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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	trpB
Gene Synonym(s)	ECK1255, b1261, JW1253^[1], JW1253
Product Desc.	tryptophan synthase, β subunit^[2]^[3]; Component of tryptophan synthase, β subunit dimer^[3]; tryptophan synthase^[2]^[3] Tryptophan synthase, beta subunit^[4]
Product Synonyms(s)	tryptophan synthase, beta subunit^[1], B1261^[2]^[1], TrpB^[2]^[1], β subunit^[2]^[1] , ECK1255, JW1253, b1261
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	trpB
Mnemonic	Tryptophan
Synonyms	ECK1255, b1261, JW1253^[1], JW1253
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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	28.35 minutes	MG1655: 1316439..1315246 <gbrowseImage> name=NC_000913:1315246..1316439 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1316009..1314816 <gbrowseImage> name=NC_012967:1314816..1316009 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4179047..4180240 <gbrowseImage> name=NC_012759:4179047..4180240 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
BW2952		NC_012759: 1206095..1207288 <gbrowseImage> name=NC_012759:1206095..1207288 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1320129..1318936 <gbrowseImage> name=NC_007779:1318936..1320129 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1405835..1404642 <gbrowseImage> name=NC_010473:1404642..1405835 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	1315249	Edman degradation	PMID:369556 PMID:3524672 PMID:6985892 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: Type	Phenotype: Description	Reference	Availability	Comments
trpB(del) (Keio:JW1253)	deletion	deletion			PMID:16738554	Shigen CGSC9130^[5]
trpB::Tn5KAN-2 (FB20277)	Insertion at nt 776 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20277	does not contain pKD46
trpBG281R		G281R		(in mutant TRPB8)			Strain variation; seeded from UniProt:P0A879
trpB114::Tn10			Auxotrophies			CGSC:7405
trpB202						CGSC:10290
trpB9579(Oc)			Auxotrophies	requires tryptophan for growth	PMID:5339605	CGSC:12160	ochre (UAA) mutation
trpB0						CGSC:27407
trpB9601(Am)			Auxotrophies		PMID:5339605	CGSC:65097	amber (UAG) mutation
trpB9676(Oc)			Auxotrophies	requires tryptophan for growth	PMID:5339605	CGSC:65099	ochre (UAA) mutation
trpB769(del)::kan					PMID:16738554	CGSC:103224
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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
JW1253	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACAACATTACTTAACCCCTA Primer 2:CCGATTTCCCCTCGTGCTTTCAA
14C4	Kohara Phage	Genobase	PMID:3038334
4F1	Kohara Phage	Genobase	PMID:3038334
oppC506::Tn10	Linked marker	CAG12169 = CGSC7369^[5]	est. P1 cotransduction: 67% ^[6] Synonyms:zch-506::Tn10, zci-506::Tn10
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[5]	est. P1 cotransduction: 92% ^[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:EG11025	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11025	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001014	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945768	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1018	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004234	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	TrpB
Synonyms	tryptophan synthase, beta subunit^[1], B1261^[2]^[1], TrpB^[2]^[1], β subunit^[2]^[1] , ECK1255, JW1253, b1261
Product description	tryptophan synthase, β subunit^[2]^[3]; Component of tryptophan synthase, β subunit dimer^[3]; tryptophan synthase^[2]^[3] Tryptophan synthase, beta 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_00133	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:IPR001926	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004834	tryptophan synthase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00133	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004834	tryptophan synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006653	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004834	tryptophan synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006654	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:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001926	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	PMID:4887511	IDA: Inferred from Direct Assay		C		complete
	GO:0005515	protein binding	PMID:378665	IDA: Inferred from Direct Assay		F	Tryptophan synthase is a tetramer consisting of a dimer of alpha and a dimer of beta subunits. EcoliWiki:trpA\|EcoliWiki:trpB	complete
	GO:0030170	pyridoxal phosphate binding	PMID:350880	IDA: Inferred from Direct Assay		F		complete
Contributes to	GO:0004834	tryptophan synthase activity	PMID:8325869	IDA: Inferred from Direct Assay		F		complete
	GO:0009073	aromatic amino acid family biosynthetic process	PMID:8325869	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0000162	tryptophan biosynthetic process	PMID:8325869	IMP: Inferred from Mutant Phenotype		P		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, β subunit dimer	could be indirect
Protein	paaJ		PMID:16606699	Experiment(s):EBI-1139350
Protein	nadE		PMID:16606699	Experiment(s):EBI-1139350
Protein	greB		PMID:16606699	Experiment(s):EBI-1139350
Protein	lacZ		PMID:16606699	Experiment(s):EBI-1139350
Protein	topA		PMID:16606699	Experiment(s):EBI-1139350
Protein	Subunits of tryptophan synthase	could be indirect
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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 MTTLLNPYFG EFGGMYVPQI LMPALRQLEE AFVSAQKDPE FQAQFNDLLK NYAGRPTALT KCQNITAGTN TTLYLKREDL LHGGAHKTNQ VLGQALLAKR MGKTEIIAET GAGQHGVASA LASALLGLKC RIYMGAKDVE RQSPNVFRMR LMGAEVIPVH SGSATLKDAC NEALRDWSGS YETAHYMLGT AAGPHPYPTI VREFQRMIGE ETKAQILERE GRLPDAVIAC VGGGSNAIGM FADFINETNV GLIGVEPGGH GIETGEHGAP LKHGRVGIYF GMKAPMMQTE DGQIEESYSI SAGLDFPSVG PQHAYLNSTG RADYVSITDD EALEAFKTLC LHEGIIPALE SSHALAHALK MMRENPDKEQ LLVVNLSGRG DKDIFTVHDI LKARGEI
Length	397
Mol. Wt	42.983 kDa
pI	6.1 (calculated)
Extinction coefficient	23,380 - 24,005 (calc based on 12 Y, 1 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
Initiator Methionine	1	Removed	UniProt:P0A879
Domain	50..378	PF00291 Pyridoxal-phosphate dependent enzyme		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=trpB 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:16129222	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945768	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004234	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A879	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11025	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11025	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945768	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001014	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1018	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 EMG2	360	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: M91-l	PMID: 9298646
Protein	E. coli K-12 MG1655	550	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	2331	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	787	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_000913:1316419..1316459 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:b1261 (EcoliWiki Page)	NCBI GEO profiles for trpB
microarray	GenExpDB:b1261 (EcoliWiki Page)	Summary of data for trpB 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 trpB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11025	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1018	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1261
EcoGene	EcoGene:EG11025	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001014	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004234	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	AT4G27070 (score: 1.000; bootstrap: 100%) AT5G54810 (score: 0.823) AT5G28237 (score: 0.196)	From Inparanoid:20070104
Oryza gramene	P43283 (score: 1.000; bootstrap: 100%) Q8W0T4 (score: 0.967) P43284 (score: 0.953) Q6YYB9 (score: 0.914) O04225 (score: 0.708)	From Inparanoid:20070104
Saccharomyces cerevisiae	YGL026C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC19A85 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000014791 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	TRPB	From SHIGELLACYC
E. coli O157	TRPB	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)	PF00291 Pyridoxal-phosphate dependent enzyme
Panther (EcoliWiki Page)	PTHR10314:SF3
Superfamily (EcoliWiki Page)	SUPERFAMILY:53686
EcoCyc	EcoCyc:EG11025	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11025	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001014	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1018	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004234	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 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 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 ^3.4 ^3.5 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).

trpB: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 trpB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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