icd:Gene Product(s)

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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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<protect> 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
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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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<protect> 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]

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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

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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

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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. ↑ 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

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