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Protein

Dimethylglycine dehydrogenase, mitochondrial

Gene

Dmgdh

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the demethylation of N,N-dimethylglycine to sarcosine. Also has activity with sarcosine in vitro.1 Publication

Catalytic activityi

N,N-dimethylglycine + electron-transfer flavoprotein + H2O = sarcosine + formaldehyde + reduced electron-transfer flavoprotein.2 Publications

Cofactori

FAD2 PublicationsNote: Binds 1 FAD covalently per monomer.2 Publications

Kineticsi

kcat is 1.43-1.48 sec1-.1 Publication
  1. KM=760 µM for N,N-dimethylglycine for precursor enzyme1 Publication
  2. KM=580 µM for N,N-dimethylglycine for mature enzyme1 Publication

    Pathwayi: betaine degradation

    This protein is involved in step 2 of the subpathway that synthesizes sarcosine from betaine.
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. Betaine--homocysteine S-methyltransferase 1 (Bhmt)
    2. Dimethylglycine dehydrogenase, mitochondrial (Dmgdh)
    This subpathway is part of the pathway betaine degradation, which is itself part of Amine and polyamine degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes sarcosine from betaine, the pathway betaine degradation and in Amine and polyamine degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei212FAD; via amide nitrogen and carbonyl oxygenCombined sources1 Publication1
    Binding sitei244FADCombined sources1 Publication1
    Binding sitei669TetrahydrofolateCombined sources1 Publication1
    Binding sitei737TetrahydrofolateCombined sources1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi52 – 53FADCombined sources1 Publication2
    Nucleotide bindingi73 – 74FADCombined sources1 Publication2
    Nucleotide bindingi80 – 88FADCombined sources1 Publication9
    Nucleotide bindingi390 – 395FADCombined sources1 Publication6

    GO - Molecular functioni

    • dimethylglycine dehydrogenase activity Source: RGD
    • flavin adenine dinucleotide binding Source: RGD
    • folic acid binding Source: RGD

    GO - Biological processi

    • amino-acid betaine catabolic process Source: UniProtKB-UniPathway
    • choline catabolic process Source: RGD
    • choline metabolic process Source: RGD
    • tetrahydrofolate interconversion Source: RGD

    Keywordsi

    Molecular functionOxidoreductase
    LigandFAD, Flavoprotein

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16117.
    BRENDAi1.5.8.4. 5301.
    UniPathwayiUPA00291; UER00433.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Dimethylglycine dehydrogenase, mitochondrial (EC:1.5.8.42 Publications)
    Alternative name(s):
    ME2GLYDH
    Gene namesi
    Name:Dmgdh
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
    Proteomesi
    • UP000002494 Componenti: Unplaced

    Organism-specific databases

    RGDi620453. Dmgdh.

    Subcellular locationi

    GO - Cellular componenti

    • mitochondrial matrix Source: GO_Central
    • mitochondrion Source: RGD

    Keywords - Cellular componenti

    Mitochondrion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 43MitochondrionSequence analysisAdd BLAST43
    ChainiPRO_000001076944 – 857Dimethylglycine dehydrogenase, mitochondrialAdd BLAST814

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei84Tele-8alpha-FAD histidineCombined sources2 Publications1
    Modified residuei107N6-acetyllysineBy similarity1
    Modified residuei141N6-acetyllysine; alternateBy similarity1
    Modified residuei141N6-succinyllysine; alternateBy similarity1
    Modified residuei161N6-acetyllysineBy similarity1
    Modified residuei216N6-acetyllysineBy similarity1
    Modified residuei310N6-succinyllysineBy similarity1
    Modified residuei312N6-succinyllysineBy similarity1
    Modified residuei328N6-acetyllysineBy similarity1
    Modified residuei353N6-acetyllysineBy similarity1
    Modified residuei427N6-acetyllysine; alternateBy similarity1
    Modified residuei427N6-succinyllysine; alternateBy similarity1
    Modified residuei469N6-acetyllysine; alternateBy similarity1
    Modified residuei469N6-succinyllysine; alternateBy similarity1
    Modified residuei516N6-acetyllysine; alternateBy similarity1
    Modified residuei516N6-succinyllysine; alternateBy similarity1
    Modified residuei648N6-acetyllysine; alternateBy similarity1
    Modified residuei648N6-succinyllysine; alternateBy similarity1
    Modified residuei757N6-acetyllysineBy similarity1
    Modified residuei786N6-acetyllysine; alternateBy similarity1
    Modified residuei786N6-succinyllysine; alternateBy similarity1
    Modified residuei788N6-succinyllysineBy similarity1

    Keywords - PTMi

    Acetylation

    Proteomic databases

    PaxDbiQ63342.
    PRIDEiQ63342.

    PTM databases

    iPTMnetiQ63342.
    PhosphoSitePlusiQ63342.

    Interactioni

    Protein-protein interaction databases

    STRINGi10116.ENSRNOP00000030481.

