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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

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei52 – 521FAD; via amide nitrogen and carbonyl oxygen
Binding sitei174 – 1741FAD; via amide nitrogen and carbonyl oxygen
Active sitei225 – 2251 Reviewed prediction
Sitei225 – 2251Important for catalytic activity
Active sitei259 – 2591 Reviewed prediction
Binding sitei259 – 2591FAD
Sitei259 – 2591Important for catalytic activity
Active sitei552 – 5521For 5,10-methylenetetrahydrofolate synthesis activity Reviewed prediction
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 – 152FAD
Nucleotide bindingi35 – 362FAD
Nucleotide bindingi45 – 484FAD
Nucleotide bindingi360 – 3634FAD

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiQ9AGP8.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the GcvT family.

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

MASTPRIVII GAGIVGTNLA DELVTRGWNN ITVLDQGPLN MPGGSTSHAP    50
GLVFQTNPSK TMASFAKYTV EKLLSLTEDG VSCFNQVGGL EVATTETRLA 100
DLKRKLGYAA AWGIEGRLLS PAECQELYPL LDGENILGGL HVPSDGLASA 150
ARAVQLLIKR TESAGVTYRG STTVTGIEQS GGRVTGVQTA DGVIPADIVV 200
SCAGFWGAKI GAMIGMAVPL LPLAHQYVKT TPVPAQQGRN DQPNGARLPI 250
LRHQDQDLYY REHGDRYGIG SYAHRPMPVD VDTLGAYAPE TVSEHHMPSR 300
LDFTLEDFLP AWEATKQLLP ALADSEIEDG FNGIFSFTPD GGPLLGESKE 350
LDGFYVAEAV WVTHSAGVAK AMAELLTTGR SETDLGECDI TRFEDVQLTP 400
EYVSETSQQN FVEIYDVLHP LQPRLSPRNL RVSPFHARHK ELGAFFLEAG 450
GWERPYWFEA NAALLKEMPA EWLPPARDAW SGMFSSPIAA AEAWKTRTAV 500
AMYDMTPLKR LEVSGPGALK LLQELTTADL AKKPGAVTYT LLLDHAGGVR 550
SDITVARLSE DTFQLGANGN IDTAYFERAA RHQTQSGSAT DWVQVRDTTG 600
GTCCIGLWGP LARDLVSKVS DDDFTNDGLK YFRAKNVVIG GIPVTAMRLS 650
YVGELGWELY TSADNGQRLW DALWQAGQPF GVIAAGRAAF SSLRLEKGYR 700
SWGTDMTTEH DPFEAGLGFA VKMAKESFIG KGALEGRTEE ASARRLRCLT 750
IDDGRSIVLG KEPVFYKEQA VGYVTSAAYG YTVAKPIAYS YLPGTVSVGD 800
SVDIEYFGRR ITATVTEDPL YDPKMTRLRG 830
Length:830
Mass (Da):89,985
Last modified:June 1, 2001 - v1
Checksum:i13DE3C4B3DF325DA
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF329477 Genomic DNA. Translation: AAK16482.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF329477 Genomic DNA. Translation: AAK16482.1 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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...

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: July 9, 2014
This is version 65 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

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