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UniProtKB - P28834 (IDH1_YEAST)

Entry version 171 (08 May 2019)
Sequence version 2 (01 Jul 1993)
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Protein

Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial

Gene

IDH1

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

Performs an essential role in the oxidative function of the citric acid cycle. Also binds RNA; specifically to the 5'-untranslated leaders of mitochondrial mRNAs.

Miscellaneous

Present with 10500 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

Allosterically regulated by several compounds including AMP, NAD+, and citrate.

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 sitei109SubstrateBy similarity1
Binding sitei140SubstrateBy 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>Sitei194Critical 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 bindingi228Magnesium or manganeseBy similarity1
Binding sitei228SubstrateBy similarity1

<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

View the complete GO annotation on QuickGO ...

GO - Biological processi

  • glutamate biosynthetic process Source: SGD
  • isocitrate metabolic process Source: SGD
  • tricarboxylic acid cycle Source: SGD
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 functionAllosteric enzyme, Oxidoreductase, RNA-binding
Biological processTricarboxylic acid cycle
LigandMagnesium, Manganese, Metal-binding, NAD

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		MetaCyc:YNL037C-MONOMER
YEAST:YNL037C-MONOMER

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		1.1.1.41 984

Reactome - a knowledgebase of biological pathways and processes

More...Reactomei		R-SCE-71403 Citric acid cycle (TCA cycle)

Protein family/group databases

MoonProt database of moonlighting proteins

More...MoonProti		P28834

<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 [NAD] subunit 1, mitochondrial (EC:1.1.1.41)
Alternative name(s):
Isocitric dehydrogenase
NAD(+)-specific ICDH
<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:IDH1
Ordered Locus Names:YNL037C
ORF Names:N2690
<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 XIV

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...EuPathDBi		FungiDB:YNL037C

Saccharomyces Genome Database

More...SGDi		S000004982 IDH1

<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

Mitochondrion

<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 transit peptide.<p><a href='/help/transit' target='_top'>More...</a></p>Transit peptidei1 – 11Mitochondrion1 PublicationAdd BLAST11
<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_000001443112 – 360Isocitrate dehydrogenase [NAD] subunit 1, mitochondrialAdd BLAST349

Proteomic databases

MaxQB - The MaxQuant DataBase

More...MaxQBi		P28834

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

More...PaxDbi		P28834

PRoteomics IDEntifications database

More...PRIDEi		P28834

<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

Octamer of two non-identical subunits IDH1 and IDH2.

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

WithEntry#Exp.IntActNotes
IDH2P282416EBI-8878,EBI-8883

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		35787, 259 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...ComplexPortali		CPX-558 Mitochondrial isocitrate dehydrogenase complex (NAD+)

Database of interacting proteins

More...DIPi		DIP-4376N

Protein interaction database and analysis system

More...IntActi		P28834, 26 interactors

Molecular INTeraction database

More...MINTi		P28834

STRING: functional protein association networks

More...STRINGi		4932.YNL037C

<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

Secondary structure

1360
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BLVX-ray3.20A/C/E/G12-360[»]
3BLWX-ray4.30A/C/E/G/I/K/M/O12-360[»]
3BLXX-ray2.70A/C/E/G/I/K/M/O12-360[»]

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

More...SMRi		P28834

Database of comparative protein structure models

More...ModBasei		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P28834

<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

<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

Keywords - Domaini

Transit peptide

Phylogenomic databases

Ensembl GeneTree

More...GeneTreei		ENSGT00950000182989

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000021113

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P28834

KEGG Orthology (KO)

More...KOi		K00030

Identification of Orthologs from Complete Genome Data

More...OMAi		KVRTADM

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR019818 IsoCit/isopropylmalate_DH_CS
IPR004434 Isocitrate_DH_NAD
IPR024084 IsoPropMal-DH-like_dom

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00180 Iso_dh, 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		TIGR00175 mito_nad_idh, 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.

