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Q9SLK0

- ICDHX_ARATH

UniProt

Q9SLK0 - ICDHX_ARATH

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Protein

Peroxisomal isocitrate dehydrogenase [NADP]

Gene

ICDH

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

Functioni

May be involved in response to oxidative stresses.By similarity

Catalytic activityi

Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.

Cofactori

Binds 1 magnesium or manganese ion per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei79 – 791SubstrateBy similarity
Binding sitei84 – 841NADPBy similarity
Binding sitei111 – 1111SubstrateBy similarity
Binding sitei134 – 1341SubstrateBy similarity
Sitei141 – 1411Critical for catalysisBy similarity
Sitei213 – 2131Critical for catalysisBy similarity
Metal bindingi253 – 2531Magnesium or manganeseBy similarity
Binding sitei261 – 2611NADPBy similarity
Metal bindingi276 – 2761Magnesium or manganeseBy similarity
Binding sitei329 – 3291NADP; via amide nitrogen and carbonyl oxygenBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi77 – 793NADPBy similarity
Nucleotide bindingi311 – 3166NADPBy similarity

GO - Molecular functioni

  1. isocitrate dehydrogenase (NADP+) activity Source: UniProtKB-EC
  2. magnesium ion binding Source: InterPro
  3. NAD binding Source: InterPro

GO - Biological processi

  1. isocitrate metabolic process Source: InterPro
  2. response to stress Source: UniProtKB-KW
  3. tricarboxylic acid cycle Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Stress response, Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NADP

Enzyme and pathway databases

BioCyciARA:AT1G54340-MONOMER.
ReactomeiREACT_214122. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
REACT_218202. NADPH regeneration.

Names & Taxonomyi

Protein namesi
Recommended name:
Peroxisomal isocitrate dehydrogenase [NADP] (EC:1.1.1.42)
Gene namesi
Name:ICDH
Ordered Locus Names:At1g54340
ORF Names:F20D21.16
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 1

Organism-specific databases

TAIRiAT1G54340.

Subcellular locationi

Peroxisome 2 Publications

GO - Cellular componenti

  1. peroxisome Source: TAIR
  2. plasma membrane Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Peroxisome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 416416Peroxisomal isocitrate dehydrogenase [NADP]PRO_0000421962Add
BLAST

Proteomic databases

PRIDEiQ9SLK0.

Expressioni

Gene expression databases

ExpressionAtlasiQ9SLK0. baseline and differential.
GenevestigatoriQ9SLK0.

Structurei

3D structure databases

ProteinModelPortaliQ9SLK0.
SMRiQ9SLK0. Positions 4-409.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni96 – 1027Substrate bindingBy similarity

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi414 – 4163Peroxisomal targeting signalCurated

Sequence similaritiesi

Phylogenomic databases

HOGENOMiHOG000019858.
InParanoidiQ9SLK0.
KOiK00031.
OMAiEANWRSK.
PhylomeDBiQ9SLK0.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR004790. Isocitrate_DH_NADP.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11822. PTHR11822. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
PIRSFiPIRSF000108. IDH_NADP. 1 hit.
TIGRFAMsiTIGR00127. nadp_idh_euk. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9SLK0 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MEFEKIKVIN PVVEMDGDEM TRVIWKFIKD KLIFPFLELD IKYFDLGLPN
60 70 80 90 100
RDFTDDKVTI ETAEATLKYN VAIKCATITP DEARVREFGL KKMWRSPNGT
110 120 130 140 150
IRNILNGTVF REPIICRNIP RLVPGWTKPI CIGRHAFGDQ YRATDLIVNE
160 170 180 190 200
PGKLKLVFEP SGSSQKTEFE VFNFTGGGVA LAMYNTDESI RAFAESSMYT
210 220 230 240 250
AYQKKWPLYL STKNTILKIY DGRFKDIFQE VYEANWRSKY EAAGIWYEHR
260 270 280 290 300
LIDDMVAYAM KSEGGYVWAC KNYDGDVQSD FLAQGYGSLG MMTSVLVCPD
310 320 330 340 350
GKTIEAEAAH GTVTRHYRVH QKGGETSTNS IASIFAWSRG LAHRAKLDSN
360 370 380 390 400
AALLSYTEKL EAACMGTVES GKMTKDLALL IHGAKVRRDQ YVNTEEFIDA
410
VAWELKRRLL GNNSRL
Length:416
Mass (Da):47,234
Last modified:May 1, 2000 - v1
Checksum:iEEAAAC9E5C6B2FA5
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF316501 mRNA. Translation: AAK06592.1.
AC005287 Genomic DNA. Translation: AAD25614.1.
CP002684 Genomic DNA. Translation: AEE33082.1.
BT025983 mRNA. Translation: ABG25072.1.
PIRiA96585.
RefSeqiNP_175836.1. NM_104312.2.
UniGeneiAt.11811.
At.37230.

