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Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Azotobacter vinelandii
Status
Reviewed-Annotation score: Annotation score: 5 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

Inhibition of this enzyme by phosphorylation regulates the branch point between the Krebs cycle and the glyoxylate bypass, which is an alternate route that accumulates carbon for biosynthesis when acetate is the sole carbon source for growth. The phosphorylation state of this enzyme is controlled by isocitrate dehydrogenase kinase/phosphatase (AceK).

Temperature dependencei

Optimum temperature is above 40 degrees Celsius.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei135NADP1
Binding sitei145Substrate1
Sitei255Critical for catalysisBy similarity1
Metal bindingi350Magnesium or manganese1
Sitei420Critical for catalysisBy similarity1
Binding sitei547Substrate1
Metal bindingi548Magnesium or manganese1
Metal bindingi552Magnesium or manganeseBy similarity1
Binding sitei589NADP1
Binding sitei649NADP1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi82 – 87NADP6
Nucleotide bindingi584 – 585NADP2
Nucleotide bindingi600 – 602NADP3

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glyoxylate bypass, Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NADP

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13167.

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
OrganismiAzotobacter vinelandii
Taxonomic identifieri354 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaeAzotobacter

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000835932 – 741Isocitrate dehydrogenase [NADP]Add BLAST740

Keywords - PTMi

Phosphoprotein

Proteomic databases

PRIDEiP16100.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi322710.Avin_28310.

Structurei

Secondary structure

1741
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 10Combined sources6
Helixi13 – 31Combined sources19
Turni32 – 34Combined sources3
Beta strandi36 – 41Combined sources6
Helixi44 – 51Combined sources8
Helixi53 – 55Combined sources3
Turni58 – 60Combined sources3
Helixi65 – 72Combined sources8
Beta strandi79 – 82Combined sources4
Helixi90 – 102Combined sources13
Helixi117 – 129Combined sources13
Beta strandi130 – 132Combined sources3
Helixi135 – 138Combined sources4
Beta strandi143 – 146Combined sources4
Helixi149 – 157Combined sources9
Beta strandi172 – 174Combined sources3
Beta strandi177 – 180Combined sources4
Helixi181 – 184Combined sources4
Beta strandi186 – 189Combined sources4
Beta strandi192 – 202Combined sources11
Beta strandi207 – 216Combined sources10
Beta strandi221 – 227Combined sources7
Helixi229 – 246Combined sources18
Beta strandi249 – 252Combined sources4
Turni256 – 258Combined sources3
Helixi262 – 274Combined sources13
Helixi276 – 281Combined sources6
Helixi283 – 288Combined sources6
Helixi293 – 295Combined sources3
Helixi297 – 303Combined sources7
Helixi304 – 306Combined sources3
Helixi309 – 325Combined sources17
Beta strandi331 – 333Combined sources3
Turni334 – 337Combined sources4
Turni340 – 342Combined sources3
Beta strandi346 – 348Combined sources3
Helixi349 – 358Combined sources10
Turni359 – 361Combined sources3
Beta strandi362 – 364Combined sources3
Beta strandi368 – 376Combined sources9
Helixi380 – 396Combined sources17
Turni401 – 403Combined sources3
Beta strandi409 – 411Combined sources3
Turni414 – 416Combined sources3
Helixi418 – 421Combined sources4
Helixi423 – 425Combined sources3
Beta strandi426 – 428Combined sources3
Beta strandi430 – 439Combined sources10
Beta strandi444 – 450Combined sources7
Beta strandi455 – 461Combined sources7
Helixi463 – 480Combined sources18
Beta strandi484 – 487Combined sources4
Helixi493 – 506Combined sources14
Beta strandi516 – 519Combined sources4
Helixi521 – 533Combined sources13
Beta strandi539 – 542Combined sources4
Helixi544 – 559Combined sources16
Beta strandi562 – 571Combined sources10
Beta strandi576 – 580Combined sources5
Helixi587 – 596Combined sources10
Helixi604 – 620Combined sources17
Helixi624 – 642Combined sources19
Beta strandi649 – 653Combined sources5
Helixi656 – 673Combined sources18
Helixi678 – 693Combined sources16
Helixi695 – 703Combined sources9
Beta strandi706 – 708Combined sources3
Beta strandi715 – 717Combined sources3
Helixi720 – 727Combined sources8
Helixi731 – 736Combined sources6
Turni737 – 739Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ITWX-ray1.95A/B/C/D1-741[»]
1J1WX-ray3.20A/B/C/D1-741[»]
ProteinModelPortaliP16100.
SMRiP16100.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP16100.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni132 – 139Substrate binding8

