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P80046 (IDH_SYNY3) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Isocitrate dehydrogenase [NADP]

Short name=IDH
EC=1.1.1.42
Alternative name(s):
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
Gene names
Name:icd
Ordered Locus Names:slr1289
OrganismSynechocystis sp. (strain PCC 6803 / Kazusa) [Reference proteome] [HAMAP]
Taxonomic identifier1111708 [NCBI]
Taxonomic lineageBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechocystis

Protein attributes

Sequence length475 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

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

Cofactor

Binds 1 magnesium or manganese ion per subunit By similarity.

Enzyme regulation

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.

Subunit structure

Homodimer.

Subcellular location

Cytoplasm.

Sequence similarities

Belongs to the isocitrate and isopropylmalate dehydrogenases family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 475475Isocitrate dehydrogenase [NADP]
PRO_0000083570

Regions

Nucleotide binding394 – 4007NADP By similarity

Sites

Metal binding3621Magnesium or manganese By similarity
Binding site1041NADP By similarity
Binding site1131Substrate By similarity
Binding site1151Substrate By similarity
Binding site1191Substrate By similarity
Binding site1291Substrate By similarity
Binding site1531Substrate By similarity
Binding site4071NADP; via amide nitrogen and carbonyl oxygen By similarity
Binding site4461NADP By similarity
Binding site4501NADP By similarity
Site1601Critical for catalysis By similarity
Site2371Critical for catalysis By similarity

Amino acid modifications

Modified residue1131Phosphoserine By similarity

Experimental info

Sequence conflict60 – 623REE → ERK in BAA16835. Ref.2
Sequence conflict83 – 842IF → YL in BAA16835. Ref.2
Sequence conflict2231K → L in BAA16835. Ref.2
Sequence conflict2471P → A in BAA16835. Ref.2
Sequence conflict2731C → L in BAA16835. Ref.2

Sequences

Sequence LengthMass (Da)Tools
P80046 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: 6F3254A8BBA75F92

FASTA47552,275
        10         20         30         40         50         60 
MYEKLQPPSV GSKITFVAGK PVVPNDPIIP YIRGDGTGVD IWPATELVIN AAIAKAYGGR 

        70         80         90        100        110        120 
EEINWFKVYA GDEACELYGT YQIFPEDTLT AIKEYGVAIK GPLTTPVGGG IRSLNVALRQ 

       130        140        150        160        170        180 
IFDLYTCVRP CRYYPGTPSP HKTPEKLDII VYRENTEDIY LGIEWAEGTE GAKKLIAYLN 

       190        200        210        220        230        240 
DELIPTTPAL GKKQIRLDSG IGIKPISKTG SQRLVRRAIL HAKRLPKAKQ MVTLVHKGNI 

       250        260        270        280        290        300 
MKFTEGPFRD WGYELATTEF RAECVTERES WICGNKESNP DLTIEANAHM IDPGYDTLTE 

       310        320        330        340        350        360 
EKQAVIKQEV EQVLNSIWES HGNGQWKEKV MVNDRIADSI FQQIQTRPDE YSILATMNLN 

       370        380        390        400        410        420 
GDYLSDAAAA VVGGLGMGPG ANIGDSAAIF EATHGTAPKH AGLDRINPGS VILSGVMMLE 

       430        440        450        460        470 
FMGWQEAADL IKKGIGAAIA NREVTYDLAR LMEPKVDKPL KCSEFAQAIV SHFDD 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X83563 Genomic DNA. Translation: CAA58549.1.
BA000022 Genomic DNA. Translation: BAA16835.1.
PIRS74684.
RefSeqNP_440155.1. NC_000911.1.
YP_005650212.1. NC_017277.1.
YP_007450038.1. NC_020286.1.

3D structure databases

ProteinModelPortalP80046.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP80046. 2 interactions.
STRING1148.slr1289.

Proteomic databases

PaxDbP80046.
PRIDEP80046.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAA16835; BAA16835; BAA16835.
GeneID12255899.
14615683.
953454.
KEGGsyn:slr1289.
syy:SYNGTS_0259.
syz:MYO_12610.
PATRIC23837428. VBISynSp132158_0286.

Phylogenomic databases

eggNOGCOG0538.
HOGENOMHOG000021113.
KOK00031.
OrthoDBEOG6SNDTP.
PhylomeDBP80046.
ProtClustDBPRK07362.

Family and domain databases

Gene3D3.40.718.10. 2 hits.
InterProIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004439. Isocitrate_DH_NADP_dimer_prok.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERPTHR11835. PTHR11835. 1 hit.
PfamPF00180. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsTIGR00183. prok_nadp_idh. 1 hit.
PROSITEPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameIDH_SYNY3
AccessionPrimary (citable) accession number: P80046
Secondary accession number(s): P72820
Entry history
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: November 1, 1997
Last modified: April 16, 2014
This is version 100 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Synechocystis PCC 6803

Synechocystis (strain PCC 6803): entries and gene names

SIMILARITY comments

Index of protein domains and families