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MDH1 malate dehydrogenase 1 [ Homo sapiens (human) ]

Gene ID: 4190, updated on 18-Sep-2024

Summary

Official Symbol
MDH1provided by HGNC
Official Full Name
malate dehydrogenase 1provided by HGNC
Primary source
HGNC:HGNC:6970
See related
Ensembl:ENSG00000014641 MIM:154200; AllianceGenome:HGNC:6970
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KAR; MDHA; MOR2; DEE88; MDH-s; EIEE88; HEL-S-32; MGC:1375
Summary
This gene encodes an enzyme that catalyzes the NAD/NADH-dependent, reversible oxidation of malate to oxaloacetate in many metabolic pathways, including the citric acid cycle. Two main isozymes are known to exist in eukaryotic cells: one is found in the mitochondrial matrix and the other in the cytoplasm. This gene encodes the cytosolic isozyme, which plays a key role in the malate-aspartate shuttle that allows malate to pass through the mitochondrial membrane to be transformed into oxaloacetate for further cellular processes. Alternatively spliced transcript variants have been found for this gene. A recent study showed that a C-terminally extended isoform is produced by use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism, and that this isoform is localized in the peroxisomes. Pseudogenes have been identified on chromosomes X and 6. [provided by RefSeq, Feb 2016]
Expression
Broad expression in heart (RPKM 313.6), fat (RPKM 131.4) and 24 other tissues See more
Orthologs
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Genomic context

See MDH1 in Genome Data Viewer
Location:
2p15
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (63588963..63607197)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (63596617..63614818)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (63816097..63834331)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene WD repeat containing planar cell polarity effector Neighboring gene uncharacterized LOC107985769 Neighboring gene MPRA-validated peak3728 silencer Neighboring gene MTFR2 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:63550648-63551224 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:63551225-63551800 Neighboring gene NANOG hESC enhancer GRCh37_chr2:63562934-63563435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15876 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:63814776-63815296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15877 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:63841564-63842426 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:63842427-63843289 Neighboring gene PRELID1 pseudogene 6 Neighboring gene ribosomal protein S4X pseudogene 5

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables L-malate dehydrogenase (NAD+) activity EXP
Inferred from Experiment
more info
PubMed 
enables L-malate dehydrogenase (NAD+) activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables diiodophenylpyruvate reductase activity IEA
Inferred from Electronic Annotation
more info
 
enables hydroxyphenylpyruvate reductase activity IEA
Inferred from Electronic Annotation
more info
 
enables malic enzyme activity TAS
Traceable Author Statement
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in NADH metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in NADH metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in NADP metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in malate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in malate-aspartate shuttle TAS
Traceable Author Statement
more info
 
involved_in oxaloacetate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in tricarboxylic acid cycle IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
located_in centrosome IDA
Inferred from Direct Assay
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in extracellular exosome HDA PubMed 
located_in extracellular space HDA PubMed 

General protein information

Preferred Names
malate dehydrogenase, cytoplasmic; malate dehydrogenase, peroxisomal
Names
aromatic alpha-keto acid reductase
cytosolic malate dehydrogenase
diiodophenylpyruvate reductase
epididymis secretory protein Li 32
malate dehydrogenase 1, NAD (soluble)
soluble malate dehydrogenase
NP_001186040.1
NP_001186041.1
NP_001303303.1
NP_005908.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001199111.2NP_001186040.1  malate dehydrogenase, cytoplasmic isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains a different 5' terminal exon, which results in translation initiation from an alternate start codon compared to variant 1. The encoded isoform (2) is longer with a distinct N-terminus compared to isoform MDH1.
    Source sequence(s)
    AC016734, AK295931, BC001484, BI667299
    Consensus CDS
    CCDS56121.1
    UniProtKB/Swiss-Prot
    P40925
    Related
    ENSP00000410073.2, ENST00000432309.6
    Conserved Domains (2) summary
    TIGR01759
    Location:20345
    MalateDH-SF1; malate dehydrogenase
    cd01336
    Location:21346
    MDH_cytoplasmic_cytosolic; Cytoplasmic and cytosolic Malate dehydrogenases
  2. NM_001199112.2NP_001186041.1  malate dehydrogenase, cytoplasmic isoform 3

    See identical proteins and their annotated locations for NP_001186041.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' region, which results in translation initiation from an in-frame downstream start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform MDH1.
    Source sequence(s)
    AC016734, AK300719, BC001484, BI667299
    UniProtKB/TrEMBL
    B9A041
    Related
    ENSP00000386719.1, ENST00000409476.5
    Conserved Domains (1) summary
    cl21454
    Location:1239
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins
  3. NM_001316374.2NP_001303303.1  malate dehydrogenase, peroxisomal isoform MDH1x

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes two isoforms, which result from the use of alternative in-frame translation termination codons. The shorter isoform (MDH1) results from translation termination at the upstream UGA stop codon, while the longer isoform (MDH1x) results from UGA stop codon readthrough to the downstream UGA termination codon. This RefSeq represents the longer, C-terminally extended isoform (MDH1x), which is localized in the peroxisomes. As the UGA stop codon has been reported to specify several alternative amino acids (tryptophan, cysteine, arginine and serine), its location in the longer isoform is denoted by an 'X'.
    Source sequence(s)
    BC001484, CB266998
    Consensus CDS
    CCDS92766.1
    UniProtKB/TrEMBL
    A0A5K1VW95
    Related
    ENSP00000438144.3, ENST00000539945.7
    Conserved Domains (2) summary
    TIGR01759
    Location:2327
    MalateDH-SF1; malate dehydrogenase
    cd01336
    Location:3328
    MDH_cytoplasmic_cytosolic; Cytoplasmic and cytosolic Malate dehydrogenases
  4. NM_005917.4NP_005908.1  malate dehydrogenase, cytoplasmic isoform MDH1

    See identical proteins and their annotated locations for NP_005908.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes two isoforms, which result from the use of alternative in-frame translation termination codons. The shorter isoform (MDH1) results from translation termination at the upstream UGA stop codon, while the longer isoform (MDH1x) results from UGA stop codon readthrough to the downstream UGA termination codon. This RefSeq represents the shorter isoform (MDH1), which is localized in the cytosol.
    Source sequence(s)
    BC001484, CB266998
    Consensus CDS
    CCDS1874.1
    UniProtKB/Swiss-Prot
    B2R5V5, B4DUN2, B7Z3I7, F5H098, P40925, Q6I9V0
    UniProtKB/TrEMBL
    V9HWF2
    Related
    ENSP00000233114.8, ENST00000233114.13
    Conserved Domains (1) summary
    cd01336
    Location:3328
    MDH_cytoplasmic_cytosolic; Cytoplasmic and cytosolic Malate dehydrogenases

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    63588963..63607197
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    63596617..63614818
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)