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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	trpA
Gene Synonym(s)	ECK1254, b1260, JW1252, try, tryp^[1], tryp
Product Desc.	tryptophan synthase, α subunit^[2]^[3]; Component of tryptophan synthase^[2]^[3] Tryptophan synthase, alpha subunit^[4]
Product Synonyms(s)	tryptophan synthase, alpha subunit^[1], B1260^[2]^[1], Try^[2]^[1], TrpA^[2]^[1], α subunit^[2]^[1], TSase α^[2]^[1] , ECK1254, JW1252, try, tryp, b1260
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): trpCBA^[2], trpLEDCBA^[2], OP00094, trp
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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otherPDB (S. typhimurium): 1BKS.^[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	trpA
Mnemonic	Tryptophan
Synonyms	ECK1254, b1260, JW1252, try, tryp^[1], tryp
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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	28.33 minutes	MG1655: 1315246..1314440 <gbrowseImage> name=NC_000913:1314440..1315246 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1314816..1314010 <gbrowseImage> name=NC_012967:1314010..1314816 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1205289..1206095 <gbrowseImage> name=NC_012759:1205289..1206095 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1318936..1318130 <gbrowseImage> name=NC_007779:1318130..1318936 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1404642..1403836 <gbrowseImage> name=NC_010473:1403836..1404642 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	1314440	Edman degradation	PMID:388433 PMID:4863752 PMID:9298646
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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
trpA(del) (Keio:JW1252)	deletion	deletion		PMID:16738554	Shigen CGSC9129^[5]
trpA::Tn5KAN-2 (FB20276)	Insertion at nt 549 in Minus orientation			PMID:15262929	E. coli Genome Project:FB20276	does not contain pKD46
trpALQGFGISAPDQVKAAI209IAGFWYFRPGSGKSSD		LQGFGISAPDQVKAAI209IAGFWYFRPGSGKSSD	(in mutant TrpA46-Asp-PR3)			Strain variation; seeded from UniProt:P0A877
trpA9605(Am)					CGSC:4520	amber (UAG) mutation
trpA49(Am)					CGSC:4688	amber (UAG) mutation
trpA33					CGSC:4770
trpA43					CGSC:5089
trpA9761(Am)					CGSC:5498	amber (UAG) mutation
trpA62					CGSC:6239
trpA58					CGSC:6521
trpA9825(Oc)					CGSC:6541	ochre (UAA) mutation
trpA36					CGSC:6727
trpA23				PMID:13906503 PMID:13906211 PMID:13906504	CGSC:6728
trpA9705(Am)					CGSC:9737	amber (UAG) mutation
trpA9767					CGSC:11092
trpA9607'(Oc, UAA15)				PMID:14008999	CGSC:89883	ochre (UAA) mutation
trpA1016(Am, UAG15)					CGSC:89936	amber (UAG) mutation
trpA1017(UGA, UGA15)					CGSC:89939	opal (UGA) mutation
trpA1015'(Oc, UAA15)					CGSC:89940	ochre (UAA) mutation
trpA1049(Am, UAG49)					CGSC:89941	amber (UAG) mutation
trpA115(Am, UAG115)					CGSC:89942	amber (UAG) mutation
trpA116(UGA, UGA115)					CGSC:89943	opal (UGA) mutation
trpA102(Am, UAG102)					CGSC:89944	amber (UAG) mutation
trpA103(Oc, UAA102)					CGSC:89945	ochre (UAA) mutation
trpA104(UGA, UGA102)					CGSC:89946	opal (UGA) mutation
trpA212(Am, UAG211)					CGSC:89949	amber (UAG) mutation
trpA213(UGA, UGA211)					CGSC:89950	opal (UGA) mutation
trpA211(Oc, UAA211)					CGSC:89951	ochre (UAA) mutation
trpA236(Am, UAG234)					CGSC:89952	amber (UAG) mutation
trpA234(UGA, UGA234)					CGSC:89953	opal (UGA) mutation
trpA235(Oc, UAA234)					CGSC:89954	ochre (UAA) mutation
trpA244(Am, UAG243)					CGSC:89955	amber (UAG) mutation
trpA245(UGA, UGA243)					CGSC:89956	opal (UGA) mutation
trpA243(Oc, UAA243)					CGSC:89957	ochre (UAA) mutation
trpA768(del)::kan				PMID:16738554	CGSC:103222
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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
JW1252	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGAACGCTACGAATCTCTGTT Primer 2:CCACTGCGCGTCGCCGCTTTCAT
14C4	Kohara Phage	Genobase	PMID:3038334
4F1	Kohara Phage	Genobase	PMID:3038334
oppC506::Tn10	Linked marker	CAG12169 = CGSC7369^[5]	est. P1 cotransduction: 69% ^[6] Synonyms:zch-506::Tn10, zci-506::Tn10
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[5]	est. P1 cotransduction: 90% ^[6] Synonyms:trpB83::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:EG11024	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11024	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001013	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946204	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1017	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004232	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	TrpA
Synonyms	tryptophan synthase, alpha subunit^[1], B1260^[2]^[1], Try^[2]^[1], TrpA^[2]^[1], α subunit^[2]^[1], TSase α^[2]^[1] , ECK1254, JW1252, try, tryp, b1260
Product description	tryptophan synthase, α subunit^[2]^[3]; Component of tryptophan synthase^[2]^[3] Tryptophan synthase, alpha subunit^[4]