    Structurei

    Secondary structure

    1857
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi41 – 48Combined sources8
    Helixi52 – 63Combined sources12
    Beta strandi68 – 72Combined sources5
    Beta strandi74 – 76Combined sources3
    Turni77 – 81Combined sources5
    Helixi82 – 84Combined sources3
    Beta strandi94 – 96Combined sources3
    Helixi98 – 116Combined sources19
    Beta strandi127 – 131Combined sources5
    Helixi134 – 147Combined sources14
    Beta strandi150 – 152Combined sources3
    Beta strandi155 – 157Combined sources3
    Helixi159 – 165Combined sources7
    Beta strandi176 – 180Combined sources5
    Helixi188 – 201Combined sources14
    Beta strandi205 – 209Combined sources5
    Beta strandi214 – 217Combined sources4
    Beta strandi223 – 227Combined sources5
    Beta strandi230 – 239Combined sources10
    Helixi242 – 244Combined sources3
    Helixi245 – 250Combined sources6
    Turni251 – 253Combined sources3
    Beta strandi259 – 268Combined sources10
    Helixi272 – 275Combined sources4
    Beta strandi283 – 286Combined sources4
    Turni287 – 290Combined sources4
    Beta strandi291 – 296Combined sources6
    Beta strandi299 – 304Combined sources6
    Turni308 – 310Combined sources3
    Helixi315 – 320Combined sources6
    Helixi336 – 338Combined sources3
    Helixi339 – 348Combined sources10
    Helixi350 – 353Combined sources4
    Beta strandi357 – 367Combined sources11
    Beta strandi374 – 377Combined sources4
    Beta strandi384 – 388Combined sources5
    Helixi393 – 410Combined sources18
    Helixi418 – 420Combined sources3
    Helixi422 – 424Combined sources3
    Helixi431 – 443Combined sources13
    Turni444 – 446Combined sources3
    Helixi467 – 471Combined sources5
    Turni472 – 474Combined sources3
    Beta strandi475 – 480Combined sources6
    Beta strandi483 – 489Combined sources7
    Helixi508 – 520Combined sources13
    Beta strandi523 – 526Combined sources4
    Beta strandi530 – 537Combined sources8
    Helixi540 – 547Combined sources8
    Beta strandi548 – 550Combined sources3
    Beta strandi557 – 564Combined sources8
    Beta strandi570 – 580Combined sources11
    Beta strandi583 – 588Combined sources6
    Helixi590 – 592Combined sources3
    Helixi593 – 606Combined sources14
    Beta strandi612 – 615Combined sources4
    Turni617 – 619Combined sources3
    Beta strandi620 – 627Combined sources8
    Helixi630 – 635Combined sources6
    Turni644 – 646Combined sources3
    Beta strandi651 – 657Combined sources7
    Beta strandi660 – 665Combined sources6
    Beta strandi671 – 680Combined sources10
    Helixi681 – 683Combined sources3
    Helixi684 – 694Combined sources11
    Turni695 – 699Combined sources5
    Helixi705 – 714Combined sources10
    Turni720 – 722Combined sources3
    Turni730 – 734Combined sources5
    Helixi736 – 738Combined sources3
    Beta strandi743 – 745Combined sources3
    Helixi750 – 759Combined sources10
    Beta strandi762 – 770Combined sources9
    Beta strandi782 – 785Combined sources4
    Beta strandi788 – 799Combined sources12
    Turni800 – 803Combined sources4
    Beta strandi804 – 812Combined sources9
    Helixi813 – 815Combined sources3
    Beta strandi821 – 826Combined sources6
    Beta strandi829 – 835Combined sources7
    Helixi844 – 857Combined sources14

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4P9SX-ray2.32A/B22-857[»]
    4PAAX-ray2.26A/B22-857[»]
    4PABX-ray1.85A/B2-857[»]
    ProteinModelPortaliQ63342.
    SMRiQ63342.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni573 – 575Tetrahydrofolate bindingCombined sources1 Publication3
    Regioni676 – 678Tetrahydrofolate bindingCombined sources1 Publication3

    Sequence similaritiesi

    Belongs to the GcvT family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG2844. Eukaryota.
    COG0404. LUCA.
    COG0665. LUCA.
    HOGENOMiHOG000251716.
    HOVERGENiHBG081945.
    InParanoidiQ63342.
    PhylomeDBiQ63342.

