icd:Gene Product(s): Difference between revisions

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*  
*  
****************************************************************************************** -->{{Product_nomenclature_help}}
****************************************************************************************** -->{{Product_nomenclature_help}}
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{|   id="O46aa58e316c3e" class=" tableEdit Product_nomenclature_table"


|-
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
e14 prophage; isocitrate dehydrogenase, specific for NADP+<ref name='LIB:Riley_2006'/>, B1136<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Icd<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, IcdE<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, IcdA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''e14 prophage; isocitrate dehydrogenase, specific for NADP+<ref name='LIB:Riley_2006'/>, B1136<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Icd<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, IcdE<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, IcdA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1122, icdA, icdE, JW1122, b1136''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
Line 58: Line 58:
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.42 1.1.1.42]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.42 1.1.1.42]<ref name='LIB:Riley_2006'/>


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*  
*  
****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z46aa58e4767b5"  class=" tableEdit GO_table_product dataTable" 
|- {{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:0005737
|
cytoplasm
|
 
|
 
|
 
|
C
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
Missing: evidence, reference
|-  
|-  
|
|
Line 88: Line 107:
magnesium ion binding
magnesium ion binding
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR001804
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0000287
|
magnesium ion binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR019818
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0000287
|
magnesium ion binding
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 96: Line 153:
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 107: Line 164:
isocitrate dehydrogenase (NADP+) activity
isocitrate dehydrogenase (NADP+) activity
|
|
GO_REF:0000002<br />GO_REF:0000003
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR004439<br />EC:1.1.1.42
InterPro:IPR004439
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 122: Line 179:


|
|
GO:0006097
GO:0004450
|
|
glyoxylate cycle
isocitrate dehydrogenase (NADP+) activity
|
|
GO_REF:0000004
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0329
EC:1.1.1.42
|
|
P
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 145: Line 202:
tricarboxylic acid cycle
tricarboxylic acid cycle
|
|
GO_REF:0000002<br />GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR004439<br />SP_KW:KW-0816
InterPro:IPR004439
|
|
P
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 160: Line 217:


|
|
GO:0008152
GO:0006099
|
|
metabolic process
tricarboxylic acid cycle
|
|
GO_REF:0000002
PMID:4932752
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
|
InterPro:IPR001804
 
|
|
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
 
|
|
complete  
complete  
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oxidoreductase activity
oxidoreductase activity
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 191: Line 248:
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 202: Line 259:
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 210: Line 267:
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 217: Line 274:


|
|
GO:0030145
GO:0016616
|
|
manganese ion binding
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0464
InterPro:IPR019818
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 236: Line 293:


|
|
GO:0046872
GO:0022900
|
|
metal ion binding
electron transport chain
|
|
GO_REF:0000004
PMID:776950
PMID:15221231
|
|
IEA: Inferred from Electronic Annotation
IMP: Inferred from Mutant Phenotype
|
|
SP_KW:KW-0479
 
|
|
F
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
 
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0005737
GO:0030145
|
|
cytoplasm
manganese ion binding
|
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0464
|
|
C
F
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|


|
|
GO:0006099
GO:0046872
|
|
tricarboxylic acid cycle
metal ion binding
|
|
GO_REF:0000002<br />GO_REF:0000004<br />PMID:13152052
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IDA: Inferred from Direct Assay
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR004439<br />SP_KW:KW-0816<br />
SP_KW:KW-0479
|
|
P
F
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 293: Line 351:


|
|
GO:0055114
GO:0051287
|
|
oxidation reduction
NAD or NADH binding
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0560
InterPro:IPR001804
|
|
P
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 312: Line 370:


|
|
GO:0000287
GO:0051287
|
|
magnesium ion binding
NAD or NADH binding
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0460
InterPro:IPR019818
|
|
F
F
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 331: Line 389:


|
|
GO:0004450
GO:0055114
|
|
isocitrate dehydrogenase (NADP+) activity
oxidation reduction
|
|
GO_REF:0000002<br />GO_REF:0000003
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR004439<br />EC:1.1.1.42
InterPro:IPR001804
|
|
F
P
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 350: Line 408:


|
|
GO:0006097
GO:0055114
|
|
glyoxylate cycle
oxidation reduction
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0329
InterPro:IPR004439
|
|
P
P
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 369: Line 427:


|
|
GO:0008152
GO:0055114
|
|
metabolic process
oxidation reduction
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001804
InterPro:IPR019818
|
|
P
P
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 388: Line 446:


