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P80046

- IDH_SYNY3

UniProt

P80046 - IDH_SYNY3

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Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
Status
Reviewed - 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 Mn(2+) ion per subunit.By similarity

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei104 – 1041NADPBy similarity
Binding sitei113 – 1131SubstrateBy similarity
Binding sitei115 – 1151SubstrateBy similarity
Binding sitei119 – 1191SubstrateBy similarity
Binding sitei129 – 1291SubstrateBy similarity
Binding sitei153 – 1531SubstrateBy similarity
Sitei160 – 1601Critical for catalysisBy similarity
Sitei237 – 2371Critical for catalysisBy similarity
Metal bindingi362 – 3621Magnesium or manganeseBy similarity
Binding sitei407 – 4071NADP; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei446 – 4461NADPBy similarity
Binding sitei450 – 4501NADPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi394 – 4007NADPBy 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. glyoxylate cycle Source: UniProtKB-KW
  2. tricarboxylic acid cycle Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glyoxylate bypass, Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NADP

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:slr1289
OrganismiSynechocystis sp. (strain PCC 6803 / Kazusa)
Taxonomic identifieri1111708 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechocystis
ProteomesiUP000001425: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 475475Isocitrate dehydrogenase [NADP]PRO_0000083570Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei113 – 1131PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP80046.
PRIDEiP80046.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

IntActiP80046. 2 interactions.
STRINGi1148.slr1289.

Structurei

3D structure databases

ProteinModelPortaliP80046.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0538.
HOGENOMiHOG000021113.
InParanoidiP80046.
KOiK00031.
OrthoDBiEOG6SNDTP.
PhylomeDBiP80046.

Family and domain databases

Gene3Di3.40.718.10. 2 hits.
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.

P80046-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MYEKLQPPSV GSKITFVAGK PVVPNDPIIP YIRGDGTGVD IWPATELVIN
60 70 80 90 100
AAIAKAYGGR EEINWFKVYA GDEACELYGT YQIFPEDTLT AIKEYGVAIK
110 120 130 140 150
GPLTTPVGGG IRSLNVALRQ IFDLYTCVRP CRYYPGTPSP HKTPEKLDII
160 170 180 190 200
VYRENTEDIY LGIEWAEGTE GAKKLIAYLN DELIPTTPAL GKKQIRLDSG
210 220 230 240 250
IGIKPISKTG SQRLVRRAIL HAKRLPKAKQ MVTLVHKGNI MKFTEGPFRD
260 270 280 290 300
WGYELATTEF RAECVTERES WICGNKESNP DLTIEANAHM IDPGYDTLTE
310 320 330 340 350
EKQAVIKQEV EQVLNSIWES HGNGQWKEKV MVNDRIADSI FQQIQTRPDE
360 370 380 390 400
YSILATMNLN GDYLSDAAAA VVGGLGMGPG ANIGDSAAIF EATHGTAPKH
410 420 430 440 450
AGLDRINPGS VILSGVMMLE FMGWQEAADL IKKGIGAAIA NREVTYDLAR
460 470
LMEPKVDKPL KCSEFAQAIV SHFDD
Length:475
Mass (Da):52,275
Last modified:November 1, 1997 - v2
Checksum:i6F3254A8BBA75F92
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti60 – 623REE → ERK in BAA16835. (PubMed:8905231)Curated
Sequence conflicti83 – 842IF → YL in BAA16835. (PubMed:8905231)Curated
Sequence conflicti223 – 2231K → L in BAA16835. (PubMed:8905231)Curated
Sequence conflicti247 – 2471P → A in BAA16835. (PubMed:8905231)Curated
Sequence conflicti273 – 2731C → L in BAA16835. (PubMed:8905231)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X83563 Genomic DNA. Translation: CAA58549.1.
BA000022 Genomic DNA. Translation: BAA16835.1.
PIRiS74684.
RefSeqiNP_440155.1. NC_000911.1.
YP_005650212.1. NC_017277.1.
YP_007450038.1. NC_020286.1.

Genome annotation databases

EnsemblBacteriaiBAA16835; BAA16835; BAA16835.
GeneIDi953454.
KEGGisyn:slr1289.
PATRICi23837428. VBISynSp132158_0286.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X83563 Genomic DNA. Translation: CAA58549.1 .
BA000022 Genomic DNA. Translation: BAA16835.1 .
PIRi S74684.
RefSeqi NP_440155.1. NC_000911.1.
YP_005650212.1. NC_017277.1.
YP_007450038.1. NC_020286.1.

3D structure databases

ProteinModelPortali P80046.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi P80046. 2 interactions.
STRINGi 1148.slr1289.

Proteomic databases

PaxDbi P80046.
PRIDEi P80046.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAA16835 ; BAA16835 ; BAA16835 .
GeneIDi 953454.
KEGGi syn:slr1289.
PATRICi 23837428. VBISynSp132158_0286.

Phylogenomic databases

eggNOGi COG0538.
HOGENOMi HOG000021113.
InParanoidi P80046.
KOi K00031.
OrthoDBi EOG6SNDTP.
PhylomeDBi P80046.

Family and domain databases

Gene3Di 3.40.718.10. 2 hits.
InterProi IPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004439. Isocitrate_DH_NADP_dimer_prok.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view ]
PANTHERi PTHR11835. PTHR11835. 1 hit.
Pfami PF00180. Iso_dh. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR00183. prok_nadp_idh. 1 hit.
PROSITEi PS00470. IDH_IMDH. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The NADP+-isocitrate dehydrogenase gene (icd) is nitrogen regulated in cyanobacteria."
    Muro-Pastor M.I., Reyes J.C., Florencio F.J.
    J. Bacteriol. 178:4070-4076(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions."
    Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.
    , Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    DNA Res. 3:109-136(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PCC 6803 / Kazusa.
  3. "Purification and properties of NADP-isocitrate dehydrogenase from the unicellular cyanobacterium Synechocystis sp. PCC 6803."
    Muro-Pastor M.I., Florencio F.J.
    Eur. J. Biochem. 203:99-105(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-20.

Entry informationi

Entry nameiIDH_SYNY3
AccessioniPrimary (citable) accession number: P80046
Secondary accession number(s): P72820
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: November 1, 1997
Last modified: November 26, 2014
This is version 105 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Synechocystis PCC 6803
    Synechocystis (strain PCC 6803): entries and gene names

External Data

Dasty 3