Isocitrate dehydrogenase [NADP] - Synechocystis sp. (strain PCC 6803)

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Reviewed, UniProtKB/Swiss-Prot P80046 (IDH_SYNY3)

Last modified November 25, 2008. Version 61. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Isocitrate dehydrogenase [NADP]
      Short name=IDH
    EC=1.1.1.42
Alternative name(s):
    Oxalosuccinate decarboxylase
    NADP(+)-specific ICDH
    IDP

Gene names

Name:	icd
Ordered Locus Names:	slr1289

Organism

Synechocystis sp. (strain PCC 6803) [Complete proteome] [HAMAP]

Taxonomic identifier

1148 [NCBI]

Taxonomic lineage

Bacteria › Cyanobacteria › Chroococcales › Synechocystis

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Protein attributes

Sequence length	475 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Catalytic activity	Isocitrate + NADP(+) = 2-oxoglutarate + CO(2) + NADPH. Oxalosuccinate + NADP(+) = 2-oxoglutarate + CO(2) + 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.

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Ontologies

Keywords
Biological process	Glyoxylate bypass Tricarboxylic acid cycle
Cellular component	Cytoplasm
Ligand	Magnesium Manganese Metal-binding NADP
Molecular function	Oxidoreductase
PTM	Phosphoprotein
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	glyoxylate cycle Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW tricarboxylic acid cycle Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	isocitrate dehydrogenase (NADP+) activity Inferred from electronic annotation. Source: InterPro magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 475

475

Isocitrate dehydrogenase [NADP]

PRO_0000083570

Regions

Nucleotide binding

394 – 400

NADP By similarity

Sites

Metal binding

362

Magnesium or manganese By similarity

Binding site

104

NADP By similarity

Binding site

113

Substrate By similarity

Binding site

115

Substrate By similarity

Binding site

119

Substrate By similarity

Binding site

129

Substrate By similarity

Binding site

153

Substrate By similarity

Binding site

407

NADP; via amide nitrogen and carbonyl oxygen By similarity

Binding site

446

NADP By similarity

Binding site

450

NADP By similarity

Site

160

Critical for catalysis By similarity

Site

237

Critical for catalysis By similarity

Amino acid modifications

Modified residue

113

Phosphoserine By similarity

Experimental info

Sequence conflict

60 – 62

REE → ERK in BAA16835. Ref.2

Sequence conflict

83 – 84

IF → YL in BAA16835. Ref.2

Sequence conflict

223

K → L in BAA16835. Ref.2

Sequence conflict

247

P → A in BAA16835. Ref.2

Sequence conflict

273

C → L in BAA16835. Ref.2

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Sequences

Sequence

Length

Mass (Da)

Tools

P80046-1 [UniParc].

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

475

52,275

        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

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References

	« Hide 'large scale' referencesShow '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: 8763933] [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. Tabata S. DNA Res. 3:109-136(1996) [PubMed: 8905231] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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: 1730247] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-20.

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Cross-references

Sequence databases
	X83563 Genomic DNA. Translation: CAA58549.1. BA000022 Genomic DNA. Translation: BAA16835.1.
PIR	S74684.
RefSeq	NP_440155.1.
3D structure databases
HSSP	HSSP built from PDB template 1PB1 based on UniProtKB P08200.
ModBase	Search...
Protein-protein interaction databases
IntAct	P80046.
Genome annotation databases
GeneID	953454.
GenomeReviews	Gene locus slr1289 in contig BA000022_GR.
KEGG	syn:slr1289.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	P80046.
Enzyme and pathway databases
BioCyc	SSP1148:SLR1289-MON.
Family and domain databases
InterPro	IPR004439. IsoCit_DHase_NADP_prok. IPR001804. IsoCit_IM_DHase. [Graphical view]
Gene3D	G3DSA:3.40.718.10. IDH_IMDH. 1 hit.
PANTHER	PTHR11835. IDH_IMDH_dimeric. 1 hit. PTHR11835:SF1. NADP_IDH_prok. 1 hit.
Pfam	PF00180. Iso_dh. 1 hit. [Graphical view]
TIGRFAMs	TIGR00183. prok_nadp_idh. 1 hit.
PROSITE	PS00470. IDH_IMDH. 1 hit. [Graphical view]
ProtoNet	Search...

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Entry information

Entry name

IDH_SYNY3

Accession

Primary (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:	November 25, 2008
This is version 61 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

SIMILARITY comments

Index of protein domains and families

Synechocystis PCC 6803

Synechocystis (strain PCC 6803): entries and gene names

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Keywords

Gene Ontology (GO)

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents