 50,475 (calc based on 15 Y, 5 W, and 5 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	26..393	PF00155 Aminotransferase class I and II		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=tyrB 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:16131880	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948563	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013278	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P04693	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11040	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11040	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948563	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001029	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1033	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	Reference(s)
Protein	E. coli K-12 MC4100	5.10E+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	E. coli K-12 MG1655	1417	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	1747	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	1342	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)
tyrB
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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_000913:4265117..4265157 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:b4054 (EcoliWiki Page)	NCBI GEO profiles for tyrB
microarray	GenExpDB:b4054 (EcoliWiki Page)	Summary of data for tyrB 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 (4264347..4264704) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ01; Well:B5^[8]
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Notes

Accessions Related to tyrB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11040	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1033	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4054
EcoGene	EcoGene:EG11040	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001029	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013278	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	ENSANGP00000016571 (score: 1.000; bootstrap: 100%) ENSANGP00000011707 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000030487 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0001124 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YLR027C (score: 1.000; bootstrap: 91%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC7251 (score: 1.000; bootstrap: 100%) SPAC10F63c (score: 0.115)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000130060 (score: 0.146) NEWSINFRUP00000162658 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000128916 (score: 0.131)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00003870001 (score: 1.000; bootstrap: 99%) GSTENP00010691001 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	TYRB	From SHIGELLACYC
E. coli O157	TYRB	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)	PF00155 Aminotransferase class I and II
Panther (EcoliWiki Page)	PTHR11879:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
EcoCyc	EcoCyc:EG11040	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11040	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001029	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1033	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013278	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 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 ^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).
↑ Powell, JT & Morrison, JF (1978) The purification and properties of the aspartate aminotransferase and aromatic-amino-acid aminotransferase from Escherichia coli. Eur. J. Biochem. 87 391-400 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

tyrB: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 tyrB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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