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Q9AGP8 (DMGO_ARTGO) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 65. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Dimethylglycine oxidase

Short name=DMGO
EC=1.5.3.10
Gene names
Name:dmg
OrganismArthrobacter globiformis
Taxonomic identifier1665 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesMicrococcineaeMicrococcaceaeArthrobacter

Protein attributes

Sequence length830 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.2 Ref.3 Ref.4

Catalytic activity

N,N-dimethylglycine + H2O + O2 = sarcosine + formaldehyde + H2O2. Ref.1

N,N-dimethylglycine + tetrahydrofolate = sarcosine + 5,10-methylenetetrahydrofolate. Ref.1

Cofactor

Binds 1 FAD per subunit. Ref.1 Ref.2

Sequence similarities

Belongs to the GcvT family.

Biophysicochemical properties

Kinetic parameters:

KM=2 mM for N,N-dimethylglycine Ref.1

pH dependence:

Optimum pH is 8.0-10.0.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 830830Dimethylglycine oxidase
PRO_0000428956

Regions

Nucleotide binding14 – 152FAD
Nucleotide binding35 – 362FAD
Nucleotide binding45 – 484FAD
Nucleotide binding360 – 3634FAD
Region658 – 6603Tetrahydrofolic acid binding

Sites

Active site2251 Potential
Active site2591 Potential
Active site5521For 5,10-methylenetetrahydrofolate synthesis activity Potential
Binding site521FAD; via amide nitrogen and carbonyl oxygen
Binding site1741FAD; via amide nitrogen and carbonyl oxygen
Binding site2591FAD
Binding site5541Tetrahydrofolic acid
Binding site5661Tetrahydrofolic acid; via carbonyl oxygen
Site2251Important for catalytic activity
Site2591Important for catalytic activity
Site5521Important for catalytic activity

Amino acid modifications

Modified residue481Pros-8alpha-FAD histidine

Experimental info

Mutagenesis2251H → Q: Reduces catalytic efficiency 3-fold and substrate affinity 30-fold. Ref.3
Mutagenesis2591Y → F: Reduces catalytic efficiency 225-fold and substrate affinity 25-fold. Ref.3
Mutagenesis5521D → A: No effect on the activity. Ref.4
Mutagenesis5521D → N: Reduces activity 3-fold. Ref.4

Secondary structure

.................................................................................................................................................................. 830
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9AGP8 [UniParc].

Last modified June 1, 2001. Version 1.
Checksum: 13DE3C4B3DF325DA

FASTA83089,985
        10         20         30         40         50         60 
MASTPRIVII GAGIVGTNLA DELVTRGWNN ITVLDQGPLN MPGGSTSHAP GLVFQTNPSK 

        70         80         90        100        110        120 
TMASFAKYTV EKLLSLTEDG VSCFNQVGGL EVATTETRLA DLKRKLGYAA AWGIEGRLLS 

       130        140        150        160        170        180 
PAECQELYPL LDGENILGGL HVPSDGLASA ARAVQLLIKR TESAGVTYRG STTVTGIEQS 

       190        200        210        220        230        240 
GGRVTGVQTA DGVIPADIVV SCAGFWGAKI GAMIGMAVPL LPLAHQYVKT TPVPAQQGRN 

       250        260        270        280        290        300 
DQPNGARLPI LRHQDQDLYY REHGDRYGIG SYAHRPMPVD VDTLGAYAPE TVSEHHMPSR 

       310        320        330        340        350        360 
LDFTLEDFLP AWEATKQLLP ALADSEIEDG FNGIFSFTPD GGPLLGESKE LDGFYVAEAV 

       370        380        390        400        410        420 
WVTHSAGVAK AMAELLTTGR SETDLGECDI TRFEDVQLTP EYVSETSQQN FVEIYDVLHP 

       430        440        450        460        470        480 
LQPRLSPRNL RVSPFHARHK ELGAFFLEAG GWERPYWFEA NAALLKEMPA EWLPPARDAW 

       490        500        510        520        530        540 
SGMFSSPIAA AEAWKTRTAV AMYDMTPLKR LEVSGPGALK LLQELTTADL AKKPGAVTYT 

       550        560        570        580        590        600 
LLLDHAGGVR SDITVARLSE DTFQLGANGN IDTAYFERAA RHQTQSGSAT DWVQVRDTTG 

       610        620        630        640        650        660 
GTCCIGLWGP LARDLVSKVS DDDFTNDGLK YFRAKNVVIG GIPVTAMRLS YVGELGWELY 

       670        680        690        700        710        720 
TSADNGQRLW DALWQAGQPF GVIAAGRAAF SSLRLEKGYR SWGTDMTTEH DPFEAGLGFA 

       730        740        750        760        770        780 
VKMAKESFIG KGALEGRTEE ASARRLRCLT IDDGRSIVLG KEPVFYKEQA VGYVTSAAYG 

       790        800        810        820        830 
YTVAKPIAYS YLPGTVSVGD SVDIEYFGRR ITATVTEDPL YDPKMTRLRG 

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References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF329477 Genomic DNA. Translation: AAK16482.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1PJ5X-ray1.61A1-830[»]
1PJ6X-ray1.65A1-830[»]
1PJ7X-ray2.10A1-830[»]
3GSIX-ray2.00A4-830[»]
ProteinModelPortalQ9AGP8.
SMRQ9AGP8. Positions 3-830.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

BRENDA1.5.3.10. 1012.

Family and domain databases

Gene3D2.40.30.110. 1 hit.
3.30.1360.120. 2 hits.
InterProIPR006076. FAD-dep_OxRdtase.
IPR013977. GCV_T_C.
IPR006222. GCV_T_N.
IPR029043. GcvT/YgfZ_C.
IPR027266. TrmE/GcvT_dom1.
[Graphical view]
PfamPF01266. DAO. 1 hit.
PF01571. GCV_T. 1 hit.
PF08669. GCV_T_C. 1 hit.
[Graphical view]
SUPFAMSSF101790. SSF101790. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ9AGP8.

Entry information

Entry nameDMGO_ARTGO
AccessionPrimary (citable) accession number: Q9AGP8
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references