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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	trpD
Gene Synonym(s)	ECK1257, b1263, JW1255, trpGD^[1], trpGD
Product Desc.	anthranilate synthase component II^[2]^[3]; Component of anthranilate synthase^[2]^[3] Tryptophan synthesis, bifunctional: anthranilate synthase component II and phosphoribosyl anthranilate transferase^[4]
Product Synonyms(s)	fused glutamine amidotransferase (component II) of anthranilate synthase^[1], anthranilate phosphoribosyl transferase^[1], B1263^[2]^[1], TrpD^[2]^[1], TrpGD^[2]^[1] , ECK1257, JW1255, trpGD, b1263
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): trpLEDCBA^[2], OP00094, trp
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	trpD
Mnemonic	Tryptophan
Synonyms	ECK1257, b1263, JW1255, trpGD^[1], trpGD
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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	28.4 minutes	MG1655: 1319408..1317813 <gbrowseImage> name=NC_000913:1317813..1319408 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1318978..1317383 <gbrowseImage> name=NC_012967:1317383..1318978 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1208662..1210257 <gbrowseImage> name=NC_012759:1208662..1210257 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1323098..1321503 <gbrowseImage> name=NC_007779:1321503..1323098 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1408804..1407209 <gbrowseImage> name=NC_010473:1407209..1408804 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	1317816	Edman degradation	PMID:4594441
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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
trpD(del) (Keio:JW1255)	deletion	deletion	Auxotrophies	requires tryptophan for growth	PMID:16738554	Shigen CGSC9132^[5]
trpD8888			Auxotrophies	requires tryptophan for growth		CGSC:27413
trpD9923			Auxotrophies	requires tryptophan for growth	PMID:4945859	CGSC:58653
trpD9778(Oc)			Auxotrophies	requires tryptophan for growth	PMID:5339605	CGSC:65103	ochre (UAA) mutation
trpD771(del)::kan			Auxotrophies	requires tryptophan for growth	PMID:16738554	CGSC:103228
trpD80	missense		Auxotrophies	requires tryptophan for growth; accumulates anthranilate	PMID:4886290
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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
JW1255	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTGACATTCTGCTGCTCGA Primer 2:CCgCCTCGTGCCGCCAGTGCGGT
4F1	Kohara Phage	Genobase	PMID:3038334
13F9	Kohara Phage	Genobase	PMID:3038334
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[5]	est. P1 cotransduction: 100% ^[6] Synonyms:trpB83::Tn10
zcj-233::Tn10	Linked marker	CAG12028 = CGSC7373^[5]	est. P1 cotransduction: 9% ^[6] Synonyms:zci-233::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:EG11027	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11027	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001016	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945109	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1020	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004241	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	TrpD
Synonyms	fused glutamine amidotransferase (component II) of anthranilate synthase^[1], anthranilate phosphoribosyl transferase^[1], B1263^[2]^[1], TrpD^[2]^[1], TrpGD^[2]^[1] , ECK1257, JW1255, trpGD, b1263
Product description	anthranilate synthase component II^[2]^[3]; Component of anthranilate synthase^[2]^[3] Tryptophan synthesis, bifunctional: anthranilate synthase component II and phosphoribosyl anthranilate transferase^[4]
EC number (for enzymes)	4.1.3.27^[1] 2.4.2.18^[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_00211	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000162	tryptophan biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005940	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:0004048	anthranilate phosphoribosyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00211	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004048	anthranilate phosphoribosyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005940	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004048	anthranilate phosphoribosyltransferase activity	PMID:4886290	IDA: Inferred from Direct Assay		F	Fig. 9	complete
Contributes to	GO:0004049	anthranilate synthase activity	PMID:5331787	IDA: Inferred from Direct Assay		F	Anthranilate synthase activity restored when extracts of trpD9778 and trpE5972 mutants are combined (Fig. 1).	complete
	GO:0004049	anthranilate synthase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.3.27	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006541	glutamine metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001317	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006541	glutamine metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011702	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006541	glutamine metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0315	P	Seeded from EcoCyc (v14.0)	complete
	GO:0004049	anthranilate synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006221	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004048	anthranilate phosphoribosyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.4.2.18	F	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 anthranilate 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
Cytoplasm		PMID:4594441, PMID:6283099.	EchoLocation:trpD
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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 MADILLLDNI DSFTYNLADQ LRSNGHNVVI YRNHIPAQTL IERLATMSNP VLMLSPGPGV PSEAGCMPEL LTRLRGKLPI IGICLGHQAI VEAYGGYVGQ AGEILHGKAS SIEHDGQAMF AGLTNPLPVA RYHSLVGSNI PAGLTINAHF NGMVMAVRHD ADRVCGFQFH PESILTTQGA RLLEQTLAWA QQKLEPANTL QPILEKLYQA QTLSQQESHQ LFSAVVRGEL KPEQLAAALV SMKIRGEHPN EIAGAATALL ENAAPFPRPD YLFADIVGTG GDGSNSINIS TASAFVAAAC GLKVAKHGNR SVSSKSGSSD LLAAFGINLD MNADKSRQAL DELGVCFLFA PKYHTGFRHA MPVRQQLKTR TLFNVLGPLI NPAHPPLALI GVYSPELVLP IAETLRVLGY QRAAVVHSGG MDEVSLHAPT IVAELHDGEI KSYQLTAEDF GLTPYHQEQL AGGTPEENRD ILTRLLQGKG DAAHEAAVAA NVAMLMRLHG HEDLQANAQT VLEVLRSGSA YDRVTALAAR G
Length	531
Mol. Wt	56.87 kDa
pI	6.5 (calculated)
Extinction coefficient	24,870 - 25,495 (calc based on 13 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:P00904
Domain	5..190	PF00117 Glutamine amidotransferase class-I		PMID:19920124
Domain	199..264	PF02885 Glycosyl transferase family, helical bundle domain		PMID:19920124
Domain	270..521	PF00591 Glycosyl transferase family, a/b domain		PMID:19920124
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<motif_map/>

Structure
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Structures

<beststructure> gene=trpD 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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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:16129224	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945109	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004241	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P00904	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11027	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11027	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945109	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001016	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1020	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 MG1655	74	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	719	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	186	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)
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_000913:1319388..1319428 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:b1263 (EcoliWiki Page)	NCBI GEO profiles for trpD
microarray	GenExpDB:b1263 (EcoliWiki Page)	Summary of data for trpD 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 trpD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11027	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1020	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1263
EcoGene	EcoGene:EG11027	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001016	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004241	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
Saccharomyces cerevisiae	YDR354W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G17990 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC16G58 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	TRPD	From SHIGELLACYC
E. coli O157	TRPD	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)	PF02885 Glycosyl transferase family, helical bundle domain
Pfam (EcoliWiki Page)	PF00591 Glycosyl transferase family, a/b domain
Pfam (EcoliWiki Page)	PF00117 Glutamine amidotransferase class-I
Superfamily (EcoliWiki Page)	SUPERFAMILY:47648
Superfamily (EcoliWiki Page)	SUPERFAMILY:52317
Superfamily (EcoliWiki Page)	SUPERFAMILY:52418
Panther (EcoliWiki Page)	PTHR11922:SF7
EcoCyc	EcoCyc:EG11027	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11027	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001016	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1020	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004241	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 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 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).

trpD:On One Page

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Gene

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Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

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Genetic Resources

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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 trpD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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