Domaini

This molecule consists of two distinct domains, a small domain and a large domain. The structure of the large domain repeats a motif observed in the dimeric IDH. Such a fusional structure by domain duplication enables a single polypeptide chain to form a structure at the catalytic site that is homologous to the dimeric IDH, the catalytic site of which is located at the interface of two identical subunits.

Sequence similaritiesi

Belongs to the monomeric-type IDH family.Curated

Phylogenomic databases

eggNOGiENOG4105E9K. Bacteria.
COG2838. LUCA.

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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P16100-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTPKIIYTL TDEAPALATY SLLPIIKAFT GSSGIAVETR DISLAGRLIA
60 70 80 90 100
TFPEYLTDTQ KISDDLAELG KLATTPDANI IKLPNISASV PQLKAAIKEL
110 120 130 140 150
QQQGYKLPDY PEEPKTDTEK DVKARYDKIK GSAVNPVLRE GNSDRRAPLS
160 170 180 190 200
VKNYARKHPH KMGAWSADSK SHVAHMDNGD FYGSEKAALI GAPGSVKIEL
210 220 230 240 250
IAKDGSSTVL KAKTSVQAGE IIDSSVMSKN ALRNFIAAEI EDAKKQGVLL
260 270 280 290 300
SVHLKATMMK VSDPIMFGQI VSEFYKDALT KHAEVLKQIG FDVNNGIGDL
310 320 330 340 350
YARIKTLPEA KQKEIEADIQ AVYAQRPQLA MVNSDKGITN LHVPSDVIVD
360 370 380 390 400
ASMPAMIRDS GKMWGPDGKL HDTKAVIPDR CYAGVYQVVI EDCKQHGAFD
410 420 430 440 450
PTTMGSVPNV GLMAQKAEEY GSHDKTFQIP ADGVVRVTDE SGKLLLEQSV
460 470 480 490 500
EAGDIWRMCQ AKDAPIQDWV KLAVNRARAT NTPAVFWLDP ARAHDAQVIA
510 520 530 540 550
KVERYLKDYD TSGLDIRILS PVEATRFSLA RIREGKDTIS VTGNVLRDYL
560 570 580 590 600
TDLFPIMELG TSAKMLSIVP LMSGGGLFET GAGGSAPKHV QQFLEEGYLR
610 620 630 640 650
WDSLGEFLAL AASLEHLGNA YKNPKALVLA STLDQATGKI LDNNKSPARK
660 670 680 690 700
VGEIDNRGSH FYLALYWAQA LAAQTEDKEL QAQFTGIAKA LTDNETKIVG
710 720 730 740
ELAAAQGKPV DIAGYYHPNT DLTSKAIRPS ATFNAALAPL A
Length:741
Mass (Da):80,390
Last modified:January 23, 2007 - v5
Checksum:i29FF35278E5AED8B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D73443 Genomic DNA. Translation: BAA11169.1.
PIRiA10759.
JC7822.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D73443 Genomic DNA. Translation: BAA11169.1.
PIRiA10759.
JC7822.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ITWX-ray1.95A/B/C/D1-741[»]
1J1WX-ray3.20A/B/C/D1-741[»]
ProteinModelPortaliP16100.
SMRiP16100.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi322710.Avin_28310.

Proteomic databases

PRIDEiP16100.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105E9K. Bacteria.
COG2838. LUCA.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13167.

Miscellaneous databases

EvolutionaryTraceiP16100.

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_AZOVI
AccessioniPrimary (citable) accession number: P16100
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 106 of the entry and version 5 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

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.