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UniProtKB - P41939 (IDHC_YEAST)

Entry version 162 (08 May 2019)
Sequence version 2 (01 Oct 1996)
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Protein

Isocitrate dehydrogenase [NADP] cytoplasmic

Gene

IDP2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

May function in the production of NADPH for fatty acid and sterol synthesis.

Miscellaneous

Present with 2620 molecules/cell in log phase SD medium.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg2+ or Mn2+ ion per subunit.By similarity

<p>This subsection of the ‘Function’ section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

By catabolite repression.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei77SubstrateBy similarity1
Binding sitei82NADPBy similarity1
Binding sitei109SubstrateBy similarity1
Binding sitei132SubstrateBy similarity1
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei139Critical for catalysisBy similarity1
Sitei212Critical for catalysisBy similarity1
<p>This subsection of the ‘Function’ section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi252Magnesium or manganeseBy similarity1
Binding sitei260NADPBy similarity1
Metal bindingi275Magnesium or manganeseBy similarity1
Binding sitei328NADP; via amide nitrogen and carbonyl oxygenBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi75 – 77NADPBy similarity3
Nucleotide bindingi310 – 315NADPBy similarity6

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

  • isocitrate dehydrogenase (NADP+) activity Source: SGD
  • magnesium ion binding Source: InterPro
  • NAD binding Source: InterPro
  • protein homodimerization activity Source: GO_Central
View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionOxidoreductase
Biological processGlyoxylate bypass, Tricarboxylic acid cycle
LigandMagnesium, Manganese, Metal-binding, NADP

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		MetaCyc:YLR174W-MONOMER
YEAST:YLR174W-MONOMER

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		1.1.1.42 984

SABIO-RK: Biochemical Reaction Kinetics Database

More...SABIO-RKi		P41939

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Isocitrate dehydrogenase [NADP] cytoplasmic (EC:1.1.1.42)
Short name:
IDH
Alternative name(s):
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:IDP2
Ordered Locus Names:YLR174W
ORF Names:L9470.12
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome XII

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...EuPathDBi		FungiDB:YLR174W

Saccharomyces Genome Database

More...SGDi		S000004164 IDP2

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000835871 – 412Isocitrate dehydrogenase [NADP] cytoplasmicAdd BLAST412

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

The N-terminus is blocked.

Proteomic databases

MaxQB - The MaxQuant DataBase

More...MaxQBi		P41939

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P41939

PRoteomics IDEntifications database

More...PRIDEi		P41939

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		31445, 93 interactors

Database of interacting proteins

More...DIPi		DIP-4252N

Protein interaction database and analysis system

More...IntActi		P41939, 2 interactors

STRING: functional protein association networks

More...STRINGi		4932.YLR174W

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P41939

Database of comparative protein structure models

More...ModBasei		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni94 – 100Substrate bindingBy similarity7

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the isocitrate and isopropylmalate dehydrogenases family.Curated

Phylogenomic databases

Ensembl GeneTree

More...GeneTreei		ENSGT00390000012547

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000019858

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P41939

KEGG Orthology (KO)

More...KOi		K00031

Identification of Orthologs from Complete Genome Data

More...OMAi		FEKHYKP

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR019818 IsoCit/isopropylmalate_DH_CS
IPR004790 Isocitrate_DH_NADP
IPR024084 IsoPropMal-DH-like_dom

