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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)DescriptionActionsGraphical viewLength
    Binding sitei52FAD; via amide nitrogen and carbonyl oxygen2 Publications1
    Binding sitei174FAD; via amide nitrogen and carbonyl oxygen2 Publications1
    Active sitei225Sequence analysis1
    Sitei225Important for catalytic activity1 Publication1
    Active sitei259Sequence analysis1
    Binding sitei259FAD2 Publications1
    Sitei259Important for catalytic activity1 Publication1
    Binding sitei539Tetrahydrofolate1 Publication1
    Active sitei552For 5,10-methylenetetrahydrofolate synthesis activitySequence analysis1
    Sitei552Important for catalytic activity1 Publication1 Publication1
    Binding sitei554Tetrahydrofolate1
    Binding sitei566Tetrahydrofolate; via carbonyl oxygen1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi14 – 15FAD2 Publications2
    Nucleotide bindingi35 – 36FAD2 Publications2
    Nucleotide bindingi45 – 48FAD2 Publications4
    Nucleotide bindingi360 – 363FAD2 Publications4

    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)DescriptionActionsGraphical viewLength
    Mutagenesisi225H → Q: Reduces catalytic efficiency 3-fold and substrate affinity 30-fold. 1 Publication1
    Mutagenesisi259Y → F: Reduces catalytic efficiency 225-fold and substrate affinity 25-fold. 1 Publication1
    Mutagenesisi552D → A: No effect on the activity. 1 Publication1
    Mutagenesisi552D → N: Reduces activity 3-fold. 1 Publication1

    Chemistry databases

    DrugBankiDB03147. Flavin adenine dinucleotide.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004289561 – 830Dimethylglycine oxidaseAdd BLAST830

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei48Pros-8alpha-FAD histidine1

    Structurei

    Secondary structure

    1830
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi7 – 10Combined sources4
    Helixi14 – 25Combined sources12
    Beta strandi31 – 34Combined sources4
    Helixi45 – 47Combined sources3
    Helixi60 – 75Combined sources16
    Beta strandi81 – 85Combined sources5
    Beta strandi89 – 95Combined sources7
    Helixi96 – 112Combined sources17
    Beta strandi117 – 119Combined sources3
    Helixi121 – 127Combined sources7
    Helixi133 – 135Combined sources3
    Beta strandi138 – 142Combined sources5
    Beta strandi146 – 148Combined sources3
    Helixi150 – 163Combined sources14
    Beta strandi167 – 169Combined sources3
    Beta strandi174 – 180Combined sources7
    Beta strandi183 – 189Combined sources7
    Beta strandi192 – 195Combined sources4
    Beta strandi197 – 201Combined sources5
    Helixi204 – 206Combined sources3
    Helixi207 – 212Combined sources6
    Turni213 – 215Combined sources3
    Beta strandi221 – 231Combined sources11
    Helixi234 – 236Combined sources3
    Turni237 – 239Combined sources3
    Turni242 – 244Combined sources3
    Beta strandi250 – 253Combined sources4
    Helixi254 – 256Combined sources3
    Beta strandi258 – 263Combined sources6
    Beta strandi266 – 271Combined sources6
    Helixi281 – 283Combined sources3
    Helixi289 – 291Combined sources3
    Helixi305 – 318Combined sources14
    Helixi320 – 324Combined sources5
    Beta strandi327 – 337Combined sources11
    Beta strandi344 – 347Combined sources4
    Beta strandi349 – 352Combined sources4
    Beta strandi354 – 359Combined sources6
    Helixi362 – 364Combined sources3
    Helixi365 – 378Combined sources14
    Turni386 – 388Combined sources3
    Helixi390 – 392Combined sources3
    Helixi395 – 398Combined sources4
    Helixi400 – 412Combined sources13
    Turni413 – 415Combined sources3
    Beta strandi425 – 427Combined sources3
    Helixi436 – 441Combined sources6
    Beta strandi444 – 449Combined sources6
    Beta strandi452 – 458Combined sources7
    Helixi459 – 467Combined sources9
    Helixi470 – 472Combined sources3
    Helixi479 – 482Combined sources4
    Helixi488 – 498Combined sources11
    Beta strandi501 – 504Combined sources4
    Beta strandi510 – 515Combined sources6
    Helixi518 – 525Combined sources8
    Beta strandi526 – 528Combined sources3
    Beta strandi536 – 543Combined sources8
    Beta strandi549 – 559Combined sources11
    Beta strandi562 – 566Combined sources5
    Helixi570 – 586Combined sources17
    Beta strandi594 – 597Combined sources4
    Helixi599 – 601Combined sources3
    Beta strandi602 – 609Combined sources8
    Helixi612 – 616Combined sources5
    Turni617 – 619Combined sources3
    Turni626 – 628Combined sources3
    Beta strandi633 – 639Combined sources7
    Beta strandi642 – 647Combined sources6
    Beta strandi653 – 662Combined sources10
    Helixi663 – 677Combined sources15
    Helixi678 – 680Combined sources3
    Beta strandi683 – 685Combined sources3
    Helixi687 – 696Combined sources10
    Turni702 – 704Combined sources3
    Turni712 – 716Combined sources5
    Helixi718 – 720Combined sources3
    Helixi731 – 734Combined sources4
    Turni739 – 741Combined sources3
    Beta strandi743 – 751Combined sources9
    Beta strandi763 – 766Combined sources4
    Beta strandi769 – 773Combined sources5
    Beta strandi776 – 780Combined sources5
    Turni781 – 784Combined sources4
    Beta strandi785 – 793Combined sources9
    Beta strandi801 – 806Combined sources6
    Beta strandi809 – 816Combined sources8
    Turni826 – 828Combined sources3

