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Protein

Dimethylglycine oxidase

Gene

dmg

Organism
Arthrobacter globiformis
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the oxidative demethylation of N,N-dimethylglycine to yield sarcosine, formaldehyde and hydrogen peroxide. The oxidation of dimethylglycine is coupled to the synthesis of 5,10-methylenetetrahydrofolate through an unusual substrate channeling mechanism. This channeling occurs by nonbiased diffusion of the iminium intermediate through a large solvent cavity connecting active site 1 (N-terminus) and active site 2 (C-terminus). The synthesis of 5,10-methylenetetrahydrofolate (at active site 2) prevents the accumulation of formaldehyde, formed by hydrolysis of the iminium intermediate product (at active site 1). Does not oxidize sarcosine.4 Publications

Catalytic activityi

N,N-dimethylglycine + H2O + O2 = sarcosine + formaldehyde + H2O2.1 Publication
N,N-dimethylglycine + tetrahydrofolate = sarcosine + 5,10-methylenetetrahydrofolate.1 Publication

Cofactori

FAD2 PublicationsNote: Binds 1 FAD per subunit.2 Publications

Kineticsi

  1. KM=2 mM for N,N-dimethylglycine1 Publication

    pH dependencei

    Optimum pH is 8.0-10.0.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei52 – 521FAD; via amide nitrogen and carbonyl oxygen2 Publications
    Binding sitei174 – 1741FAD; via amide nitrogen and carbonyl oxygen2 Publications
    Active sitei225 – 2251Sequence Analysis
    Sitei225 – 2251Important for catalytic activity
    Active sitei259 – 2591Sequence Analysis
    Binding sitei259 – 2591FAD2 Publications
    Sitei259 – 2591Important for catalytic activity
    Active sitei552 – 5521For 5,10-methylenetetrahydrofolate synthesis activitySequence Analysis
    Sitei552 – 5521Important for catalytic activity
    Binding sitei554 – 5541Tetrahydrofolic acid
    Binding sitei566 – 5661Tetrahydrofolic acid; via carbonyl oxygen

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi14 – 152FAD2 Publications
    Nucleotide bindingi35 – 362FAD2 Publications
    Nucleotide bindingi45 – 484FAD2 Publications
    Nucleotide bindingi360 – 3634FAD2 Publications

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    FAD, Flavoprotein, Nucleotide-binding

    Enzyme and pathway databases

    BRENDAi1.5.3.10. 444.
    SABIO-RKQ9AGP8.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Dimethylglycine oxidase (EC:1.5.3.10)
    Short name:
    DMGO
    Gene namesi
    Name:dmg
    OrganismiArthrobacter globiformis
    Taxonomic identifieri1665 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaMicrococcalesMicrococcaceaeArthrobacter

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi225 – 2251H → Q: Reduces catalytic efficiency 3-fold and substrate affinity 30-fold. 1 Publication
    Mutagenesisi259 – 2591Y → F: Reduces catalytic efficiency 225-fold and substrate affinity 25-fold. 1 Publication
    Mutagenesisi552 – 5521D → A: No effect on the activity. 1 Publication
    Mutagenesisi552 – 5521D → N: Reduces activity 3-fold. 1 Publication

    Chemistry

    DrugBankiDB03147. Flavin adenine dinucleotide.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 830830Dimethylglycine oxidasePRO_0000428956Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei48 – 481Pros-8alpha-FAD histidine

