tdh:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

tdh

Gene Synonym(s)

ECK3606, b3616, JW3591[1], JW3591

Product Desc.

Tdh[2][3];

Component of threonine dehydrogenase[2][3]

Threonine dehydrogenase[4]

Product Synonyms(s)

threonine 3-dehydrogenase, NAD(P)-binding[1], B3616[2][1], Tdh[2][1] , ECK3606, JW3591, b3616

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): kbl-tdh[2], OP00316, tdh

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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

tdh

Mnemonic

Threonine dehydrogenase

Synonyms

ECK3606, b3616, JW3591[1], JW3591

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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

81.65 minutes 

MG1655: 3789368..3788343
<gbrowseImage> name=NC_000913:3788343..3789368 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3732111..3731086
<gbrowseImage> name=NC_012967:3731086..3732111 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3676669..3677694
<gbrowseImage> name=NC_012759:3676669..3677694 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3849070..3850095
<gbrowseImage> name=NC_007779:3849070..3850095 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3886945..3885920
<gbrowseImage> name=NC_010473:3885920..3886945 source=DH10B preset=GeneLocation </gbrowseImage>

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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

3788343

Edman degradation

PMID:2647748


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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

Δtdh (Keio:JW3591)

deletion

deletion

PMID:16738554

Shigen
CGSC10645[5]

tdh::Tn5KAN-I-SceI (FB21347)

Insertion at nt 283 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21347

does not contain pKD46

tdh::Tn5KAN-I-SceI (FB21348)

Insertion at nt 283 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21348

contains pKD46

tdh-1::cat1212

CGSC:13063

Δtdh-728::kan

PMID:16738554

CGSC:103118


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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

JW3591

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAAGCGTTATCCAAACTGAA

Primer 2:CCATCCCAGCTCAGAATAACTTT

16B11

Kohara Phage

Genobase

PMID:3038334

5D2

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: % [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: 19% [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:EG10993

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10993

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000982

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948139

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0986

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011830

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Tdh

Synonyms

threonine 3-dehydrogenase, NAD(P)-binding[1], B3616[2][1], Tdh[2][1] , ECK3606, JW3591, b3616

Product description

Tdh[2][3];

Component of threonine dehydrogenase[2][3]

Threonine dehydrogenase[4]

EC number (for enzymes)
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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:0008743

L-threonine 3-dehydrogenase activity

PMID:6780553

IDA: Inferred from Direct Assay

F

complete

GO:0005488

binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

F

Seeded from EcoCyc (v14.0)

complete

GO:0005829

cytosol

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0006564

L-serine biosynthetic process

PMID:3108237

IGI: Inferred from Genetic Interaction

EcoliWiki:serC


P

tdh serC double mutants are unable to synthesize serine by the alternate pathway (Tut cycle) and cannot grow on LRKTM:240 medium (minimal medium containing 240 mg/liter of leucine, arginine, lysine, threonine, and methionine)

complete

GO:0006567

threonine catabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00627

P

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

PMID:6780553

IDA: Inferred from Direct Assay

C

complete

GO:0006567

threonine catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004627

P

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002085

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

PMID:6780553

IDA: Inferred from Direct Assay

F

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002328

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

PMID:6780553

IDA: Inferred from Direct Assay

F

complete

GO:0046870

cadmium ion binding

PMID:3056527

IDA: Inferred from Direct Assay

F

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013149

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

PMID:2007567

IDA: Inferred from Direct Assay

F

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0008743

L-threonine 3-dehydrogenase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00627

F

Seeded from EcoCyc (v14.0)

complete

GO:0006564

L-serine biosynthetic process

PMID:3108237

IGI: Inferred from Genetic Interaction

EcoliWiki:serB


P

tdh serB double mutants are unable to synthesize serine by the alternate pathway (Tut cycle) and cannot grow on LRKTM:240 medium (minimal medium containing 240 mg/liter of leucine, arginine, lysine, threonine, and methionine)

complete

GO:0008743

L-threonine 3-dehydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004627

F

Seeded from EcoCyc (v14.0)

complete

GO:0006564

L-serine biosynthetic process

PMID:3108237

IGI: Inferred from Genetic Interaction

EcoliWiki:serA


P

tdh serA double mutants are unable to synthesize serine by the alternate pathway (Tut cycle) and cannot grow on LRKTM:240 medium (minimal medium containing 240 mg/liter of leucine, arginine, lysine, threonine, and methionine)

complete

GO:0008743

L-threonine 3-dehydrogenase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.1.103

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

GO:0050897

cobalt ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0170

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002328

P

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

PMID:3518793

IDA: Inferred from Direct Assay

F

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 threonine dehydrogenase

could be indirect

Protein

ebgR

PMID:16606699

Experiment(s):EBI-1146260

Protein

groL

PMID:16606699

Experiment(s):EBI-1146260

Protein

nadE

PMID:16606699

Experiment(s):EBI-1146260
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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 

MKALSKLKAE EGIWMTDVPV PELGHNDLLI KIRKTAICGT DVHIYNWDEW SQKTIPVPMV
VGHEYVGEVV GIGQEVKGFK IGDRVSGEGH ITCGHCRNCR GGRTHLCRNT IGVGVNRPGC
FAEYLVIPAF NAFKIPDNIS DDLAAIFDPF GNAVHTALSF DLVGEDVLVS GAGPIGIMAA
AVAKHVGARN VVITDVNEYR LELARKMGIT RAVNVAKENL NDVMAELGMT EGFDVGLEMS
GAPPAFRTML DTMNHGGRIA MLGIPPSDMS IDWTKVIFKG LFIKGIYGRE MFETWYKMAA
LIQSGLDLSP IITHRFSIDD FQKGFDAMRS GQSGKVILSW D
Length

341

Mol. Wt

37.239 kDa

pI

6.4 (calculated)

Extinction coefficient

41,940 - 42,690 (calc based on 6 Y, 6 W, and 6 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

174..304

PF00107 Zinc-binding dehydrogenase

PMID:19920124

Domain

25..135

PF08240 Alcohol dehydrogenase GroES-like domain

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=tdh 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:16131487

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948139

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011830

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P07913

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10993

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10993

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948139

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000982

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0986

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

4.94E+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

4448

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

263

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

2284

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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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

kbl-tdh

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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_000913:3789348..3789388 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:b3616 (EcoliWiki Page)

NCBI GEO profiles for tdh

microarray

GenExpDB:b3616 (EcoliWiki Page)

Summary of data for tdh 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 tdh Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10993

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0986

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3616

EcoGene

EcoGene:EG10993

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000982

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011830

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Ciona intestinalis

  • ENSCINP00000019198 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000021010 (score: 1.000; bootstrap: 65%)

From Inparanoid:20070104

Shigella flexneri

TDH

From SHIGELLACYC

E. coli O157

TDH

From ECOO157CYC

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Do-It-Yourself Web Tools

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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)

PF00107 Zinc-binding dehydrogenase

Superfamily (EcoliWiki Page)

SUPERFAMILY:50129

Superfamily (EcoliWiki Page)

SUPERFAMILY:51735

Pfam (EcoliWiki Page)

PF08240 Alcohol dehydrogenase GroES-like domain

EcoCyc

EcoCyc:EG10993

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10993

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000982

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0986

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011830

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 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. ↑ 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. ↑ 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. ↑ 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).

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