tdcB:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
catabolic threonine dehydratase, PLP-dependent<ref name='LIB:Riley_2006'/>, B3117<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Tdc<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, TdcB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''catabolic threonine dehydratase, PLP-dependent<ref name='LIB:Riley_2006'/>, B3117<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Tdc<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, TdcB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK3106, JW3088, b3117''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.19 4.3.1.19]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.19 4.3.1.19]<ref name='LIB:Riley_2006'/>


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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-  
|-  
|
|


|
|
GO:0030170
GO:0005737
|
|
pyridoxal phosphate binding
cytoplasm
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|
GO_REF:0000002<br />GO_REF:0000002
 
|
|
IEA: Inferred from Electronic Annotation
 
|
InterPro:IPR000634<br />InterPro:IPR001926
|
F
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|
complete
|-
|
|


|
|
GO:0004794
C
|
L-threonine ammonia-lyase activity
|
GO_REF:0000003
|
IEA: Inferred from Electronic Annotation
|
EC:4.3.1.19
|
F
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|
complete
|-
|
|
GO:0005737
|
cytoplasm
|
|
|
|
C  
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
|
|
required fields missing 
Missing: evidence, reference
|-  
|-  
|
|


|
|
GO:0003824
GO:0005737
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|
catalytic activity
cytoplasm
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|
GO_REF:0000002<br />GO_REF:0000004
PMID:3540965
|
|
IEA: Inferred from Electronic Annotation
IC: Inferred by Curator
|
|
InterPro:IPR001926<br />SP_KW:KW-0021
 
|
|
F
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
 
|
|
complete
Missing: with/from
|-  
|-  
|
|


|
|
GO:0003941
GO:0004793
|
|
L-serine ammonia-lyase activity
threonine aldolase activity
|
|
PMID:4889010
PMID:3540965
|
|
IDA: Inferred from Direct Assay
IDA: Inferred from Direct Assay
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F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
 
|
|
complete  
complete  
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|
|
GO:0006520
GO:0006567
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|
amino acid metabolic process
threonine catabolic process
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|
GO_REF:0000002
PMID:6751404
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
|
InterPro:IPR000634
 
|
|
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
 
|
|
complete  
complete  
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|
|
GO:0006565
GO:0016597
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|
L-serine catabolic process
amino acid binding
|
|
PMID:4889010
PMID:3540965
|
|
IDA: Inferred from Direct Assay
IDA: Inferred from Direct Assay
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|
|
P
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
 
|
|
complete  
complete  
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|
|
GO:0008152
GO:0030170
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|
metabolic process
pyridoxal phosphate binding
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|
GO_REF:0000002
PMID:6751404
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|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
InterPro:IPR001926
|
P
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
|-
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GO:0009063
|
amino acid catabolic process
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|
|
|
P
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
|
required fields missing 
|-
|
|


|
GO:0016829
|
lyase activity
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0456
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
 
|
|
complete  
complete  


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1144834<br />  
Experiment(s):EBI-1144834<br />  


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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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!align=left {{table heading style}} |Name
||


|-
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SRPGNLTYEI VRELVDDIVL VSEDEIRNSM IALIQRNKVV TEGAGALACA ALLSGKLDQY
SRPGNLTYEI VRELVDDIVL VSEDEIRNSM IALIQRNKVV TEGAGALACA ALLSGKLDQY
IQNRKTVSII SGGNIDLSRV SQITGFVDA</pre>  
IQNRKTVSII SGGNIDLSRV SQITGFVDA</pre>  
|-
!align=left {{table heading style}} |Length
||
329
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
35.23 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
35.232 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.0 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
11920 - 12670 (calc based on 8 Y, 0 W, and 6 C residues)  
11,920 - 12,670 (calc based on 8 Y, 0 W, and 6 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
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|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
22..312
|
[http://pfam.janelia.org/family/PF00291 PF00291  Pyridoxal-phosphate dependent enzyme]
|
 
|
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</table>


<span id="Structure"></span><big>'''Structure'''</big>
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
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|-
|-
!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>tdcB
<beststructure>
562</beststructure>
gene=tdcB
 
taxon=562,83333
</beststructure>
|-
|-
!align=left {{table heading style}} |Models
!align=left {{table heading style}} |Models
||
||
View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=tdcB&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P77528 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=tdcB&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AGF6 PSI-PRED (P0AGF6)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AGF6 Genomes TO Protein (P0AGF6)] (GTOP)
* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)


