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Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.

Cofactori

Mg2+, Mn2+Note: Binds 1 Mg(2+) or Mn2+ ion per subunit.

Enzyme regulationi

Weakly inhibited by oxaloacetate, 2-oxoglutarate, and citrate. Severely inhibited by oxaloacetate plus glyoxylate.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei133 – 1331NADPBy similarity
Binding sitei143 – 1431SubstrateBy similarity
Sitei253 – 2531Critical for catalysisBy similarity
Metal bindingi346 – 3461Magnesium or manganese1 Publication
Sitei416 – 4161Critical for catalysisBy similarity
Binding sitei543 – 5431SubstrateBy similarity
Metal bindingi544 – 5441Magnesium or manganese1 Publication
Metal bindingi548 – 5481Magnesium or manganese1 Publication
Binding sitei585 – 5851NADPBy similarity
Binding sitei645 – 6451NADPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi80 – 856NADPBy similarity
Nucleotide bindingi580 – 5812NADPBy similarity
Nucleotide bindingi596 – 5983NADPBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glyoxylate bypass, Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Metal-binding, NADP

Enzyme and pathway databases

BRENDAi1.1.1.42. 960.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NADP] (EC:1.1.1.42)
Short name:
IDH
Alternative name(s):
Oxalosuccinate decarboxylase
Gene namesi
Name:icd
Ordered Locus Names:Cgl0664, cg0766
OrganismiCorynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Taxonomic identifieri196627 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeCorynebacteriaceaeCorynebacterium
ProteomesiUP000001009 Componenti: Chromosome UP000000582 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 738738Isocitrate dehydrogenase [NADP]PRO_0000083595Add
BLAST

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi196627.cg0766.

Structurei

Secondary structure

1
738
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi11 – 2919Combined sources
Turni30 – 323Combined sources
Beta strandi34 – 396Combined sources
Helixi42 – 476Combined sources
Helixi51 – 533Combined sources
Turni56 – 583Combined sources
Helixi63 – 708Combined sources
Beta strandi77 – 804Combined sources
Helixi88 – 10013Combined sources
Helixi115 – 12511Combined sources
Beta strandi128 – 1303Combined sources
Helixi132 – 1365Combined sources
Beta strandi141 – 1444Combined sources
Helixi147 – 1559Combined sources
Beta strandi170 – 1723Combined sources
Beta strandi175 – 1784Combined sources
Helixi179 – 1824Combined sources
Beta strandi184 – 1874Combined sources
Beta strandi192 – 1998Combined sources
Beta strandi205 – 21410Combined sources
Beta strandi219 – 2257Combined sources
Helixi227 – 24418Combined sources
Beta strandi247 – 2504Combined sources
Turni254 – 2563Combined sources
Helixi260 – 27213Combined sources
Helixi274 – 28613Combined sources
Helixi294 – 3029Combined sources
Helixi308 – 32114Combined sources
Beta strandi327 – 3293Combined sources
Helixi330 – 3323Combined sources
Beta strandi342 – 3443Combined sources
Helixi345 – 35410Combined sources
Turni355 – 3573Combined sources
Beta strandi358 – 3603Combined sources
Beta strandi366 – 3727Combined sources
Helixi376 – 39217Combined sources
Turni397 – 3993Combined sources
Beta strandi405 – 4073Combined sources
Turni410 – 4123Combined sources
Helixi414 – 4174Combined sources
Helixi419 – 4213Combined sources
Beta strandi422 – 4243Combined sources
Beta strandi427 – 4348Combined sources
Beta strandi440 – 4467Combined sources
Beta strandi451 – 4577Combined sources
Helixi459 – 47618Combined sources
Beta strandi480 – 4834Combined sources
Helixi489 – 50214Combined sources
Beta strandi512 – 5154Combined sources
Helixi517 – 52913Combined sources
Beta strandi535 – 5384Combined sources
Helixi540 – 55516Combined sources
Beta strandi558 – 5603Combined sources
Beta strandi562 – 5676Combined sources
Beta strandi572 – 5754Combined sources
Helixi583 – 59210Combined sources
Helixi600 – 61718Combined sources
Helixi620 – 63819Combined sources
Helixi652 – 66918Combined sources
Helixi674 – 70027Combined sources
Beta strandi711 – 7133Combined sources
Helixi716 – 7238Combined sources
Helixi727 – 7359Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2B0TX-ray1.75A1-738[»]
3MBCX-ray1.90A/B1-738[»]
ProteinModelPortaliP50216.
SMRiP50216. Positions 2-736.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50216.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni130 – 1378Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the monomeric-type IDH family.Curated

Phylogenomic databases

eggNOGiCOG2838.
HOGENOMiHOG000240860.
KOiK00031.
OMAiDENRAHD.
OrthoDBiEOG6DVJPP.

Family and domain databases

Gene3Di3.40.718.10. 3 hits.
InterProiIPR004436. Isocitrate_DH_NADP_mono.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PfamiPF03971. IDH. 1 hit.
[Graphical view]
PIRSFiPIRSF009407. IDH_monmr. 1 hit.
TIGRFAMsiTIGR00178. monomer_idh. 1 hit.

Sequencei

Sequence statusi: Complete.