    Structurei

    Secondary structure

    1
    830
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi7 – 104Combined sources
    Helixi14 – 2512Combined sources
    Beta strandi31 – 344Combined sources
    Helixi45 – 473Combined sources
    Helixi60 – 7516Combined sources
    Beta strandi81 – 855Combined sources
    Beta strandi89 – 957Combined sources
    Helixi96 – 11217Combined sources
    Beta strandi117 – 1193Combined sources
    Helixi121 – 1277Combined sources
    Helixi133 – 1353Combined sources
    Beta strandi138 – 1425Combined sources
    Beta strandi146 – 1483Combined sources
    Helixi150 – 16314Combined sources
    Beta strandi167 – 1693Combined sources
    Beta strandi174 – 1807Combined sources
    Beta strandi183 – 1897Combined sources
    Beta strandi192 – 1954Combined sources
    Beta strandi197 – 2015Combined sources
    Helixi204 – 2063Combined sources
    Helixi207 – 2126Combined sources
    Turni213 – 2153Combined sources
    Beta strandi221 – 23111Combined sources
    Helixi234 – 2363Combined sources
    Turni237 – 2393Combined sources
    Turni242 – 2443Combined sources
    Beta strandi250 – 2534Combined sources
    Helixi254 – 2563Combined sources
    Beta strandi258 – 2636Combined sources
    Beta strandi266 – 2716Combined sources
    Helixi281 – 2833Combined sources
    Helixi289 – 2913Combined sources
    Helixi305 – 31814Combined sources
    Helixi320 – 3245Combined sources
    Beta strandi327 – 33711Combined sources
    Beta strandi344 – 3474Combined sources
    Beta strandi349 – 3524Combined sources
    Beta strandi354 – 3596Combined sources
    Helixi362 – 3643Combined sources
    Helixi365 – 37814Combined sources
    Turni386 – 3883Combined sources
    Helixi390 – 3923Combined sources
    Helixi395 – 3984Combined sources
    Helixi400 – 41213Combined sources
    Turni413 – 4153Combined sources
    Beta strandi425 – 4273Combined sources
    Helixi436 – 4416Combined sources
    Beta strandi444 – 4496Combined sources
    Beta strandi452 – 4587Combined sources
    Helixi459 – 4679Combined sources
    Helixi470 – 4723Combined sources
    Helixi479 – 4824Combined sources
    Helixi488 – 49811Combined sources
    Beta strandi501 – 5044Combined sources
    Beta strandi510 – 5156Combined sources
    Helixi518 – 5258Combined sources
    Beta strandi526 – 5283Combined sources
    Beta strandi536 – 5438Combined sources
    Beta strandi549 – 55911Combined sources
    Beta strandi562 – 5665Combined sources
    Helixi570 – 58617Combined sources
    Beta strandi594 – 5974Combined sources
    Helixi599 – 6013Combined sources
    Beta strandi602 – 6098Combined sources
    Helixi612 – 6165Combined sources
    Turni617 – 6193Combined sources
    Turni626 – 6283Combined sources
    Beta strandi633 – 6397Combined sources
    Beta strandi642 – 6476Combined sources
    Beta strandi653 – 66210Combined sources
    Helixi663 – 67715Combined sources
    Helixi678 – 6803Combined sources
    Beta strandi683 – 6853Combined sources
    Helixi687 – 69610Combined sources
    Turni702 – 7043Combined sources
    Turni712 – 7165Combined sources
    Helixi718 – 7203Combined sources
    Helixi731 – 7344Combined sources
    Turni739 – 7413Combined sources
    Beta strandi743 – 7519Combined sources
    Beta strandi763 – 7664Combined sources
    Beta strandi769 – 7735Combined sources
    Beta strandi776 – 7805Combined sources
    Turni781 – 7844Combined sources
    Beta strandi785 – 7939Combined sources
    Beta strandi801 – 8066Combined sources
    Beta strandi809 – 8168Combined sources
    Turni826 – 8283Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1PJ5X-ray1.61A1-830[»]
    1PJ6X-ray1.65A1-830[»]
    1PJ7X-ray2.10A1-830[»]
    3GSIX-ray2.00A4-830[»]
    ProteinModelPortaliQ9AGP8.
    SMRiQ9AGP8. Positions 3-830.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9AGP8.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni658 – 6603Tetrahydrofolic acid binding