    Family and domain databases

    Gene3Di2.40.30.110. 1 hit.
    InterProiView protein in InterPro
    IPR006076. FAD-dep_OxRdtase.
    IPR023753. FAD/NAD-binding_dom.
    IPR032503. FAO_M.
    IPR013977. GCV_T_C.
    IPR006222. GCV_T_N.
    IPR029043. GcvT/YgfZ_C.
    PfamiView protein in Pfam
    PF01266. DAO. 1 hit.
    PF16350. FAO_M. 1 hit.
    PF01571. GCV_T. 1 hit.
    PF08669. GCV_T_C. 1 hit.
    SUPFAMiSSF101790. SSF101790. 1 hit.
    SSF51905. SSF51905. 2 hits.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q63342-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLRLGALRLR GLALRSSQGR PSSAGLREGQ ESPPSPPEWK DRAETVIIGG
    60 70 80 90 100
    GCVGVSLAYH LAKAGMRDVV LLEKSELTAG STWHAAGLTT YFHPGINLKK
    110 120 130 140 150
    IHYDSIKLYE RLEEETGQVV GFHQPGSIRL ATTPERVDEF KYQMTRTNWH
    160 170 180 190 200
    ATEQYIIEPE KIHELFPLLN MDKILAGLYN PGDGHIDPYS LTMALATGAR
    210 220 230 240 250
    KYGVLLKYPA PVTSLKPRPD GTWDVETPQG SVRANRIVNA AGFWAREVGK
    260 270 280 290 300
    MIGLDHPLIP VQHQYVVTST IPEVKALKRE LPVLRDLEGS YYLRQERDGL
    310 320 330 340 350
    LFGPYESQEK MKLQASWVAH GVPPGFGKEL FESDLDRITE HVEAAMEMVP
    360 370 380 390 400
    VLKKADIINI VNGPITYSPD ILPMVGPHQG VRNYWVAIGF GYGIIHAGGV
    410 420 430 440 450
    GKYLSDWILH GEPPFDLIEL DPNRYGKWTT TQYTEAKARE SYGFNNIVGY
    460 470 480 490 500
    PKEERFAGRP TQRVSGLYKI LESKCSMGFH AGWEQPHWFY KPGQDTQYRP
    510 520 530 540 550
    SFRRTNWFRP VGSEYKQVMQ RVGVIDLSPF GKFNIKGQDS TQLLDHLCAN
    560 570 580 590 600
    VIPKVGFTNI SHMLTPRGRV YAELTVSHQS PGEFLLITGS GSELHDLRWI
    610 620 630 640 650
    EEAAVRGGYD VEIRNITDEL GVLGVAGPYA RRVLQKLTSE DLSDDVFKFL
    660 670 680 690 700
    QTKSLKISDI PVTAIRISYT GELGWELYHR REDSAALYER IMNAGQEEGI
    710 720 730 740 750
    DNFGTYALNA LRLEKAFRAW GSEMNCDTNP LEAGLDYFIK LNKPADFTGK
    760 770 780 790 800
    QALKQIKAKG LKRRLVCLTL ATDDVDPEGN ESVWYKGKVI GNTTSGSYSY
    810 820 830 840 850
    SIQKSLAFAY VPVELSEVGQ QVEVELLGKN YPATIIQEPL VLTEPTRTRL

    QKDGRKS
    Length:857
    Mass (Da):96,048
    Last modified:November 1, 1996 - v1
    Checksum:iA6FED946B8AB9878
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X55995 mRNA. Translation: CAA39468.1.
    PIRiS16133.
    UniGeneiRn.3646.

    Genome annotation databases

    UCSCiRGD:620453. rat.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X55995 mRNA. Translation: CAA39468.1.
    PIRiS16133.
    UniGeneiRn.3646.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4P9SX-ray2.32A/B22-857[»]
    4PAAX-ray2.26A/B22-857[»]
    4PABX-ray1.85A/B2-857[»]
    ProteinModelPortaliQ63342.
    SMRiQ63342.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi10116.ENSRNOP00000030481.

    PTM databases

    iPTMnetiQ63342.
    PhosphoSitePlusiQ63342.

    Proteomic databases

    PaxDbiQ63342.
    PRIDEiQ63342.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    UCSCiRGD:620453. rat.

    Organism-specific databases

    RGDi620453. Dmgdh.

    Phylogenomic databases

    eggNOGiKOG2844. Eukaryota.
    COG0404. LUCA.
    COG0665. LUCA.
    HOGENOMiHOG000251716.
    HOVERGENiHBG081945.
    InParanoidiQ63342.
    PhylomeDBiQ63342.

    Enzyme and pathway databases

    UniPathwayiUPA00291; UER00433.
    BioCyciMetaCyc:MONOMER-16117.
    BRENDAi1.5.8.4. 5301.

    Miscellaneous databases

    PROiPR:Q63342.

    Family and domain databases

    Gene3Di2.40.30.110. 1 hit.
    InterProiView protein in InterPro
    IPR006076. FAD-dep_OxRdtase.
    IPR023753. FAD/NAD-binding_dom.
    IPR032503. FAO_M.
    IPR013977. GCV_T_C.
    IPR006222. GCV_T_N.
    IPR029043. GcvT/YgfZ_C.
    PfamiView protein in Pfam
    PF01266. DAO. 1 hit.
    PF16350. FAO_M. 1 hit.
    PF01571. GCV_T. 1 hit.
    PF08669. GCV_T_C. 1 hit.
    SUPFAMiSSF101790. SSF101790. 1 hit.
    SSF51905. SSF51905. 2 hits.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiM2GD_RAT
    AccessioniPrimary (citable) accession number: Q63342
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1996
    Last modified: May 10, 2017
    This is version 124 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

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

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.