dsdC:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
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DNA-binding transcriptional dual regulator<ref name='LIB:Riley_2006'/>, B2364<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DsdC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, D-serine dehydratase (deaminase) transcriptional activator<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''DNA-binding transcriptional dual regulator<ref name='LIB:Riley_2006'/>, B2364<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DsdC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, D-serine dehydratase (deaminase) transcriptional activator<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2360, JW2361, b2364''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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!|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
|-  
|-  
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GO:0006350
GO:0003677
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|
transcription
DNA binding
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GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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SP_KW:KW-0804
SP_KW:KW-0238
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P
F
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|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
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transcription factor activity
transcription factor activity
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GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
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GO:0003677
GO:0006350
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DNA binding
transcription
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GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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SP_KW:KW-0238
SP_KW:KW-0804
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F
P
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|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
|-
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GO:0009063
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amino acid catabolic process
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P
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
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required fields missing 
|-
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GO:0005737
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cytoplasm
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C
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Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
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required fields missing 
|-
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GO:0016563
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transcription activator activity
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F
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
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required fields missing 
|-  
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regulation of transcription, DNA-dependent
regulation of transcription, DNA-dependent
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GO_REF:0000002<br />GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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InterPro:IPR000847<br />SP_KW:KW-0805
InterPro:IPR000847
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P
P
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|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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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-1142650<br />  
Experiment(s):EBI-1142650<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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AVIAAMNHIG VAMGRKRLVQ KRLASGELVA PFGDMTVKCH QHYYITTLPG RQWPKIEAFI
AVIAAMNHIG VAMGRKRLVQ KRLASGELVA PFGDMTVKCH QHYYITTLPG RQWPKIEAFI
IWLREQVKTT S</pre>  
IWLREQVKTT S</pre>  
|-
!align=left {{table heading style}} |Length
||
311
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
35.33 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
35.332 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.88<ref name='LIB:EcoCyc10.6'/>
7.1 (calculated)
|-
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!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
55920 - 56545 (calc based on 8 Y, 8 W, and 5 C residues)  
55,920 - 56,545 (calc based on 8 Y, 8 W, and 5 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
|-  
|-  
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Domain
Domain
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|
15 - 72
98..308
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[[interpro:IPR000847|HTH lysR-type]]
[http://pfam.janelia.org/family/PF03466 PF03466  LysR substrate binding domain]
|
|
[http://www.uniprot.org/uniprot/P46068#section_features UniProt:P46068]


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PMID:19920124
|-
|
Domain
|
17..76
|
[http://pfam.janelia.org/family/PF00126 PF00126  Bacterial regulatory helix-turn-helix protein, lysR family]
|
 
|
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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|-
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!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>dsdC
<beststructure>
562</beststructure>
gene=dsdC
 
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=dsdC&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P46068 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=dsdC&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P46068 PSI-PRED (P46068)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P46068 Genomes TO Protein (P46068)] (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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!|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/16130296 GI:16130296]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/NP_416865.1 GeneID:948828]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[ASAP]]
|
ASAP:ABE-0007797
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=PD00297 EcoCyc:PD00297]
[http://www.uniprot.org/uniprot/P46068 UniProtKB/Swiss-Prot:P46068]
|
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Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoCyc]]
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[[uniprot:P46068|UniProt:P46068]]
EcoCyc:EG13161
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00126 PFAM:PF00126]
EcoGene:EG13161
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_416865 RefSeq:NP_416865]
[http://www.ncbi.nlm.nih.gov/gene?term=948828 GeneID:948828]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P46068 ModBase:P46068]
RegulonDB:ECK120002429
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z0885-MONOMER ECOO157CYC:Z0885-MONOMER]
EchoBASE:EB2953
|
|
''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:0009063_!_amino acid catabolic process]][[Category:GO:0006350_!_transcription]][[Category:GO:0005737_!_cytoplasm]][[Category:GO:0016563_!_transcription activator activity]]

Latest revision as of 20:50, 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

DsdC

Synonyms

DNA-binding transcriptional dual regulator[1], B2364[2][1], DsdC[2][1], D-serine dehydratase (deaminase) transcriptional activator[2][1] , ECK2360, JW2361, b2364

Product description

DsdC transcriptional dual regulator[2][3]

Activator of dsdA transcription[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:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000847

F

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000847

P

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

yghA

PMID:16606699[5]

Experiment(s):EBI-1142650

Protein

rmlA2

PMID:16606699[5]

Experiment(s):EBI-1142650

Protein

yfeT

PMID:16606699[5]

Experiment(s):EBI-1142650

Protein

groL

PMID:16606699[5]

Experiment(s):EBI-1142650

Protein

rplO

PMID:16606699[5]

Experiment(s):EBI-1142650
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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 

MEPLREIRNR LLNGWQLSKM HTFEVAARHQ SFALAAEELS LSPSAVSHRI NQLEEELGIQ
LFVRSHRKVE LTHEGKRVYW ALKSSLDTLN QEILDIKNQE LSGTLTLYSR PSIAQCWLVP
ALGDFTRRYP SISLTVLTGN DNVNLQRAGI DLAIYFDDAP SAQLTHHFLM DEEILPVCSP
EYAQRHALTN TVINLCHCTL LHDRQAWSND SGTDEWHSWA QHYAVNLPTS SGIGFDRSDL
AVIAAMNHIG VAMGRKRLVQ KRLASGELVA PFGDMTVKCH QHYYITTLPG RQWPKIEAFI
IWLREQVKTT S
Length

311

Mol. Wt

35.332 kDa

pI

7.1 (calculated)

Extinction coefficient

55,920 - 56,545 (calc based on 8 Y, 8 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

Domain

98..308

PF03466 LysR substrate binding domain

PMID:19920124[6]

Domain

17..76

PF00126 Bacterial regulatory helix-turn-helix protein, lysR family

PMID:19920124[6]

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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=dsdC 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:16130296

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948828

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007797

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P46068

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG13161

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13161

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948828

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002429

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2953

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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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 5.3 5.4 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ 6.0 6.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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