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PDBsum entry 1pj5

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protein ligands metals links
Oxidoreductase PDB id
1pj5
Jmol
Contents
Protein chain
827 a.a. *
Ligands
ACT
FAD
Metals
_NA
Waters ×1740
* Residue conservation analysis
PDB id:
1pj5
Name: Oxidoreductase
Title: Crystal structure of dimethylglycine oxidase of arthrobacter globiformis in complex with acetate
Structure: N,n-dimethylglycine oxidase. Chain: a. Engineered: yes
Source: Arthrobacter globiformis. Organism_taxid: 1665. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.61Å     R-factor:   0.162     R-free:   0.198
Authors: D.Leys,J.Basran,N.S.Scrutton
Key ref: D.Leys et al. (2003). Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase. EMBO J, 22, 4038-4048. PubMed id: 12912903
Date:
01-Jun-03     Release date:   07-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9AGP8  (Q9AGP8_ARTGO) -  Dimethylglycine oxidase
Seq:
Struc:
 
Seq:
Struc:
830 a.a.
827 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.5.3.10  - Dimethylglycine oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: N,N-dimethylglycine + H2O + O2 = sarcosine + formaldehyde + H2O2
N,N-dimethylglycine
+ H(2)O
+ O(2)
= sarcosine
+ formaldehyde
+ H(2)O(2)
      Cofactor: FAD
FAD
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
EMBO J 22:4038-4048 (2003)
PubMed id: 12912903  
 
 
Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase.
D.Leys, J.Basran, N.S.Scrutton.
 
