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Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Bacillus subtilis (strain 168)
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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei95NADPBy similarity1
Binding sitei96Substrate1
Binding sitei104Substrate1
Binding sitei106Substrate1
Binding sitei110Substrate1
Binding sitei120SubstrateBy similarity1
Binding sitei144Substrate1
Sitei151Critical for catalysisBy similarity1
Sitei221Critical for catalysisBy similarity1
Metal bindingi311Magnesium or manganeseBy similarity1
Binding sitei358NADP; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei397NADPBy similarity1
Binding sitei401NADPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi345 – 351NADPBy 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

BioCyciBSUB:BSU29130-MONOMER.
SABIO-RKP39126.

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
Synonyms:citC
Ordered Locus Names:BSU29130
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000835491 – 423Isocitrate dehydrogenase [NADP]Add BLAST423

Proteomic databases

PaxDbiP39126.
PRIDEiP39126.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
mdhP498143EBI-7829570,EBI-7827708

Protein-protein interaction databases

IntActiP39126. 2 interactors.
MINTiMINT-1711252.
STRINGi224308.Bsubs1_010100015896.

Structurei

Secondary structure

1423
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 5Combined sources3
Beta strandi8 – 10Combined sources3
Beta strandi13 – 15Combined sources3
Beta strandi18 – 25Combined sources8
Helixi31 – 50Combined sources20
Beta strandi57 – 60Combined sources4
Helixi65 – 71Combined sources7
Helixi77 – 86Combined sources10
Beta strandi88 – 91Combined sources4
Beta strandi98 – 102Combined sources5
Helixi105 – 112Combined sources8
Beta strandi117 – 123Combined sources7
Beta strandi131 – 133Combined sources3
Helixi135 – 137Combined sources3
Beta strandi139 – 145Combined sources7
Helixi149 – 152Combined sources4
Helixi161 – 173Combined sources13
Helixi182 – 184Combined sources3
Beta strandi185 – 193Combined sources9
Helixi194 – 211Combined sources18
Beta strandi214 – 220Combined sources7
Turni222 – 224Combined sources3
Turni226 – 228Combined sources3
Helixi229 – 244Combined sources16
Helixi245 – 247Combined sources3
Beta strandi248 – 250Combined sources3
Helixi251 – 275Combined sources25
Beta strandi279 – 285Combined sources7
Helixi286 – 295Combined sources10
Helixi297 – 299Combined sources3
Beta strandi301 – 305Combined sources5
Helixi307 – 320Combined sources14
Turni324 – 326Combined sources3
Beta strandi328 – 332Combined sources5
Turni334 – 336Combined sources3
Beta strandi339 – 344Combined sources6
Helixi349 – 351Combined sources3
Turni352 – 355Combined sources4
Helixi360 – 373Combined sources14
Helixi376 – 391Combined sources16
Helixi397 – 400Combined sources4
Beta strandi403 – 405Combined sources3
Helixi411 – 420Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HQSX-ray1.55A/B1-423[»]
ProteinModelPortaliP39126.
SMRiP39126.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39126.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108HMX. Bacteria.
COG0538. LUCA.
HOGENOMiHOG000021113.
InParanoidiP39126.
KOiK00031.
OMAiTERESWI.
PhylomeDBiP39126.

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.

P39126-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQGEKITVS NGVLNVPNNP IIPFIEGDGT GPDIWNAASK VLEAAVEKAY
60 70 80 90 100
KGEKKITWKE VYAGEKAYNK TGEWLPAETL DVIREYFIAI KGPLTTPVGG
110 120 130 140 150
GIRSLNVALR QELDLFVCLR PVRYFTGVPS PVKRPEDTDM VIFRENTEDI
160 170 180 190 200
YAGIEYAKGS EEVQKLISFL QNELNVNKIR FPETSGIGIK PVSEEGTSRL
210 220 230 240 250
VRAAIDYAIE HGRKSVTLVH KGNIMKFTEG AFKNWGYELA EKEYGDKVFT
260 270 280 290 300
WAQYDRIAEE QGKDAANKAQ SEAEAAGKII IKDSIADIFL QQILTRPNEF
310 320 330 340 350
DVVATMNLNG DYISDALAAQ VGGIGIAPGA NINYETGHAI FEATHGTAPK
360 370 380 390 400
YAGLDKVNPS SVILSGVLLL EHLGWNEAAD LVIKSMEKTI ASKVVTYDFA
410 420
RLMDGATEVK CSEFGEELIK NMD
Length:423
Mass (Da):46,418
Last modified:February 1, 1995 - v1
Checksum:iCC69E694EB66D0D8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U05257 Genomic DNA. Translation: AAA96342.1.
AF008220 Genomic DNA. Translation: AAC00346.1.
AL009126 Genomic DNA. Translation: CAB14873.1.
PIRiI40382.
RefSeqiNP_390791.1. NC_000964.3.
WP_003229433.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB14873; CAB14873; BSU29130.
GeneIDi938183.
KEGGibsu:BSU29130.
PATRICi18977720. VBIBacSub10457_3048.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U05257 Genomic DNA. Translation: AAA96342.1.
AF008220 Genomic DNA. Translation: AAC00346.1.
AL009126 Genomic DNA. Translation: CAB14873.1.
PIRiI40382.
RefSeqiNP_390791.1. NC_000964.3.
WP_003229433.1. NZ_JNCM01000036.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HQSX-ray1.55A/B1-423[»]
ProteinModelPortaliP39126.
SMRiP39126.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP39126. 2 interactors.
MINTiMINT-1711252.
STRINGi224308.Bsubs1_010100015896.

Proteomic databases

PaxDbiP39126.
PRIDEiP39126.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14873; CAB14873; BSU29130.
GeneIDi938183.
KEGGibsu:BSU29130.
PATRICi18977720. VBIBacSub10457_3048.

Phylogenomic databases

eggNOGiENOG4108HMX. Bacteria.
COG0538. LUCA.
HOGENOMiHOG000021113.
InParanoidiP39126.
KOiK00031.
OMAiTERESWI.
PhylomeDBiP39126.

Enzyme and pathway databases

BioCyciBSUB:BSU29130-MONOMER.
SABIO-RKP39126.

Miscellaneous databases

EvolutionaryTraceiP39126.

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_BACSU
AccessioniPrimary (citable) accession number: P39126
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: November 2, 2016
This is version 138 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The enzyme can be phosphorylated in vitro by the E.coli isocitrate dehydrogenase kinase/phosphatase, but B.subtilis lacks such an enzyme.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.