Dmgdh dimethylglycine dehydrogenase [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Dmgdhprovided by RGD
Official Full Name: dimethylglycine dehydrogenaseprovided by RGD
Primary source: RGD:620453
See related: Ensembl: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. Located in mitochondrion. Orthologous to human DMGDH (dimethylglycine dehydrogenase). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Liver (RPKM 416.1) and Kidney (RPKM 254.1) See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

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
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info

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

Go to the top of the page Help

Preferred Names: dimethylglycine dehydrogenase, mitochondrial

NP_620802.2

EC 1.5.8.4

XP_038957650.1

EC 1.5.8.4

XP_038957651.1

EC 1.5.8.4

XP_063137364.1

EC 1.5.8.4

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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)

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, ENSRNOT00000032783.5

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

NC_086020.1 Reference GRCr8

Range

26647540..26722496

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063281294.1 → XP_063137364.1 dimethylglycine dehydrogenase, mitochondrial isoform X3
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
XM_039101722.2 → XP_038957650.1 dimethylglycine dehydrogenase, mitochondrial isoform X1

UniProtKB/Swiss-Prot

Q63342

UniProtKB/TrEMBL

A0A0G2K9Y2

Related

ENSRNOP00000075177.1

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