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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 Mg(2+) or Mn2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei95 – 951NADPBy similarity
Binding sitei96 – 961Substrate
Binding sitei104 – 1041Substrate
Binding sitei106 – 1061Substrate
Binding sitei110 – 1101Substrate
Binding sitei120 – 1201SubstrateBy similarity
Binding sitei144 – 1441Substrate
Sitei151 – 1511Critical for catalysisBy similarity
Sitei221 – 2211Critical for catalysisBy similarity
Metal bindingi311 – 3111Magnesium or manganeseBy similarity
Binding sitei358 – 3581NADP; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei397 – 3971NADPBy similarity
Binding sitei401 – 4011NADPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi345 – 3517NADPBy 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, 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
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU29130. [Micado]

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 423423Isocitrate dehydrogenase [NADP]PRO_0000083549Add
BLAST

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 interactions.
MINTiMINT-1711252.
STRINGi224308.Bsubs1_010100015896.

Structurei

Secondary structure

1
423
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 53Combined sources
Beta strandi8 – 103Combined sources
Beta strandi13 – 153Combined sources
Beta strandi18 – 258Combined sources
Helixi31 – 5020Combined sources
Beta strandi57 – 604Combined sources
Helixi65 – 717Combined sources
Helixi77 – 8610Combined sources
Beta strandi88 – 914Combined sources
Beta strandi98 – 1025Combined sources
Helixi105 – 1128Combined sources
Beta strandi117 – 1237Combined sources
Beta strandi131 – 1333Combined sources
Helixi135 – 1373Combined sources
Beta strandi139 – 1457Combined sources
Helixi149 – 1524Combined sources
Helixi161 – 17313Combined sources
Helixi182 – 1843Combined sources
Beta strandi185 – 1939Combined sources
Helixi194 – 21118Combined sources
Beta strandi214 – 2207Combined sources
Turni222 – 2243Combined sources
Turni226 – 2283Combined sources
Helixi229 – 24416Combined sources
Helixi245 – 2473Combined sources
Beta strandi248 – 2503Combined sources
Helixi251 – 27525Combined sources
Beta strandi279 – 2857Combined sources
Helixi286 – 29510Combined sources
Helixi297 – 2993Combined sources
Beta strandi301 – 3055Combined sources
Helixi307 – 32014Combined sources
Turni324 – 3263Combined sources
Beta strandi328 – 3325Combined sources
Turni334 – 3363Combined sources
Beta strandi339 – 3446Combined sources
Helixi349 – 3513Combined sources
Turni352 – 3554Combined sources
Helixi360 – 37314Combined sources
Helixi376 – 39116Combined sources
Helixi397 – 4004Combined sources
Beta strandi403 – 4053Combined sources
Helixi411 – 42010Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP39126.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0538.
HOGENOMiHOG000021113.
InParanoidiP39126.
KOiK00031.
OMAiFRDWGYE.
OrthoDBiEOG6SNDTP.
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. 1 hit.
PfamiPF00180. 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
EntryMethodResolution (Å)ChainPositionsPDBsum
1HQSX-ray1.55A/B1-423[»]
ProteinModelPortaliP39126.
SMRiP39126. Positions 1-423.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP39126. 2 interactions.
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.

Organism-specific databases

GenoListiBSU29130. [Micado]

Phylogenomic databases

eggNOGiCOG0538.
HOGENOMiHOG000021113.
InParanoidiP39126.
KOiK00031.
OMAiFRDWGYE.
OrthoDBiEOG6SNDTP.
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. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00183. prok_nadp_idh. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Identification of two distinct Bacillus subtilis citrate synthase genes."
    Jin S., Sonenshein A.L.
    J. Bacteriol. 176:4669-4679(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / SMY.
  2. "Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region."
    Lapidus A., Galleron N., Sorokin A., Ehrlich S.D.
    Microbiology 143:3431-3441(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  4. "Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/phosphatase."
    Singh S.K., Miller S.P., Dean A., Banaszak L.J., LaPorte D.C.
    J. Biol. Chem. 277:7567-7573(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION.
  5. "Crystal structure of Bacillus subtilis isocitrate dehydrogenase at 1.55 A. Insights into the nature of substrate specificity exhibited by Escherichia coli isocitrate dehydrogenase kinase/phosphatase."
    Singh S.K., Matsuno K., LaPorte D.C., Banaszak L.J.
    J. Biol. Chem. 276:26154-26163(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEX WITH CITRATE, SUBUNIT.

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: June 24, 2015
This is version 128 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

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.