|
|
GO:0016491
GO:0055114
|
|
oxidoreductase activity
oxidation reduction
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 398: Line 456:
SP_KW:KW-0560
SP_KW:KW-0560
|
|
F
P
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 407: Line 465:


|
|
GO:0016616
GO:0004450
|
|
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
isocitrate dehydrogenase (NADP+) activity
|
|
GO_REF:0000002
PMID 3112144
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
|
InterPro:IPR001804
 
|
|
F
F
|
|
Seeded from EcoCyc
 
|
|
complete
Missing: reference
|-  
|-  
|
|


|
|
GO:0030145
GO:0005737
|
|
manganese ion binding
cytoplasm
|
|
GO_REF:0000004
PMID:34215
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
|
SP_KW:KW-0464
 
|
|
F
C
|
|
Seeded from EcoCyc
 
|
|
complete  
complete  
Line 445: Line 503:


|
|
GO:0046872
GO:0006097
|
|
metal ion binding
glyoxylate cycle
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0479
SP_KW:KW-0329
|
|
F
P
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 464: Line 522:


|
|
GO:0055114
GO:0006099
|
|
oxidation reduction
tricarboxylic acid cycle
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0560
SP_KW:KW-0816
|
|
P
P
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-
|
|
GO:0009061
|
anaerobic respiration
|
|
|
|
P
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
|
required fields missing 


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****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46aa58f31fc83"  class=" tableEdit Product_interactions_table dataTable"   
|- {{table heading style}}
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1138992<br />  
Experiment(s):EBI-1138992<br />  


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****************************************************************************************** -->{{Product_localization_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a7ebe18453c"  class=" tableEdit Product_localization_table"   
|- {{table heading style}}
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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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{|   id="Q46aa58f541d8d" class=" tableEdit Product_phys_prop_table"
 
|-
!align=left {{table heading style}} |Name
||


|-
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55,350 - 56,100 (calc based on 15 Y, 6 W, and 6 C residues)
55,350 - 56,100 (calc based on 15 Y, 6 W, and 6 C residues)


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*  
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****************************************************************************************** -->{{Product_domains_motifs_help}}
****************************************************************************************** -->{{Product_domains_motifs_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46aa58f59edb0"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-  
|-  
|
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Line 667: Line 710:
113
113
|
|
Phosphoserine
phosphorylation site at S113
|
[[PHOSIDA#p-values|probability greater than 75%]]
|
PMID:17938405
|-
|
Domain
|
28..412
|
[http://pfam.janelia.org/family/PF00180 PF00180  Isocitrate/isopropylmalate dehydrogenase]
|
|
[http://www.uniprot.org/uniprot/P08200#section_features UniProt:P08200]


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PMID:19920124
 
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View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P08200 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P08200 PSI-PRED (P08200)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P08200 Genomes TO Protein (P08200)] (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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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=MONOMER0-2778 EcoCyc:MONOMER0-2778]
[http://www.ncbi.nlm.nih.gov/protein/16129099 GI:16129099]
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Escherichia coli str. K-12 substr. MG1655
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/NP_415654.1 GeneID:945702]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0003823
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''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/P08200 UniProtKB/Swiss-Prot:P08200]
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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:P08200|UniProt:P08200]]
EcoCyc:EG10489
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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]])
[[EcoGene]]
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[http://pfam.sanger.ac.uk/family?acc=PF00180 PFAM:PF00180]
EcoGene:EG10489
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_415654 RefSeq:NP_415654]
[http://www.ncbi.nlm.nih.gov/gene?term=945702 GeneID:945702]
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Escherichia coli str. K-12 substr. MG1655
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[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[RegulonDB]]
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[http://salilab.org/modbase/searchbyid?databaseID=P08200 ModBase:P08200]
RegulonDB:ECK120000482
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.rcsb.org/pdb PDB] ([[PDB|EcoliWiki Page]])
[[EchoBASE]]
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[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1IKA PDB:1IKA]
EchoBASE:EB0484
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006099_!_tricarboxylic acid cycle]][[Category:GO:0009061_!_anaerobic respiration]][[Category:Complex:isocitrate dehydrogenase]][[Category:Products with structures in PDB]]

Latest revision as of 20:35, 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

Icd

Synonyms

e14 prophage; isocitrate dehydrogenase, specific for NADP+[1], B1136[2][1], Icd[2][1], IcdE[2][1], IcdA[2][1] , ECK1122, icdA, icdE, JW1122, b1136

