mdaB:Gene Product(s): Difference between revisions

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!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
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MdaB product
MdaB  
|-
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!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
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NADPH quinone reductase product<ref name='LIB:Riley_2006'/>, B3028 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, MdaB product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''NADPH quinone reductase<ref name='LIB:Riley_2006'/>, B3028<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, MdaB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK3019, JW2996, mda66, b3028''
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!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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EG12656-MONOMER<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>;  
EG12656<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>;  


Component of ; [[:Category:Complex:NADPH quinone reductase|NADPH quinone reductase]]<ref name='LIB:EcoCyc11.1'/>
Component of [[:Category:Complex:quinone reductase|quinone reductase]]<ref name='LIB:EcoCyc11.1'/>


FMN-dependent NADH-quinone reductase; MdaB and YgiN form an enzymatic quinone reduction-oxidation cycle in vitro; possibly mitigates toxicity of quinols and quinones in vivo; dimeric<ref name='LIB:EcoGene'/>
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!{{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
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** [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.99.6 1.6.99.6]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.99.6 1.6.99.6]<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.26450.B46aacd250e547-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.26450.B46aacd250e547-->
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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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[[Category:GO:0016491_!_oxidoreductase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016491_!_oxidoreductase_activity GO:0016491]
GO:0005737
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oxidoreductase activity
cytoplasm
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GO_REF:0000002
 
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IEA: Inferred from Electronic Annotation
 
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InterPro:IPR003680
 
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F
C
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Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
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complete
|-
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[[Category:GO:0005737_!_cytoplasm]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0005737_!_cytoplasm GO:0005737]
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cytoplasm
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C  
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Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
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required fields missing 
Missing: evidence, reference
|-  
|-  
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[[Category:GO:0042493_!_response_to_drug]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0042493_!_response_to_drug GO:0042493]
GO:0009055
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response to drug
electron carrier activity
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GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
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InterPro:IPR003680
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P
F
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Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
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required fields missing 
complete
|-  
|-  
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[[Category:GO:0009053_!_electron_donor_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0009053_!_electron_donor_activity GO:0009053]
GO:0016491
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electron donor activity  
oxidoreductase activity
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GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
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InterPro:IPR003680
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F  
F
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Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
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required fields missing 
complete
|-  
|-  
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[[Category:GO:0050662_!_coenzyme_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0050662_!_coenzyme_binding GO:0050662]
GO:0050662
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coenzyme binding
coenzyme binding
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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 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  


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Protein
Protein
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Subunits of [[:Category:Complex:NADPH quinone reductase|NADPH quinone reductase]]  
Subunits of [[:Category:Complex:NADPH quinone reductase|NADPH quinone reductase]]  
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could be indirect   
could be indirect  
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Protein
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groL<br />
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PMID:16606699
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Experiment(s):EBI-1144586<br />
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Protein
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nrfA<br />
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PMID:16606699
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Experiment(s):EBI-1144586<br />
 
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===Notes===
===Notes===
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!Compartment!!Description!!Evidence!!Notes
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!align=left {{table heading style}} |Name
||
 
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!{{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
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[http://biocyc.org/ECOLI/sequence-aa?object=EG12656-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=EG12656-MONOMER at EcoCyc]  
<pre>MSNILIINGA KKFAHSNGQL NDTLTEVADG TLRDLGHDVR IVRADSDYDV KAEVQNFLWA
<pre>MSNILIINGA KKFAHSNGQL NDTLTEVADG TLRDLGHDVR IVRADSDYDV KAEVQNFLWA
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TEEYRKHLVE IFG</pre>  
TEEYRKHLVE IFG</pre>  
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!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
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21.89 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
193
|-
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!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
||
21.89 kDa
|-
|-
!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
44920 (calc based on 8 Y, 6 W, and 0 C residues)  
6.2 (calculated)
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!align=left {{table heading style}} |Extinction coefficient
||
44,920 (calc based on 8 Y, 6 W, and 0 C residues)
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.26450.U46aacd3835ff1-->
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!Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
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Domain
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2..190
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[http://pfam.janelia.org/family/PF02525 PF02525  Flavodoxin-like fold]
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PMID:19920124
 
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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
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<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>mdaB
<beststructure>
562</beststructure>
gene=mdaB
 
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=mdaB&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P0AEY5 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=mdaB&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AEY5 PSI-PRED (P0AEY5)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AEY5 Genomes TO Protein (P0AEY5)] (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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===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16130924 GI:16130924]
|
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_417500.1 GeneID:947512]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0009946
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
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[http://www.uniprot.org/uniprot/P0AEY5 UniProtKB/Swiss-Prot:P0AEY5]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12656-MONOMER EcoCyc:EG12656-MONOMER] 
EcoCyc:EG12656
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
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[[uniprot:P0AEY5|UniProt:P0AEY5]] 
EcoGene:EG12656
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[http://pfam.sanger.ac.uk/family?acc=PF02525 PFAM:PF02525]
[http://www.ncbi.nlm.nih.gov/gene?term=947512 GeneID:947512]
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Escherichia coli str. K-12 substr. MG1655
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417500 RefSeq:NP_417500] 
RegulonDB:ECK120002346
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''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=P0AEY5 ModBase:P0AEY5] 
EchoBASE:EB2524
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0042493_!_response to drug]][[Category:GO:0009053_!_electron donor activity]][[Category:Complex:NADPH quinone reductase]]

Latest revision as of 20:58, 17 February 2015

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

MdaB

Synonyms

NADPH quinone reductase[1], B3028[2][1], MdaB[2][1] , ECK3019, JW2996, mda66, b3028

Product description

EG12656[2][3];

Component of quinone reductase[3]

FMN-dependent NADH-quinone reductase; MdaB and YgiN form an enzymatic quinone reduction-oxidation cycle in vitro; possibly mitigates toxicity of quinols and quinones in vivo; dimeric[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:0009055

electron carrier activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003680

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003680

F

Seeded from EcoCyc (v14.0)

complete

GO:0050662

coenzyme binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003680

F

Seeded from EcoCyc (v14.0)

complete

edit table

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 NADPH quinone reductase

could be indirect

Protein

groL

PMID:16606699[5]

Experiment(s):EBI-1144586

Protein

nrfA

PMID:16606699[5]

Experiment(s):EBI-1144586
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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 

MSNILIINGA KKFAHSNGQL NDTLTEVADG TLRDLGHDVR IVRADSDYDV KAEVQNFLWA
DVVIWQMPGW WMGAPWTVKK YIDDVFTEGH GTLYASDGRT RKDPSKKYGS GGLVQGKKYM
LSLTWNAPME AFTEKDQFFH GVGVDGVYLP FHKANQFLGM EPLPTFIAND VIKMPDVPRY
TEEYRKHLVE IFG
Length

193

Mol. Wt

21.89 kDa

pI

6.2 (calculated)

Extinction coefficient

44,920 (calc based on 8 Y, 6 W, and 0 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

2..190

PF02525 Flavodoxin-like fold

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=mdaB 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:16130924

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947512

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009946

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AEY5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12656

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12656

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947512

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002346

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2524

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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 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 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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