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiQ9AGP8.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni658 – 660Tetrahydrofolate binding3

    Sequence similaritiesi

    Belongs to the GcvT family.Curated

    Family and domain databases

    Gene3Di2.40.30.110. 1 hit.
    3.30.1360.120. 2 hits.
    3.50.50.60. 3 hits.
    InterProiIPR006076. FAD-dep_OxRdtase.
    IPR023753. FAD/NAD-binding_dom.
    IPR032503. FAO_M.
    IPR013977. GCV_T_C.
    IPR006222. GCV_T_N.
    IPR029043. GcvT/YgfZ_C.
    IPR027266. TrmE/GcvT_dom1.
    [Graphical view]
    PfamiPF01266. DAO. 1 hit.
    PF16350. FAO_M. 1 hit.
    PF01571. GCV_T. 1 hit.
    PF08669. GCV_T_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF101790. SSF101790. 1 hit.
    SSF51905. SSF51905. 2 hits.

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1PJ5X-ray1.61A1-830[»]
    1PJ6X-ray1.65A1-830[»]
    1PJ7X-ray2.10A1-830[»]
    3GSIX-ray2.00A4-830[»]
    ProteinModelPortaliQ9AGP8.
    SMRiQ9AGP8.
    ModBaseiSearch...
    MobiDBiSearch...

    Chemistry databases

    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.
    3.50.50.60. 3 hits.
    InterProiIPR006076. FAD-dep_OxRdtase.
    IPR023753. FAD/NAD-binding_dom.
    IPR032503. FAO_M.
    IPR013977. GCV_T_C.
    IPR006222. GCV_T_N.
    IPR029043. GcvT/YgfZ_C.
    IPR027266. TrmE/GcvT_dom1.
    [Graphical view]
    PfamiPF01266. DAO. 1 hit.
    PF16350. FAO_M. 1 hit.
    PF01571. GCV_T. 1 hit.
    PF08669. GCV_T_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF101790. SSF101790. 1 hit.
    SSF51905. SSF51905. 2 hits.
    ProtoNetiSearch...

    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: November 2, 2016
    This is version 78 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

    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.