    Sequence similaritiesi

    Belongs to the GcvT family.Curated

    Family and domain databases

    Gene3Di2.40.30.110. 1 hit.
    3.30.1360.120. 2 hits.
    InterProiIPR006076. FAD-dep_OxRdtase.
    IPR013977. GCV_T_C.
    IPR006222. GCV_T_N.
    IPR029043. GcvT/YgfZ_C.
    IPR027266. TrmE/GcvT_dom1.
    [Graphical view]
    PfamiPF01266. DAO. 1 hit.
    PF01571. GCV_T. 1 hit.
    PF08669. GCV_T_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF101790. SSF101790. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q9AGP8-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MASTPRIVII GAGIVGTNLA DELVTRGWNN ITVLDQGPLN MPGGSTSHAP
    60 70 80 90 100
    GLVFQTNPSK TMASFAKYTV EKLLSLTEDG VSCFNQVGGL EVATTETRLA
    110 120 130 140 150
    DLKRKLGYAA AWGIEGRLLS PAECQELYPL LDGENILGGL HVPSDGLASA
    160 170 180 190 200
    ARAVQLLIKR TESAGVTYRG STTVTGIEQS GGRVTGVQTA DGVIPADIVV
    210 220 230 240 250
    SCAGFWGAKI GAMIGMAVPL LPLAHQYVKT TPVPAQQGRN DQPNGARLPI
    260 270 280 290 300
    LRHQDQDLYY REHGDRYGIG SYAHRPMPVD VDTLGAYAPE TVSEHHMPSR
    310 320 330 340 350
    LDFTLEDFLP AWEATKQLLP ALADSEIEDG FNGIFSFTPD GGPLLGESKE
    360 370 380 390 400
    LDGFYVAEAV WVTHSAGVAK AMAELLTTGR SETDLGECDI TRFEDVQLTP
    410 420 430 440 450
    EYVSETSQQN FVEIYDVLHP LQPRLSPRNL RVSPFHARHK ELGAFFLEAG
    460 470 480 490 500
    GWERPYWFEA NAALLKEMPA EWLPPARDAW SGMFSSPIAA AEAWKTRTAV
    510 520 530 540 550
    AMYDMTPLKR LEVSGPGALK LLQELTTADL AKKPGAVTYT LLLDHAGGVR
    560 570 580 590 600
    SDITVARLSE DTFQLGANGN IDTAYFERAA RHQTQSGSAT DWVQVRDTTG
    610 620 630 640 650
    GTCCIGLWGP LARDLVSKVS DDDFTNDGLK YFRAKNVVIG GIPVTAMRLS
    660 670 680 690 700
    YVGELGWELY TSADNGQRLW DALWQAGQPF GVIAAGRAAF SSLRLEKGYR
    710 720 730 740 750
    SWGTDMTTEH DPFEAGLGFA VKMAKESFIG KGALEGRTEE ASARRLRCLT
    760 770 780 790 800
    IDDGRSIVLG KEPVFYKEQA VGYVTSAAYG YTVAKPIAYS YLPGTVSVGD
    810 820 830
    SVDIEYFGRR ITATVTEDPL YDPKMTRLRG
    Length:830
    Mass (Da):89,985
    Last modified:June 1, 2001 - v1
    Checksum:i13DE3C4B3DF325DA
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF329477 Genomic DNA. Translation: AAK16482.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF329477 Genomic DNA. Translation: AAK16482.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1PJ5X-ray1.61A1-830[»]
    1PJ6X-ray1.65A1-830[»]
    1PJ7X-ray2.10A1-830[»]
    3GSIX-ray2.00A4-830[»]
    ProteinModelPortaliQ9AGP8.
    SMRiQ9AGP8. Positions 3-830.
    ModBaseiSearch...
    MobiDBiSearch...

    Chemistry

    DrugBankiDB03147. Flavin adenine dinucleotide.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BRENDAi1.5.3.10. 444.
    SABIO-RKQ9AGP8.

    Miscellaneous databases

    EvolutionaryTraceiQ9AGP8.

    Family and domain databases

    Gene3Di2.40.30.110. 1 hit.
    3.30.1360.120. 2 hits.
    InterProiIPR006076. FAD-dep_OxRdtase.
    IPR013977. GCV_T_C.
    IPR006222. GCV_T_N.
    IPR029043. GcvT/YgfZ_C.
    IPR027266. TrmE/GcvT_dom1.
    [Graphical view]
    PfamiPF01266. DAO. 1 hit.
    PF01571. GCV_T. 1 hit.
    PF08669. GCV_T_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF101790. SSF101790. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Organization of the genes involved in dimethylglycine and sarcosine degradation in Arthrobacter spp.: implications for glycine betaine catabolism."
      Meskys R., Harris R.J., Casaite V., Basran J., Scrutton N.S.
      Eur. J. Biochem. 268:3390-3398(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: NRRL B-2979.
    2. "Mechanistic aspects of the covalent flavoprotein dimethylglycine oxidase of Arthrobacter globiformis studied by stopped-flow spectrophotometry."
      Basran J., Bhanji N., Basran A., Nietlispach D., Mistry S., Meskys R., Scrutton N.S.
      Biochemistry 41:4733-4743(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 27-58, FUNCTION, FAD-BINDING AT HIS-48.
      Strain: NRRL B-2979.
    3. "Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase."
      Leys D., Basran J., Scrutton N.S.
      EMBO J. 22:4038-4048(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.61 ANGSTROMS) IN COMPLEX WITH FAD AND TETRAHYDROFOLATE, FUNCTION, MUTAGENESIS OF HIS-225 AND TYR-259.
      Strain: NRRL B-2979.
    4. "An internal reaction chamber in dimethylglycine oxidase provides efficient protection from exposure to toxic formaldehyde."
      Tralau T., Lafite P., Levy C., Combe J.P., Scrutton N.S., Leys D.
      J. Biol. Chem. 284:17826-17834(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 4-830 IN COMPLEX WITH FAD AND TETRAHYDROFOLATE, FUNCTION, MUTAGENESIS OF ASP-552.
      Strain: NRRL B-2979.

    Entry informationi

    Entry nameiDMGO_ARTGO
    AccessioniPrimary (citable) accession number: Q9AGP8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 14, 2014
    Last sequence update: June 1, 2001
    Last modified: June 24, 2015
    This is version 72 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

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

    External Data

    Dasty 3

    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 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.