EC number (for enzymes)	4.2.1.20^[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:0000162	tryptophan biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00131	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000162	tryptophan biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0822	P	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011060	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013785	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004834	tryptophan synthase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00131	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004834	tryptophan synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002028	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004834	tryptophan synthase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.2.1.20	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:378665	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0456	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043199	sulfate binding	PMID:15451433	IPI: Inferred from Physical Interaction		F		Missing: with/from
	GO:0005515	protein binding	PMID:378665	IDA: Inferred from Direct Assay		F	Tryptophan synthase is a heterotetramer (2 alpha subunits & 2 beta subunits) EcoliWiki:trpA\|EcoliWiki:trpB	complete
Contributes to	GO:0004834	tryptophan synthase activity	PMID:8463331	IDA: Inferred from Direct Assay		F		complete
	GO:0009073	aromatic amino acid family biosynthetic process	PMID:8463331	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0000162	tryptophan biosynthetic process	PMID:8463331	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0005737	cytoplasm	PMID:4887511	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	Subunits of tryptophan synthase	could be indirect
Protein	yciE		PMID:16606699	Experiment(s):EBI-1139344
Protein	yhhY		PMID:16606699	Experiment(s):EBI-1139344
Protein	nadE		PMID:16606699	Experiment(s):EBI-1139344
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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 MERYESLFAQ LKERKEGAFV PFVTLGDPGI EQSLKIIDTL IEAGADALEL GIPFSDPLAD GPTIQNATLR AFAAGVTPAQ CFEMLALIRQ KHPTIPIGLL MYANLVFNKG IDEFYAQCEK VGVDSVLVAD VPVEESAPFR QAALRHNVAP IFICPPNADD DLLRQIASYG RGYTYLLSRA GVTGAENRAA LPLNHLVAKL KEYNAAPPLQ GFGISAPDQV KAAIDAGAAG AISGSAIVKI IEQHINEPEK MLAALKVFVQ PMKAATRS
Length	268
Mol. Wt	28.724 kDa
pI	5.3 (calculated)
Extinction coefficient	10,430 - 10,805 (calc based on 7 Y, 0 W, and 3 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	8..267	PF00290 Tryptophan synthase alpha chain		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=trpA taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

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:16129221	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946204	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004232	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A877	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11024	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11024	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946204	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001013	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1017	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	2.23E+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 EMG2	280	molecules/cell	Medium: MOPS glucose minimal Temperature (°C): 37 Doubling time (min): Growth phase: Exponential OD: OD600 = 0.2 to 0.25 other: aerated	Quantitative protein sequencing	Spot ID: M121	PMID: 9298646
Protein	E. coli K-12 MG1655	544	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	2506	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	653	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)
trpCBA
trpLEDCBA
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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_000913:1315226..1315266 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:b1260 (EcoliWiki Page)	NCBI GEO profiles for trpA
microarray	GenExpDB:b1260 (EcoliWiki Page)	Summary of data for trpA 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 trpA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11024	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1017	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1260
EcoGene	EcoGene:EG11024	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001013	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004232	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	AT4G02610 (score: 1.000; bootstrap: 100%) AT3G54640 (score: 0.661)	From Inparanoid:20070104
Oryza gramene	Q6ZL61 (score: 1.000; bootstrap: 100%) Q7Y1H9 (score: 0.577) Q9FQ75 (score: 0.529) Q7Y1I9 (score: 0.497) Q9FQ77 (score: 0.495) Q7Y1I6 (score: 0.490) Q7Y1J1 (score: 0.479) Q58A36 (score: 0.464) Q7XAK6 (score: 0.453) Q58A35 (score: 0.447) P42390 (score: 0.438) Q5QIT0 (score: 0.430) Q9FQ76 (score: 0.072)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000014780 (score: 1.000; bootstrap: 70%)	From Inparanoid:20070104
Shigella flexneri	TRPA	From SHIGELLACYC
E. coli O157	TRPA	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:51366
Panther (EcoliWiki Page)	PTHR10314:SF28
Pfam (EcoliWiki Page)	PF00290 Tryptophan synthase alpha chain
EcoCyc	EcoCyc:EG11024	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11024	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001013	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1017	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004232	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 ^1.12 ^1.13 ^1.14 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 ^2.13 ^2.14 ^2.15 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).

trpA: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 trpA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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