<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 in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P28834-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLNRTIAKRT LATAAQAERT LPKKYGGRFT VTLIPGDGVG KEITDSVRTI 
        60         70         80         90        100
FEAENIPIDW ETINIKQTDH KEGVYEAVES LKRNKIGLKG LWHTPADQTG 
       110        120        130        140        150
HGSLNVALRK QLDIYANVAL FKSLKGVKTR IPDIDLIVIR ENTEGEFSGL 
       160        170        180        190        200
EHESVPGVVE SLKVMTRPKT ERIARFAFDF AKKYNRKSVT AVHKANIMKL 
       210        220        230        240        250
GDGLFRNIIT EIGQKEYPDI DVSSIIVDNA SMQAVAKPHQ FDVLVTPSMY 
       260        270        280        290        300
GTILGNIGAA LIGGPGLVAG ANFGRDYAVF EPGSRHVGLD IKGQNVANPT 
       310        320        330        340        350
AMILSSTLML NHLGLNEYAT RISKAVHETI AEGKHTTRDI GGSSSTTDFT 
       360
NEIINKLSTM
Length:360
Mass (Da):39,324
Last modified:July 1, 1993 - 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:i0932E7B3CD685240
GO

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
M95203 Genomic DNA Translation: AAA34711.1
Z71313 Genomic DNA Translation: CAA95904.1
BK006947 Genomic DNA Translation: DAA10508.1

Protein sequence database of the Protein Information Resource

More...PIRi		S31264

NCBI Reference Sequences

More...RefSeqi		NP_014361.1, NM_001182876.1

Genome annotation databases

Ensembl fungal genome annotation project

More...EnsemblFungii		YNL037C_mRNA; YNL037C_mRNA; YNL037C

Database of genes from NCBI RefSeq genomes

More...GeneIDi		855691

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		sce:YNL037C

<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
M95203 Genomic DNA Translation: AAA34711.1
Z71313 Genomic DNA Translation: CAA95904.1
BK006947 Genomic DNA Translation: DAA10508.1
PIRiS31264
RefSeqiNP_014361.1, NM_001182876.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BLVX-ray3.20A/C/E/G12-360[»]
3BLWX-ray4.30A/C/E/G/I/K/M/O12-360[»]
3BLXX-ray2.70A/C/E/G/I/K/M/O12-360[»]
SMRiP28834
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35787, 259 interactors
ComplexPortaliCPX-558 Mitochondrial isocitrate dehydrogenase complex (NAD+)
DIPiDIP-4376N
IntActiP28834, 26 interactors
MINTiP28834
STRINGi4932.YNL037C

Protein family/group databases

MoonProtiP28834

Proteomic databases

MaxQBiP28834
PaxDbiP28834
PRIDEiP28834

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL037C_mRNA; YNL037C_mRNA; YNL037C
GeneIDi855691
KEGGisce:YNL037C

Organism-specific databases

EuPathDBiFungiDB:YNL037C
SGDiS000004982 IDH1

Phylogenomic databases

GeneTreeiENSGT00950000182989
HOGENOMiHOG000021113
InParanoidiP28834
KOiK00030
OMAiKVRTADM

Enzyme and pathway databases

BioCyciMetaCyc:YNL037C-MONOMER
YEAST:YNL037C-MONOMER
BRENDAi1.1.1.41 984
ReactomeiR-SCE-71403 Citric acid cycle (TCA cycle)

Miscellaneous databases

EvolutionaryTraceiP28834

Protein Ontology

More...PROi		PR:P28834

Family and domain databases

InterProiView protein in InterPro
IPR019818 IsoCit/isopropylmalate_DH_CS
IPR004434 Isocitrate_DH_NAD
IPR024084 IsoPropMal-DH-like_dom
PfamiView protein in Pfam
PF00180 Iso_dh, 1 hit
SMARTiView protein in SMART
SM01329 Iso_dh, 1 hit
TIGRFAMsiTIGR00175 mito_nad_idh, 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 nameiIDH1_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: P28834
Secondary accession number(s): D6W1E2
<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: December 1, 1992
Last sequence update: July 1, 1993
Last modified: May 8, 2019
This is version 171 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

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