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<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


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|- {{table_heading_style}}
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16131010 GI:16131010]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/NP_417587.1 GeneID:947633]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=THREDEHYDCAT-MONOMER EcoCyc:THREDEHYDCAT-MONOMER]
Escherichia coli str. K-12 substr. MG1655
|-  
|
|
[[ASAP]]
|
ASAP:ABE-0010249
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P0AGF6 UniProtKB/Swiss-Prot:P0AGF6]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG10990
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:P0AGF6|UniProt:P0AGF6]]
EcoGene:EG10990
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00291 PFAM:PF00291]
[http://www.ncbi.nlm.nih.gov/gene?term=947633 GeneID:947633]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417587 RefSeq:NP_417587]
RegulonDB:ECK120000979
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
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[http://salilab.org/modbase/searchbyid?databaseID=P0AGF6 ModBase:P0AGF6]
EchoBASE:EB0983
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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===Categories===
===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0009063_!_amino acid catabolic process]][[Category:Complex:threonine dehydratase (catabolic)]]
[[Category:RefGenome_Annotated_Gene]]

Latest revision as of 20:59, 17 February 2015

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

TdcB

Synonyms

catabolic threonine dehydratase, PLP-dependent[1], B3117[2][1], Tdc[2][1], TdcB[2][1] , ECK3106, JW3088, b3117

Product description

TdcB[2][3];

Component of threonine dehydratase (catabolic)[2][3]

Threonine dehydratase[4]

EC number (for enzymes)
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Notes

Function

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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

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0005737

cytoplasm

PMID:3540965[5]

IC: Inferred by Curator

C

Missing: with/from

GO:0004793

threonine aldolase activity

PMID:3540965[5]

IDA: Inferred from Direct Assay

F

complete

GO:0006567

threonine catabolic process

PMID:6751404[6]

IDA: Inferred from Direct Assay

P

complete

GO:0016597

amino acid binding

PMID:3540965[5]

IDA: Inferred from Direct Assay

F

complete

GO:0030170

pyridoxal phosphate binding

PMID:6751404[6]

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 dehydratase (catabolic)

could be indirect

Protein

yijP

PMID:16606699[7]

Experiment(s):EBI-1144834

Protein

yqjG

PMID:16606699[7]

Experiment(s):EBI-1144834
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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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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 

MHITYDLPVA IDDIIEAKQR LAGRIYKTGM PRSNYFSERC KGEIFLKFEN MQRTGSFKIR
GAFNKLSSLT DAEKRKGVVA CSAGNHAQGV SLSCAMLGID GKVVMPKGAP KSKVAATCDY
SAEVVLHGDN FNDTIAKVSE IVEMEGRIFI PPYDDPKVIA GQGTIGLEIM EDLYDVDNVI
VPIGGGGLIA GIAVAIKSIN PTIRVIGVQS ENVHGMAASF HSGEITTHRT TGTLADGCDV
SRPGNLTYEI VRELVDDIVL VSEDEIRNSM IALIQRNKVV TEGAGALACA ALLSGKLDQY
IQNRKTVSII SGGNIDLSRV SQITGFVDA
Length

329

Mol. Wt

35.232 kDa

pI

6.0 (calculated)

Extinction coefficient

11,920 - 12,670 (calc based on 8 Y, 0 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

22..312

PF00291 Pyridoxal-phosphate dependent enzyme

PMID:19920124[8]

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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=tdcB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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:16131010

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947633

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010249

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AGF6

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10990

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10990

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947633

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000979

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0983

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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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 Datta, P et al. (1987) Covalent structure of biodegradative threonine dehydratase of Escherichia coli: homology with other dehydratases. Proc. Natl. Acad. Sci. U.S.A. 84 393-7 PubMed
  6. ↑ 6.0 6.1 Kim, SS & Datta, P (1982) Chemical characterization of biodegradative threonine dehydratases from two enteric bacteria. Biochim. Biophys. Acta 706 27-35 PubMed
  7. ↑ 7.0 7.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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