icd:Gene Product(s): Difference between revisions

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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(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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GO:0000287
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magnesium ion binding
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GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-0460
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F
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
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GO:0004450
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isocitrate dehydrogenase (NADP+) activity
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PMID:776950
PMID:15221231
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IMP: Inferred from Mutant Phenotype
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F
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
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GO:0006097
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glyoxylate cycle
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GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-0329
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P
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
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GO:0006099
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tricarboxylic acid cycle
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GO_REF:0000002<br />GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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InterPro:IPR004439<br />SP_KW:KW-0816
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P
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Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
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complete
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GO:0008152
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metabolic process
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GO_REF:0000002
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IEA: Inferred from Electronic Annotation
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InterPro:IPR001804
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P
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
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GO:0016491
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oxidoreductase activity
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GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-0560
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F
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
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GO:0016616
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oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
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GO_REF:0000002
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IEA: Inferred from Electronic Annotation
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InterPro:IPR001804
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F
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
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GO:0030145
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manganese ion binding
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GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-0464
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F
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
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GO:0046872
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metal ion binding
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GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-0479
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F
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
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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 
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GO:0055114
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oxidation reduction
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GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-0560
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P
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
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GO:0009061
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anaerobic respiration
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P
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Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
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required fields missing   
required fields missing   
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Revision as of 21:22, 10 June 2010

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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

Icd

Synonyms

e14 prophage; isocitrate dehydrogenase, specific for NADP+[1], B1136[2][1], Icd[2][1], IcdE[2][1], IcdA[2][1]

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(s) Evidence Code with/from Aspect Notes Status
GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

required fields missing

GO:0022900

electron transport chain

PMID:776950[5] PMID:15221231[6]

IMP: Inferred from Mutant Phenotype

P

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[7]

Experiment(s):EBI-1138992

Protein

yibL

PMID:16606699[7]

Experiment(s):EBI-1138992

Protein

yfdS

PMID:16606699[7]

Experiment(s):EBI-1138992

Protein

nadE

PMID:16606699[7]

Experiment(s):EBI-1138992
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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 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.

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[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=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

EcoCyc (EcoliWiki Page)

EcoCyc:MONOMER0-2778

UniProt (EcoliWiki Page)

UniProt:P08200

PFAM (EcoliWiki Page)

PFAM:PF00180

RefSeq (EcoliWiki Page)

RefSeq:NP_415654


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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 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. ↑ Lakshmi, TM & Helling, RB (1976) Selection for citrate synthase deficiency in icd mutants of Escherichia coli. J. Bacteriol. 127 76-83 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 7.2 7.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ 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

Categories

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