Genome annotation databases

EnsemblPlantsiAT1G54340.1; AT1G54340.1; AT1G54340.
GeneIDi841875.
KEGGiath:AT1G54340.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF316501 mRNA. Translation: AAK06592.1 .
AC005287 Genomic DNA. Translation: AAD25614.1 .
CP002684 Genomic DNA. Translation: AEE33082.1 .
BT025983 mRNA. Translation: ABG25072.1 .
PIRi A96585.
RefSeqi NP_175836.1. NM_104312.2.
UniGenei At.11811.
At.37230.

3D structure databases

ProteinModelPortali Q9SLK0.
SMRi Q9SLK0. Positions 4-409.
ModBasei Search...
MobiDBi Search...

Proteomic databases

PRIDEi Q9SLK0.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT1G54340.1 ; AT1G54340.1 ; AT1G54340 .
GeneIDi 841875.
KEGGi ath:AT1G54340.

Organism-specific databases

TAIRi AT1G54340.

Phylogenomic databases

HOGENOMi HOG000019858.
InParanoidi Q9SLK0.
KOi K00031.
OMAi EANWRSK.
PhylomeDBi Q9SLK0.

Enzyme and pathway databases

BioCyci ARA:AT1G54340-MONOMER.
Reactomei REACT_214122. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
REACT_218202. NADPH regeneration.

Gene expression databases

ExpressionAtlasi Q9SLK0. baseline and differential.
Genevestigatori Q9SLK0.

Family and domain databases

Gene3Di 3.40.718.10. 1 hit.
InterProi IPR019818. IsoCit/isopropylmalate_DH_CS.
IPR004790. Isocitrate_DH_NADP.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view ]
PANTHERi PTHR11822. PTHR11822. 1 hit.
Pfami PF00180. Iso_dh. 1 hit.
[Graphical view ]
PIRSFi PIRSF000108. IDH_NADP. 1 hit.
TIGRFAMsi TIGR00127. nadp_idh_euk. 1 hit.
PROSITEi PS00470. IDH_IMDH. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation of cDNA encoding NADP-specific isocitrate dehydrogenase from Arabidopsis thaliana."
    Kihara T., Ito N., Koyama H., Hara T.
    Submitted (OCT-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. Columbia.
  2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Arabidopsis ORF clones."
    Shinn P., Chen H., Kim C.J., Quinitio C., Ecker J.R.
    Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Proteome analysis of Arabidopsis leaf peroxisomes reveals novel targeting peptides, metabolic pathways, and defense mechanisms."
    Reumann S., Babujee L., Ma C., Wienkoop S., Siemsen T., Antonicelli G.E., Rasche N., Lueder F., Weckwerth W., Jahn O.
    Plant Cell 19:3170-3193(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 32-51, SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  6. "In-depth proteome analysis of Arabidopsis leaf peroxisomes combined with in vivo subcellular targeting verification indicates novel metabolic and regulatory functions of peroxisomes."
    Reumann S., Quan S., Aung K., Yang P., Manandhar-Shrestha K., Holbrook D., Linka N., Switzenberg R., Wilkerson C.G., Weber A.P., Olsen L.J., Hu J.
    Plant Physiol. 150:125-143(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiICDHX_ARATH
AccessioniPrimary (citable) accession number: Q9SLK0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2013
Last sequence update: May 1, 2000
Last modified: October 29, 2014
This is version 106 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3