  ABSTRACT  
 
Here we report crystal structures of dimethylglycine oxidase (DMGO) from the bacterium Arthrobacter globiformis, a bifunctional enzyme that catalyzes the oxidation of N,N-dimethyl glycine and the formation of 5,10-methylene tetrahydrofolate. The N-terminal region binds FAD covalently and oxidizes dimethylglycine to a labile iminium intermediate. The C-terminal region binds tetrahydrofolate, comprises three domains arranged in a ring-like structure and is related to the T-protein of the glycine cleavage system. The complex with folinic acid indicates that this enzyme selectively activates the N10 amino group for initial attack on the substrate. Dead-end reactions with oxidized folate are avoided by the strict stereochemical constraints imposed by the folate-binding funnel. The active sites in DMGO are approximately 40 A apart, connected by a large irregular internal cavity. The tetrahydrofolate-binding funnel serves as a transient entry-exit port, and access to the internal cavity is controlled kinetically by tetrahydrofolate binding. The internal cavity enables sequestration of the reactive iminium intermediate prior to reaction with tetrahydrofolate and avoids formation of toxic formaldehyde. This mode of channelling in DMGO is distinct from other channelling mechanisms.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21188587 V.Casaitė, S.Povilonienė, R.Meškienė, R.Rutkienė, and R.Meškys (2011).
Studies of dimethylglycine oxidase isoenzymes in Arthrobacter globiformis cells.
  Curr Microbiol, 62, 1267-1273.  
20133651 D.Srivastava, J.P.Schuermann, T.A.White, N.Krishnan, N.Sanyal, G.L.Hura, A.Tan, M.T.Henzl, D.F.Becker, and J.J.Tanner (2010).
Crystal structure of the bifunctional proline utilization A flavoenzyme from Bradyrhizobium japonicum.
  Proc Natl Acad Sci U S A, 107, 2878-2883.
PDB code: 3haz
19651103 P.F.Fitzpatrick (2010).
Oxidation of amines by flavoproteins.
  Arch Biochem Biophys, 493, 13-25.  
19438712 D.P.Heuts, N.S.Scrutton, W.S.McIntire, and M.W.Fraaije (2009).
What's in a covalent bond? On the role and formation of covalently bound flavin cofactors.
  FEBS J, 276, 3405-3427.  
19369258 T.Tralau, P.Lafite, C.Levy, J.P.Combe, N.S.Scrutton, and D.Leys (2009).
An internal reaction chamber in dimethylglycine oxidase provides efficient protection from exposure to toxic formaldehyde.
  J Biol Chem, 284, 17826-17834.
PDB code: 3gsi
18423846 C.Brizio, R.Brandsch, M.Douka, R.Wait, and M.Barile (2008).
The purified recombinant precursor of rat mitochondrial dimethylglycine dehydrogenase binds FAD via an autocatalytic reaction.
  Int J Biol Macromol, 42, 455-462.  
18849431 C.R.Reisch, M.A.Moran, and W.B.Whitman (2008).
Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi.
  J Bacteriol, 190, 8018-8024.  
18390652 E.Kalliri, S.B.Mulrooney, and R.P.Hausinger (2008).
Identification of Escherichia coli YgaF as an L-2-hydroxyglutarate oxidase.
  J Bacteriol, 190, 3793-3798.  
18937046 R.P.McAndrew, J.Vockley, and J.J.Kim (2008).
Molecular basis of dimethylglycine dehydrogenase deficiency associated with pathogenic variant H109R.
  J Inherit Metab Dis, 31, 761-768.  
17697998 C.J.Carrell, R.C.Bruckner, D.Venci, G.Zhao, M.S.Jorns, and F.S.Mathews (2007).
NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: structures of closed and open forms at 1.15 and 1.90 A resolution.
  Structure, 15, 928-941.
PDB codes: 2oln 2olo 2q6u
17371548 P.J.Monaghan, D.Leys, and N.S.Scrutton (2007).
Mechanistic aspects and redox properties of hyperthermophilic L-proline dehydrogenase from Pyrococcus furiosus related to dimethylglycine dehydrogenase/oxidase.
  FEBS J, 274, 2070-2087.  
17922651 P.V.Vrzheshch (2007).
Steady-state kinetics of bifunctional enzymes. Taking into account kinetic hierarchy of fast and slow catalytic cycles in a generalized model.
  Biochemistry (Mosc), 72, 936-943.  
16359333 T.Ote, M.Hashimoto, Y.Ikeuchi, M.Su'etsugu, T.Suzuki, T.Katayama, and J.Kato (2006).
Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation.
  Mol Microbiol, 59, 265-275.  
15616586 A.Scrima, I.R.Vetter, M.E.Armengod, and A.Wittinghofer (2005).
The structure of the TrmE GTP-binding protein and its implications for tRNA modification.
  EMBO J, 24, 23-33.
PDB codes: 1xzp 1xzq
16187342 M.Tress, C.H.Tai, G.Wang, I.Ezkurdia, G.López, A.Valencia, B.Lee, and R.L.Dunbrack (2005).
Domain definition and target classification for CASP6.
  Proteins, 61, 8.  
15609340 N.K.Lokanath, C.Kuroishi, N.Okazaki, and N.Kunishima (2005).
Crystal structure of a component of glycine cleavage system: T-protein from Pyrococcus horikoshii OT3 at 1.5 A resolution.
  Proteins, 58, 769-773.
PDB code: 1v5v
  16511149 P.J.Monaghan, D.Leys, and N.S.Scrutton (2005).
Crystallization and preliminary X-ray diffraction analysis of a flavoenzyme amine dehydrogenase/oxidase from Pyrococcus furiosus DSM 3638.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 756-758.  
15489424 A.Teplyakov, G.Obmolova, E.Sarikaya, S.Pullalarevu, W.Krajewski, A.Galkin, A.J.Howard, O.Herzberg, and G.L.Gilliland (2004).
Crystal structure of the YgfZ protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism.
  J Bacteriol, 186, 7134-7140.
PDB code: 1nrk
15606755 C.B.Chiribau, C.Sandu, M.Fraaije, E.Schiltz, and R.Brandsch (2004).
A novel gamma-N-methylaminobutyrate demethylating oxidase involved in catabolism of the tobacco alkaloid nicotine by Arthrobacter nicotinovorans pAO1.
  Eur J Biochem, 271, 4677-4684.  
15355973 H.H.Lee, D.J.Kim, H.J.Ahn, J.Y.Ha, and S.W.Suh (2004).
Crystal structure of T-protein of the glycine cleavage system. Cofactor binding, insights into H-protein recognition, and molecular basis for understanding nonketotic hyperglycinemia.
  J Biol Chem, 279, 50514-50523.
PDB codes: 1woo 1wop 1wor 1wos
15159392 H.S.Toogood, A.van Thiel, J.Basran, M.J.Sutcliffe, N.S.Scrutton, and D.Leys (2004).
Extensive domain motion and electron transfer in the human electron transferring flavoprotein.medium chain Acyl-CoA dehydrogenase complex.
  J Biol Chem, 279, 32904-32912.
PDB code: 1t9g
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.