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Q9AGP8

- DMGO_ARTGO

UniProt

Q9AGP8 - DMGO_ARTGO

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Protein

Dimethylglycine oxidase

Gene

dmg

Organism
Arthrobacter globiformis
Status
Reviewed - 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

  1. aminomethyltransferase activity Source: InterPro
  2. dimethylglycine oxidase activity Source: UniProtKB-EC
  3. nucleotide binding Source: UniProtKB-KW

GO - Biological processi

  1. glycine catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

FAD, Flavoprotein, Nucleotide-binding

Enzyme and pathway databases

BRENDAi1.5.3.10. 1012.

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 lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesMicrococcineaeMicrococcaceaeArthrobacter

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: InterPro
Complete GO annotation...

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

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
Entry Method Resolution (Å) Chain Positions PDBsum
1PJ5 X-ray 1.61 A 1-830 [» ]
1PJ6 X-ray 1.65 A 1-830 [» ]
1PJ7 X-ray 2.10 A 1-830 [» ]
3GSI X-ray 2.00 A 4-830 [» ]
ProteinModelPortali Q9AGP8.
SMRi Q9AGP8. Positions 3-830.
ModBasei Search...
MobiDBi Search...

Chemistry

DrugBanki DB03147. Flavin adenine dinucleotide.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

BRENDAi 1.5.3.10. 1012.

Miscellaneous databases

EvolutionaryTracei Q9AGP8.

Family and domain databases

Gene3Di 2.40.30.110. 1 hit.
3.30.1360.120. 2 hits.
InterProi IPR006076. FAD-dep_OxRdtase.
IPR013977. GCV_T_C.
IPR006222. GCV_T_N.
IPR029043. GcvT/YgfZ_C.
IPR027266. TrmE/GcvT_dom1.
[Graphical view ]
Pfami PF01266. DAO. 1 hit.
PF01571. GCV_T. 1 hit.
PF08669. GCV_T_C. 1 hit.
[Graphical view ]
SUPFAMi SSF101790. SSF101790. 1 hit.
ProtoNeti Search...

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: November 26, 2014
This is version 68 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