The PANTHER Classification System

More...PANTHERi		PTHR11822 PTHR11822, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00180 Iso_dh, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF000108 IDH_NADP, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM01329 Iso_dh, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00127 nadp_idh_euk, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00470 IDH_IMDH, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P41939-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTKIKVANPI VEMDGDEQTR IIWHLIRDKL VLPYLDVDLK YYDLSVEYRD 
        60         70         80         90        100
QTNDQVTVDS ATATLKYGVA VKCATITPDE ARVEEFHLKK MWKSPNGTIR 
       110        120        130        140        150
NILGGTVFRE PIIIPRIPRL VPQWEKPIII GRHAFGDQYK ATDVIVPEEG 
       160        170        180        190        200
ELRLVYKSKS GTHDVDLKVF DYPEHGGVAM MMYNTTDSIE GFAKASFELA 
       210        220        230        240        250
IERKLPLYST TKNTILKKYD GKFKDVFEAM YARSYKEKFE SLGIWYEHRL 
       260        270        280        290        300
IDDMVAQMLK SKGGYIIAMK NYDGDVESDI VAQGFGSLGL MTSVLITPDG 
       310        320        330        340        350
KTFESEAAHG TVTRHFRQHQ QGKETSTNSI ASIFAWTRGI IQRGKLDNTP 
       360        370        380        390        400
DVVKFGQILE SATVNTVQED GIMTKDLALI LGKSERSAYV TTEEFIDAVE 
       410 
SRLKKEFEAA AL
Length:412
Mass (Da):46,562
Last modified:October 1, 1996 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i83EB54CC56A29857
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti24 – 27HLIR → SFNQ in AAA64516 (PubMed:8068643).Curated4
Sequence conflicti68G → R in AAA64516 (PubMed:8068643).Curated1
Sequence conflicti185T → N in AAA64516 (PubMed:8068643).Curated1
Sequence conflicti232 – 239ARSYKEKF → LEVIKRSL in AAA64516 (PubMed:8068643).Curated8
Sequence conflicti267I → M in AAA64516 (PubMed:8068643).Curated1
Sequence conflicti306 – 307EA → DR in AAA64516 (PubMed:8068643).Curated2
Sequence conflicti316 – 323FRQHQQGK → LTDYDKGR in AAA64516 (PubMed:8068643).Curated8

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
L26312 Genomic DNA Translation: AAA64516.1
U17246 Genomic DNA Translation: AAB67464.1
BK006945 Genomic DNA Translation: DAA09494.1

Protein sequence database of the Protein Information Resource

More...PIRi		S51419

NCBI Reference Sequences

More...RefSeqi		NP_013275.1, NM_001182061.1

Genome annotation databases

Ensembl fungal genome annotation project

More...EnsemblFungii		YLR174W_mRNA; YLR174W_mRNA; YLR174W

Database of genes from NCBI RefSeq genomes

More...GeneIDi		850871

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		sce:YLR174W

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L26312 Genomic DNA Translation: AAA64516.1
U17246 Genomic DNA Translation: AAB67464.1
BK006945 Genomic DNA Translation: DAA09494.1
PIRiS51419
RefSeqiNP_013275.1, NM_001182061.1

3D structure databases

SMRiP41939
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31445, 93 interactors
DIPiDIP-4252N
IntActiP41939, 2 interactors
STRINGi4932.YLR174W

Proteomic databases

MaxQBiP41939
PaxDbiP41939
PRIDEiP41939

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR174W_mRNA; YLR174W_mRNA; YLR174W
GeneIDi850871
KEGGisce:YLR174W

Organism-specific databases

EuPathDBiFungiDB:YLR174W
SGDiS000004164 IDP2

Phylogenomic databases

GeneTreeiENSGT00390000012547
HOGENOMiHOG000019858
InParanoidiP41939
KOiK00031
OMAiFEKHYKP

Enzyme and pathway databases

BioCyciMetaCyc:YLR174W-MONOMER
YEAST:YLR174W-MONOMER
BRENDAi1.1.1.42 984
SABIO-RKiP41939

Miscellaneous databases

Protein Ontology

More...PROi		PR:P41939

Family and domain databases

InterProiView protein in InterPro
IPR019818 IsoCit/isopropylmalate_DH_CS
IPR004790 Isocitrate_DH_NADP
IPR024084 IsoPropMal-DH-like_dom
PANTHERiPTHR11822 PTHR11822, 1 hit
PfamiView protein in Pfam
PF00180 Iso_dh, 1 hit
PIRSFiPIRSF000108 IDH_NADP, 1 hit
SMARTiView protein in SMART
SM01329 Iso_dh, 1 hit
TIGRFAMsiTIGR00127 nadp_idh_euk, 1 hit
PROSITEiView protein in PROSITE
PS00470 IDH_IMDH, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiIDHC_YEAST
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P41939
Secondary accession number(s): D6VYH8
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: October 1, 1996
Last modified: May 8, 2019
This is version 162 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. Yeast chromosome XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names
  3. SIMILARITY comments
    Index of protein domains and families
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