P50216-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKIIWTRTD EAPLLATYSL KPVVEAFAAT AGIEVETRDI SLAGRILAQF
60 70 80 90 100
PERLTEDQKV GNALAELGEL AKTPEANIIK LPNISASVPQ LKAAIKELQD
110 120 130 140 150
QGYDIPELPD NATTDEEKDI LARYNAVKGS AVNPVLREGN SDRRAPIAVK
160 170 180 190 200
NFVKKFPHRM GEWSADSKTN VATMDANDFR HNEKSIILDA ADEVQIKHIA
210 220 230 240 250
ADGTETILKD SLKLLEGEVL DGTVLSAKAL DAFLLEQVAR AKAEGILFSA
260 270 280 290 300
HLKATMMKVS DPIIFGHVVR AYFADVFAQY GEQLLAAGLN GENGLAAILS
310 320 330 340 350
GLESLDNGEE IKAAFEKGLE DGPDLAMVNS ARGITNLHVP SDVIVDASMP
360 370 380 390 400
AMIRTSGHMW NKDDQEQDTL AIIPDSSYAG VYQTVIEDCR KNGAFDPTTM
410 420 430 440 450
GTVPNVGLMA QKAEEYGSHD KTFRIEADGV VQVVSSNGDV LIEHDVEAND
460 470 480 490 500
IWRACQVKDA PIQDWVKLAV TRSRLSGMPA VFWLDPERAH DRNLASLVEK
510 520 530 540 550
YLADHDTEGL DIQILSPVEA TQLSIDRIRR GEDTISVTGN VLRDYNTDLF
560 570 580 590 600
PILELGTSAK MLSVVPLMAG GGLFETGAGG SAPKHVQQVQ EENHLRWDSL
610 620 630 640 650
GEFLALAESF RHELNNNGNT KAGVLADALD KATEKLLNEE KSPSRKVGEI
660 670 680 690 700
DNRGSHFWLT KFWADELAAQ TEDADLAATF APVAEALNTG AADIDAALLA
710 720 730
VQGGATDLGG YYSPNEEKLT NIMRPVAQFN EIVDALKK
Length:738
Mass (Da):80,081
Last modified:October 1, 1996 - v1
Checksum:iEAC4C5FA38C33F63
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X71489 Genomic DNA. Translation: CAA50590.1.
BA000036 Genomic DNA. Translation: BAB98057.1.
BX927149 Genomic DNA. Translation: CAF19369.1.
PIRiI40719.
RefSeqiNP_599896.1. NC_003450.3.
WP_011013800.1. NC_006958.1.
YP_224955.1. NC_006958.1.

Genome annotation databases

EnsemblBacteriaiBAB98057; BAB98057; BAB98057.
CAF19369; CAF19369; cg0766.
GeneIDi1018663.
23501940.
KEGGicgb:cg0766.
cgl:NCgl0634.
PATRICi21493369. VBICorGlu203724_0650.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X71489 Genomic DNA. Translation: CAA50590.1.
BA000036 Genomic DNA. Translation: BAB98057.1.
BX927149 Genomic DNA. Translation: CAF19369.1.
PIRiI40719.
RefSeqiNP_599896.1. NC_003450.3.
WP_011013800.1. NC_006958.1.
YP_224955.1. NC_006958.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2B0TX-ray1.75A1-738[»]
3MBCX-ray1.90A/B1-738[»]
ProteinModelPortaliP50216.
SMRiP50216. Positions 2-736.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi196627.cg0766.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB98057; BAB98057; BAB98057.
CAF19369; CAF19369; cg0766.
GeneIDi1018663.
23501940.
KEGGicgb:cg0766.
cgl:NCgl0634.
PATRICi21493369. VBICorGlu203724_0650.

Phylogenomic databases

eggNOGiCOG2838.
HOGENOMiHOG000240860.
KOiK00031.
OMAiDENRAHD.
OrthoDBiEOG6DVJPP.

Enzyme and pathway databases

BRENDAi1.1.1.42. 960.

Miscellaneous databases

EvolutionaryTraceiP50216.

Family and domain databases

Gene3Di3.40.718.10. 3 hits.
InterProiIPR004436. Isocitrate_DH_NADP_mono.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PfamiPF03971. IDH. 1 hit.
[Graphical view]
PIRSFiPIRSF009407. IDH_monmr. 1 hit.
TIGRFAMsiTIGR00178. monomer_idh. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, sequence analysis, expression, and inactivation of the Corynebacterium glutamicum icd gene encoding isocitrate dehydrogenase and biochemical characterization of the enzyme."
    Eikmanns B.J., Rittmann D., Sahm H.
    J. Bacteriol. 177:774-782(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
  2. "The Corynebacterium glutamicum genome: features and impacts on biotechnological processes."
    Ikeda M., Nakagawa S.
    Appl. Microbiol. Biotechnol. 62:99-109(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
  4. "Substrate-free structure of a monomeric NADP isocitrate dehydrogenase: an open conformation phylogenetic relationship of isocitrate dehydrogenase."
    Imabayashi F., Aich S., Prasad L., Delbaere L.T.
    Proteins 63:100-112(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, SUBUNIT.

Entry informationi

Entry nameiIDH_CORGL
AccessioniPrimary (citable) accession number: P50216
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: May 27, 2015
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.