Product description

Icd[2][3];

Component of isocitrate dehydrogenase[2][3]

Isocitrate dehydrogenase, NADP+-specific; e14 attachment site[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:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001804

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019818

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0004450

isocitrate dehydrogenase (NADP+) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004439

F

Seeded from EcoCyc (v14.0)

complete

GO:0004450

isocitrate dehydrogenase (NADP+) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.1.42

F

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004439

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

PMID:4932752[5]

IDA: Inferred from Direct Assay

P

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0016616

oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001804

F

Seeded from EcoCyc (v14.0)

complete

GO:0016616

oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019818

F

Seeded from EcoCyc (v14.0)

complete

GO:0022900

electron transport chain

PMID:776950[6] PMID:15221231[7]

IMP: Inferred from Mutant Phenotype

P

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:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0051287

NAD or NADH binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001804

F

Seeded from EcoCyc (v14.0)

complete

GO:0051287

NAD or NADH binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019818

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001804

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004439

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019818

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc (v14.0)

complete

GO:0004450

isocitrate dehydrogenase (NADP+) activity

PMID 3112144

IDA: Inferred from Direct Assay

F

Missing: reference

GO:0005737

cytoplasm

PMID:34215[8]

IDA: Inferred from Direct Assay

C

complete

GO:0006097

glyoxylate cycle

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0329

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0816

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

Subunits of isocitrate dehydrogenase

could be indirect

Protein

yneG

PMID:16606699[9]

Experiment(s):EBI-1138992

Protein

yibL

PMID:16606699[9]

Experiment(s):EBI-1138992

Protein

yfdS

PMID:16606699[9]

Experiment(s):EBI-1138992

Protein

nadE

PMID:16606699[9]

Experiment(s):EBI-1138992
edit table


Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table


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 

MESKVVVPAQ GKKITLQNGK LNVPENPIIP YIEGDGIGVD VTPAMLKVVD AAVEKAYKGE
RKISWMEIYT GEKSTQVYGQ DVWLPAETLD LIREYRVAIK GPLTTPVGGG IRSLNVALRQ
ELDLYICLRP VRYYQGTPSP VKHPELTDMV IFRENSEDIY AGIEWKADSA DAEKVIKFLR
EEMGVKKIRF PEHCGIGIKP CSEEGTKRLV RAAIEYAIAN DRDSVTLVHK GNIMKFTEGA
FKDWGYQLAR EEFGGELIDG GPWLKVKNPN TGKEIVIKDV IADAFLQQIL LRPAEYDVIA
CMNLNGDYIS DALAAQVGGI GIAPGANIGD ECALFEATHG TAPKYAGQDK VNPGSIILSA
EMMLRHMGWT EAADLIVKGM EGAINAKTVT YDFERLMDGA KLLKCSEFGD AIIENM
Length

416

Mol. Wt

45.757 kDa

pI

5.0 (calculated)

Extinction coefficient

55,350 - 56,100 (calc based on 15 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

Modification Site

113

phosphorylation site at S113

probability greater than 75%

PMID:17938405[10]

Domain

28..412

PF00180 Isocitrate/isopropylmalate dehydrogenase

PMID:19920124[11]

edit table

<motif_map/>

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

Structures

<beststructure> gene=icd 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:16129099

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945702

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003823

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P08200

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10489

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10489

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945702

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000482

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0484

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]




References

[back to top]


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 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 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. ↑ Holms, WH & Bennett, PM (1971) Regulation of isocitrate dehydrogenase activity in Escherichia coli on adaptation to acetate. J. Gen. Microbiol. 65 57-68 PubMed
  6. ↑ Lakshmi, TM & Helling, RB (1976) Selection for citrate synthase deficiency in icd mutants of Escherichia coli. J. Bacteriol. 127 76-83 PubMed
  7. ↑ Kabir, MM & Shimizu, K (2004) Metabolic regulation analysis of icd-gene knockout Escherichia coli based on 2D electrophoresis with MALDI-TOF mass spectrometry and enzyme activity measurements. Appl. Microbiol. Biotechnol. 65 84-96 PubMed
  8. ↑ Garnak, M & Reeves, HC (1979) Phosphorylation of Isocitrate dehydrogenase of Escherichia coli. Science 203 1111-2 PubMed
  9. ↑ 9.0 9.1 9.2 9.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  10. ↑ Macek, B et al. (2008) Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol. Cell Proteomics 7 299-307 PubMed
  11. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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