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Entry version 177 (26 Feb 2020)
Sequence version 3 (23 Jan 2007)
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Protein

Malate dehydrogenase, peroxisomal

Gene

MDH3

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

Miscellaneous

Yeast contains at least 3 malate dehydrogenase isoenzymes: a mitochondrial (MDH1), a cytoplasmic (MDH2) and a peroxisomal (MDH3).
Present with 3300 molecules/cell in log phase SD medium.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> 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 sitei34NADBy similarity1
Binding sitei80SubstratePROSITE-ProRule annotation1
Binding sitei86SubstratePROSITE-ProRule annotation1
Binding sitei93NADBy similarity1
Binding sitei118SubstratePROSITE-ProRule annotation1
Binding sitei152SubstratePROSITE-ProRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei187Proton acceptorBy similarity1
Binding sitei237NADBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> 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 bindingi8 – 14NADBy similarity7
Nucleotide bindingi116 – 118NADBy similarity3

<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

GO - Biological processi

<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
LigandNAD

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:YDL078C-MONOMER

<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%5Fand%5Ftaxonomy%5Fsection">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:
Malate dehydrogenase, peroxisomal (EC:1.1.1.37)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:MDH3
Ordered Locus Names:YDL078C
ORF Names:D2468
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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 lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fmanual">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 IV

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YDL078C

Saccharomyces Genome Database

More...
SGDi
S000002236 MDH3

<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

Peroxisome

<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 <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved1 Publication
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001133422 – 343Malate dehydrogenase, peroxisomalAdd BLAST342

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P32419

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

More...
PaxDbi
P32419

PRoteomics IDEntifications database

More...
PRIDEi
P32419

2D gel databases

University College Dublin 2-DE Proteome Database

More...
UCD-2DPAGEi
P32419

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P32419

<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%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
31983, 162 interactors

Database of interacting proteins

More...
DIPi
DIP-6473N

Protein interaction database and analysis system

More...
IntActi
P32419, 7 interactors

Molecular INTeraction database

More...
MINTi
P32419

STRING: functional protein association networks

More...
STRINGi
4932.YDL078C

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
P32419 protein

<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

1343
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

More...
SMRi
P32419

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
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

<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 LDH/MDH superfamily. MDH type 1 family.Curated

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_047181_1_1_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P32419

KEGG Orthology (KO)

More...
KOi
K00026

Identification of Orthologs from Complete Genome Data

More...
OMAi
EIYQLGP

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.90.110.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001557 L-lactate/malate_DH
IPR022383 Lactate/malate_DH_C
IPR001236 Lactate/malate_DH_N
IPR015955 Lactate_DH/Glyco_Ohase_4_C
IPR001252 Malate_DH_AS
IPR010097 Malate_DH_type1
IPR036291 NAD(P)-bd_dom_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF02866 Ldh_1_C, 1 hit
PF00056 Ldh_1_N, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF000102 Lac_mal_DH, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF51735 SSF51735, 1 hit
SSF56327 SSF56327, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR01772 MDH_euk_gproteo, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00068 MDH, 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%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

P32419-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MVKVAILGAS GGVGQPLSLL LKLSPYVSEL ALYDIRAAEG IGKDLSHINT
60 70 80 90 100
NSSCVGYDKD SIENTLSNAQ VVLIPAGVPR KPGLTRDDLF KMNAGIVKSL
110 120 130 140 150
VTAVGKFAPN ARILVISNPV NSLVPIAVET LKKMGKFKPG NVMGVTNLDL
160 170 180 190 200
VRAETFLVDY LMLKNPKIGQ EQDKTTMHRK VTVIGGHSGE TIIPIITDKS
210 220 230 240 250
LVFQLDKQYE HFIHRVQFGG DEIVKAKQGA GSATLSMAFA GAKFAEEVLR
260 270 280 290 300
SFHNEKPETE SLSAFVYLPG LKNGKKAQQL VGDNSIEYFS LPIVLRNGSV
310 320 330 340
VSIDTSVLEK LSPREEQLVN TAVKELRKNI EKGKSFILDS SKL
Length:343
Mass (Da):37,186
Last modified:January 23, 2007 - v3
<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:i54725114B2CAD6A5
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 conflicti240A → R in AAA34767 (PubMed:1447211).Curated1

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
M98763 Genomic DNA Translation: AAA34767.1
Z74126 Genomic DNA Translation: CAA98644.1
BK006938 Genomic DNA Translation: DAA11781.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S67614 DEBYMP

NCBI Reference Sequences

More...
RefSeqi
NP_010205.1, NM_001180137.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YDL078C_mRNA; YDL078C; YDL078C

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
851481

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YDL078C

<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
M98763 Genomic DNA Translation: AAA34767.1
Z74126 Genomic DNA Translation: CAA98644.1
BK006938 Genomic DNA Translation: DAA11781.1
PIRiS67614 DEBYMP
RefSeqiNP_010205.1, NM_001180137.1

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
5ZI2X-ray2.00A/B1-343[»]
5ZI3X-ray2.10A/B1-343[»]
5ZI4X-ray2.10A/B1-343[»]
SMRiP32419
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi31983, 162 interactors
DIPiDIP-6473N
IntActiP32419, 7 interactors
MINTiP32419
STRINGi4932.YDL078C

PTM databases

iPTMnetiP32419

2D gel databases

UCD-2DPAGEiP32419

Proteomic databases

MaxQBiP32419
PaxDbiP32419
PRIDEiP32419

Genome annotation databases

EnsemblFungiiYDL078C_mRNA; YDL078C; YDL078C
GeneIDi851481
KEGGisce:YDL078C

Organism-specific databases

EuPathDBiFungiDB:YDL078C
SGDiS000002236 MDH3

Phylogenomic databases

HOGENOMiCLU_047181_1_1_1
InParanoidiP32419
KOiK00026
OMAiEIYQLGP

Enzyme and pathway databases

BioCyciYEAST:YDL078C-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P32419
RNActiP32419 protein

Family and domain databases

Gene3Di3.90.110.10, 1 hit
InterProiView protein in InterPro
IPR001557 L-lactate/malate_DH
IPR022383 Lactate/malate_DH_C
IPR001236 Lactate/malate_DH_N
IPR015955 Lactate_DH/Glyco_Ohase_4_C
IPR001252 Malate_DH_AS
IPR010097 Malate_DH_type1
IPR036291 NAD(P)-bd_dom_sf
PfamiView protein in Pfam
PF02866 Ldh_1_C, 1 hit
PF00056 Ldh_1_N, 1 hit
PIRSFiPIRSF000102 Lac_mal_DH, 1 hit
SUPFAMiSSF51735 SSF51735, 1 hit
SSF56327 SSF56327, 1 hit
TIGRFAMsiTIGR01772 MDH_euk_gproteo, 1 hit
PROSITEiView protein in PROSITE
PS00068 MDH, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
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 nameiMDHP_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: P32419
Secondary accession number(s): D6VRS1, Q12689
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: January 23, 2007
Last modified: February 26, 2020
This is version 177 of the entry and version 3 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, Direct protein sequencing, Reference proteome

Documents

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