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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 Mg2+ 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)DescriptionActionsGraphical viewLength
Binding sitei133NADPBy similarity1
Binding sitei143SubstrateBy similarity1
Sitei253Critical for catalysisBy similarity1
Metal bindingi346Magnesium or manganese1 Publication1
Sitei416Critical for catalysisBy similarity1
Binding sitei543SubstrateBy similarity1
Metal bindingi544Magnesium or manganese1 Publication1
Metal bindingi548Magnesium or manganese1 Publication1
Binding sitei585NADPBy similarity1
Binding sitei645NADPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi80 – 85NADPBy similarity6
Nucleotide bindingi580 – 581NADPBy similarity2
Nucleotide bindingi596 – 598NADPBy similarity3

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

BioCyciCORYNE:G18NG-10226-MONOMER.
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 lineageiBacteriaActinobacteriaCorynebacterialesCorynebacteriaceaeCorynebacterium
Proteomesi
  • UP000000582 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000835951 – 738Isocitrate dehydrogenase [NADP]Add BLAST738

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi196627.cg0766.

Structurei

Secondary structure

1738
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Helixi11 – 29Combined sources19
Turni30 – 32Combined sources3
Beta strandi34 – 39Combined sources6
Helixi42 – 47Combined sources6
Helixi51 – 53Combined sources3
Turni56 – 58Combined sources3
Helixi63 – 70Combined sources8
Beta strandi77 – 80Combined sources4
Helixi88 – 100Combined sources13
Helixi115 – 125Combined sources11
Beta strandi128 – 130Combined sources3
Helixi132 – 136Combined sources5
Beta strandi141 – 144Combined sources4
Helixi147 – 155Combined sources9
Beta strandi170 – 172Combined sources3
Beta strandi175 – 178Combined sources4
Helixi179 – 182Combined sources4
Beta strandi184 – 187Combined sources4
Beta strandi192 – 199Combined sources8
Beta strandi205 – 214Combined sources10
Beta strandi219 – 225Combined sources7
Helixi227 – 244Combined sources18
Beta strandi247 – 250Combined sources4
Turni254 – 256Combined sources3
Helixi260 – 272Combined sources13
Helixi274 – 286Combined sources13
Helixi294 – 302Combined sources9
Helixi308 – 321Combined sources14
Beta strandi327 – 329Combined sources3
Helixi330 – 332Combined sources3
Beta strandi342 – 344Combined sources3
Helixi345 – 354Combined sources10
Turni355 – 357Combined sources3
Beta strandi358 – 360Combined sources3
Beta strandi366 – 372Combined sources7
Helixi376 – 392Combined sources17
Turni397 – 399Combined sources3
Beta strandi405 – 407Combined sources3
Turni410 – 412Combined sources3
Helixi414 – 417Combined sources4
Helixi419 – 421Combined sources3
Beta strandi422 – 424Combined sources3
Beta strandi427 – 434Combined sources8
Beta strandi440 – 446Combined sources7
Beta strandi451 – 457Combined sources7
Helixi459 – 476Combined sources18
Beta strandi480 – 483Combined sources4
Helixi489 – 502Combined sources14
Beta strandi512 – 515Combined sources4
Helixi517 – 529Combined sources13
Beta strandi535 – 538Combined sources4
Helixi540 – 555Combined sources16
Beta strandi558 – 560Combined sources3
Beta strandi562 – 567Combined sources6
Beta strandi572 – 575Combined sources4
Helixi583 – 592Combined sources10
Helixi600 – 617Combined sources18
Helixi620 – 638Combined sources19
Helixi652 – 669Combined sources18
Helixi674 – 700Combined sources27
Beta strandi711 – 713Combined sources3
Helixi716 – 723Combined sources8
Helixi727 – 735Combined sources9

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP50216.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni130 – 137Substrate bindingBy similarity8

Sequence similaritiesi

Belongs to the monomeric-type IDH family.Curated

Phylogenomic databases

eggNOGiENOG4105E9K. Bacteria.
COG2838. LUCA.
HOGENOMiHOG000240860.
KOiK00031.
OMAiRDSGKMW.

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.

Genome annotation databases

EnsemblBacteriaiBAB98057; BAB98057; BAB98057.
CAF19369; CAF19369; cg0766.
GeneIDi1018663.
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2B0TX-ray1.75A1-738[»]
3MBCX-ray1.90A/B1-738[»]
ProteinModelPortaliP50216.
SMRiP50216.
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.
KEGGicgb:cg0766.
cgl:NCgl0634.
PATRICi21493369. VBICorGlu203724_0650.

Phylogenomic databases

eggNOGiENOG4105E9K. Bacteria.
COG2838. LUCA.
HOGENOMiHOG000240860.
KOiK00031.
OMAiRDSGKMW.

Enzyme and pathway databases

BioCyciCORYNE:G18NG-10226-MONOMER.
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...

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: November 2, 2016
This is version 106 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

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 one 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.