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Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
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+By similarity, Mn2+By similarityNote: Binds 1 Mg2+ or Mn2+ ion per subunit.By similarity

Kineticsi

  1. KM=118 µM for D,L-isocitrate
  2. KM=30 µM for NADP
  3. KM=5.4 mM for NAD
  1. Vmax=141 µmol/min/mg enzyme towards NADP at 60 degrees Celsius
  2. Vmax=14.5 µmol/min/mg enzyme towards NAD

pH dependencei

Optimum pH is 8.6.

Temperature dependencei

Optimum temperature is 90 degrees Celsius. Thermostable.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei100NADPBy similarity1
Binding sitei109SubstrateBy similarity1
Binding sitei111SubstrateBy similarity1
Binding sitei115SubstrateBy similarity1
Binding sitei125SubstrateBy similarity1
Binding sitei149SubstrateBy similarity1
Sitei156Critical for catalysisBy similarity1
Sitei223Critical for catalysisBy similarity1
Metal bindingi301Magnesium or manganeseBy similarity1
Binding sitei346NADP; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei385NADPBy similarity1
Binding sitei389NADPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi333 – 339NADPBy similarity7

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

BRENDAi1.1.1.42. 414.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NADP] (EC:1.1.1.42)
Short name:
IDH
Alternative name(s):
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
Gene namesi
Name:icd
Ordered Locus Names:AF_0647
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
Proteomesi
  • UP000002199 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000835721 – 412Isocitrate dehydrogenase [NADP]Add BLAST412

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei109PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

STRINGi224325.AF0647.

Structurei

Secondary structure

1412
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi16 – 18Combined sources3
Beta strandi21 – 23Combined sources3
Beta strandi26 – 33Combined sources8
Helixi39 – 57Combined sources19
Beta strandi62 – 65Combined sources4
Helixi70 – 76Combined sources7
Helixi82 – 91Combined sources10
Beta strandi93 – 96Combined sources4
Beta strandi103 – 108Combined sources6
Helixi109 – 117Combined sources9
Beta strandi122 – 128Combined sources7
Beta strandi136 – 138Combined sources3
Helixi140 – 142Combined sources3
Beta strandi144 – 150Combined sources7
Beta strandi152 – 154Combined sources3
Helixi155 – 157Combined sources3
Helixi166 – 179Combined sources14
Beta strandi187 – 195Combined sources9
Helixi196 – 212Combined sources17
Beta strandi216 – 222Combined sources7
Turni224 – 226Combined sources3
Turni228 – 230Combined sources3
Helixi231 – 245Combined sources15
Turni247 – 249Combined sources3
Helixi253 – 260Combined sources8
Beta strandi269 – 275Combined sources7
Helixi276 – 278Combined sources3
Helixi279 – 285Combined sources7
Helixi287 – 289Combined sources3
Beta strandi292 – 295Combined sources4
Helixi297 – 310Combined sources14
Helixi314 – 316Combined sources3
Beta strandi318 – 323Combined sources6
Beta strandi326 – 333Combined sources8
Turni338 – 341Combined sources4
Helixi348 – 360Combined sources13
Helixi364 – 379Combined sources16
Helixi385 – 391Combined sources7
Beta strandi393 – 395Combined sources3
Helixi398 – 411Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2IV0X-ray2.50A/B1-412[»]
ProteinModelPortaliO29610.
SMRiO29610.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO29610.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiarCOG01164. Archaea.
COG0538. LUCA.
KOiK00031.
OMAiTERESWI.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004439. Isocitrate_DH_NADP_dimer_prok.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 3 hits.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00183. prok_nadp_idh. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O29610-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQYEKVKPPE NGEKIRYENG KLIVPDNPII PYFEGDGIGK DVVPAAIRVL
60 70 80 90 100
DAAADKIGKE VVWFQVYAGE DAYKLYGNYL PDDTLNAIKE FRVALKGPLT
110 120 130 140 150
TPVGGGYRSL NVTIRQVLDL YANVRPVYYL KGVPSPIKHP EKVNFVIFRE
160 170 180 190 200
NTEDVYAGIE WPRGSEEALK LIRFLKNEFG VTIREDSGIG IKPISEFATK
210 220 230 240 250
RLVRMAIRYA IENNRKSVTL VHKGNIMKYT EGAFRDWGYE VAKQEFGEYC
260 270 280 290 300
ITEDELWDKY GGKQPEGKIV VKDRIADNMF QQILTRTDEY DVIALPNLNG
310 320 330 340 350
DYLSDAAAAL IGGLGIAPGS NIGDGIGVFE PVHGSAPKYA GQNKVNPTAE
360 370 380 390 400
ILTGALMFEY IGWKDASEMI KKAVEMTISS GIVTYDIHRH MGGTKVGTRE
410
FAEAVVENLQ SL
Length:412
Mass (Da):45,842
Last modified:January 1, 1998 - v1
Checksum:iA2E1A3AA7662D3EA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z96105 Genomic DNA. Translation: CAB09535.1.
AE000782 Genomic DNA. Translation: AAB90591.1.
PIRiG69330.
RefSeqiWP_010878150.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90591; AAB90591; AF_0647.
GeneIDi1483865.
KEGGiafu:AF_0647.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z96105 Genomic DNA. Translation: CAB09535.1.
AE000782 Genomic DNA. Translation: AAB90591.1.
PIRiG69330.
RefSeqiWP_010878150.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2IV0X-ray2.50A/B1-412[»]
ProteinModelPortaliO29610.
SMRiO29610.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224325.AF0647.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB90591; AAB90591; AF_0647.
GeneIDi1483865.
KEGGiafu:AF_0647.

Phylogenomic databases

eggNOGiarCOG01164. Archaea.
COG0538. LUCA.
KOiK00031.
OMAiTERESWI.

Enzyme and pathway databases

BRENDAi1.1.1.42. 414.

Miscellaneous databases

EvolutionaryTraceiO29610.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004439. Isocitrate_DH_NADP_dimer_prok.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 3 hits.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00183. prok_nadp_idh. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiIDH_ARCFU
AccessioniPrimary (citable) accession number: O29610
Secondary accession number(s): O31221
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 29, 2001
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 118 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, Direct protein sequencing, 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.