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    Dmgdh dimethylglycine dehydrogenase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 245961, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Dmgdhprovided by RGD
    Official Full Name
    dimethylglycine dehydrogenaseprovided by RGD
    Primary source
    RGD:620453
    See related
    EnsemblRapid:ENSRNOG00000023588 AllianceGenome:RGD:620453
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Me2GlyDH
    Summary
    Enables dimethylglycine dehydrogenase activity; flavin adenine dinucleotide binding activity; and folic acid binding activity. Involved in tetrahydrofolate interconversion. Predicted to be active in mitochondrial matrix. Human ortholog(s) of this gene implicated in dimethylglycine dehydrogenase deficiency. Orthologous to human DMGDH (dimethylglycine dehydrogenase). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Liver (RPKM 416.1) and Kidney (RPKM 254.1) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Dmgdh in Genome Data Viewer
    Location:
    2q12
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (26647540..26722496)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (24912600..24987533)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (23289376..23370360)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene ribosomal protein L36 like 7 Neighboring gene betaine-homocysteine S-methyltransferase 2 Neighboring gene arylsulfatase B Neighboring gene small nucleolar RNA SNORA48 Neighboring gene small nucleolar RNA SNORA24

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Folate in demethylation: the crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate. Luka Z, et al. Biochem Biophys Res Commun, 2014 Jul 11. PMID 24858690, Free PMC Article
    2. Rat liver dimethylglycine dehydrogenase. Flavinylation of the enzyme in hepatocytes in primary culture and characterization of a cDNA clone. Lang H, et al. Eur J Biochem, 1991 Jun 15. PMID 1710985
    3. Identification of folate binding protein of mitochondria as dimethylglycine dehydrogenase. Wittwer AJ, et al. Proc Natl Acad Sci U S A, 1980 Aug. PMID 6159630, Free PMC Article
    4. The purified recombinant precursor of rat mitochondrial dimethylglycine dehydrogenase binds FAD via an autocatalytic reaction. Brizio C, et al. Int J Biol Macromol, 2008 Jun 1. PMID 18423846
    5. Over-expression in Escherichia coli, functional characterization and refolding of rat dimethylglycine dehydrogenase. Brizio C, et al. Protein Expr Purif, 2004 Oct. PMID 15358367

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. crystal structures of mature and precursor forms of DMGDH in presence of tetrahydrofolate; folate binding site is connected with enzyme active center via an intramolecular channel suggesting possible transfer of the intermediate imine of dimethylglycine from the active center to the bound THF where they could react producing a 5,10-methylenetetrahydrofolate
      Title: Folate in demethylation: the crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate.
    2. covalent attachment of FAD to dimethylglycine dehydrogenase apoenzyme can proceed in vitro autocatalytically
      Title: The purified recombinant precursor of rat mitochondrial dimethylglycine dehydrogenase binds FAD via an autocatalytic reaction.
    3. characterization and folding of rat dimethylglycine dehydrogenase
      Title: Over-expression in Escherichia coli, functional characterization and refolding of rat dimethylglycine dehydrogenase.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables dimethylglycine dehydrogenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables dimethylglycine dehydrogenase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables dimethylglycine dehydrogenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables dimethylglycine dehydrogenase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables dimethylglycine dehydrogenase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables flavin adenine dinucleotide binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables flavin adenine dinucleotide binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables folic acid binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in amino-acid betaine catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in choline catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in choline catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in choline catabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in choline metabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in tetrahydrofolate interconversion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in mitochondrial matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    dimethylglycine dehydrogenase, mitochondrial
    NP_620802.2
    XP_038957650.1
    XP_038957651.1
    XP_063137364.1

    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_139102.2 → NP_620802.2  dimethylglycine dehydrogenase, mitochondrial precursor

      See identical proteins and their annotated locations for NP_620802.2

      Status: VALIDATED

      Source sequence(s)
      BC085697
      UniProtKB/Swiss-Prot
      Q63342
      UniProtKB/TrEMBL
      Q5RKL4
      Related
      ENSRNOP00000030481.3, ENSRNOT00000032783.6
      Conserved Domains (6) summary
      COG0404
      Location:481 → 850
      GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
      COG0665
      Location:40 → 428
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:475 → 738
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:746 → 838
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
      pfam16350
      Location:410 → 465
      FAO_M; FAD dependent oxidoreductase central domain
      cl21454
      Location:38 → 83
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086020.1 Reference GRCr8

      Range
      26647540..26722496
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063281294.1 → XP_063137364.1  dimethylglycine dehydrogenase, mitochondrial isoform X3

      Related
      ENSRNOP00000108170.1, ENSRNOT00000132864.1

    2. XM_039101723.2 → XP_038957651.1  dimethylglycine dehydrogenase, mitochondrial isoform X2

      UniProtKB/TrEMBL
      A6I4V9
      Conserved Domains (3) summary
      COG0665
      Location:67 → 455
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:502 → 765
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam16350
      Location:437 → 492
      FAO_M; FAD dependent oxidoreductase central domain

    3. XM_039101722.2 → XP_038957650.1  dimethylglycine dehydrogenase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      Q63342
      UniProtKB/TrEMBL
      A0A0G2K9Y2
      Related
      ENSRNOP00000075177.1, ENSRNOT00000090666.3
      Conserved Domains (3) summary
      COG0404
      Location:508 → 877
      GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
      COG0665
      Location:67 → 455
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam16350
      Location:437 → 492
      FAO_M; FAD dependent oxidoreductase central domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q63342.1 GenPept UniProtKB/Swiss-Prot:Q63342

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