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PDBsum entry 2gb0

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2gb0
Jmol
Contents
Protein chains
387 a.a. *
Ligands
PO4 ×4
FAD ×2
Metals
_CL ×2
Waters ×671
* Residue conservation analysis
PDB id:
2gb0
Name: Oxidoreductase
Title: Monomeric sarcosine oxidase: structure of a covalently flavi amine oxidizing enzyme
Structure: Monomeric sarcosine oxidase. Chain: a, b. Synonym: msox. Engineered: yes
Source: Bacillus sp.. Organism_taxid: 69000. Strain: b-0618. Gene: soxa, sox. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.85Å     R-factor:   0.165     R-free:   0.198
Authors: P.Trickey,M.A.Wagner,M.S.Jorns,F.S.Mathews
Key ref:
P.Trickey et al. (1999). Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme. Structure Fold Des, 7, 331-345. PubMed id: 10368302 DOI: 10.1016/S0969-2126(99)80043-4
Date:
09-Mar-06     Release date:   21-Mar-06    
Supersedes: 1l9f
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P40859  (MSOX_BACB0) -  Monomeric sarcosine oxidase
Seq:
Struc:
390 a.a.
387 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.5.3.1  - Sarcosine oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Sarcosine + H2O + O2 = glycine + formaldehyde + H2O2
Sarcosine
+ H(2)O
+ O(2)
= glycine
+ formaldehyde
+ H(2)O(2)
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
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   2 terms 
  Biochemical function     oxidoreductase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(99)80043-4 Structure Fold Des 7:331-345 (1999)
PubMed id: 10368302  
 
 
Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme.
P.Trickey, M.A.Wagner, M.S.Jorns, F.S.Mathews.
 
  ABSTRACT  
 
BACKGROUND: Monomeric sarcosine oxidases (MSOXs) are among the simplest members of a recently recognized family of eukaryotic and prokaryotic enzymes that catalyze similar oxidative reactions with various secondary or tertiary amino acids and contain covalently bound flavins. Other members of this family include heterotetrameric sarcosine oxidase, N-methyltryptophan oxidase and pipecolate oxidase. Mammalian sarcosine dehydrogenase and dimethylglycine dehydrogenase may be more distantly related family members. RESULTS: The X-ray crystal structure of MSOX from Bacillus sp. B-0618, expressed in Escherichia coli, has been solved at 2.0 A resolution by multiwavelength anomalous dispersion (MAD) from crystals of the selenomethionine-substituted enzyme. Fourteen selenium sites, belonging to two MSOX molecules in the asymmetric unit, were used for MAD phasing and to define the local twofold symmetry axis for electron-density averaging. The structures of the native enzyme and of two enzyme-inhibitor complexes were also determined. CONCLUSIONS: MSOX is a two-domain protein with an overall topology most similar to that of D-amino acid oxidase, with which it shares 14% sequence identity. The flavin ring is located in a very basic environment, making contact with sidechains of arginine, lysine, histidine and the N-terminal end of a helix dipole. The flavin is covalently attached through an 8alpha-S-cysteinyl linkage to Cys315 of the catalytic domain. Covalent attachment is probably self-catalyzed through interactions with the positive sidechains and the helix dipole. Substrate binding is probably stabilized by hydrogen bonds between the substrate carboxylate and two basic sidechains, Arg52 and Lys348, located above the re face of the flavin ring.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. Proposed mechanism for covalent flavinylation in MSOX (Scheme III).
 
  The above figure is reprinted by permission from Cell Press: Structure Fold Des (1999, 7, 331-345) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21491497 L.Gabison, C.Chopard, N.Colloc'h, F.Peyrot, B.Castro, M.E.Hajji, M.Altarsha, G.Monard, M.Chiadmi, and T.Prangé (2011).
X-ray, ESR, and quantum mechanics studies unravel a spin well in the cofactor-less urate oxidase.
  Proteins, 79, 1964-1976.
PDB code: 3obp
20936278 T.Satomura, X.D.Zhang, Y.Hara, K.Doi, H.Sakuraba, and T.Ohshima (2011).
Characterization of a novel dye-linked L-proline dehydrogenase from an aerobic hyperthermophilic archaeon, Pyrobaculum calidifontis.
  Appl Microbiol Biotechnol, 89, 1075-1082.  
20353187 M.S.Jorns, Z.W.Chen, and F.S.Mathews (2010).
Structural characterization of mutations at the oxygen activation site in monomeric sarcosine oxidase .
  Biochemistry, 49, 3631-3639.
PDB codes: 3m0o 3m12 3m13
19651103 P.F.Fitzpatrick (2010).
Oxidation of amines by flavoproteins.
  Arch Biochem Biophys, 493, 13-25.  
20383736 S.Kim, E.Nibe, S.Ferri, W.Tsugawa, and K.Sode (2010).
Engineering of dye-mediated dehydrogenase property of fructosyl amino acid oxidases by site-directed mutagenesis studies of its putative proton relay system.
  Biotechnol Lett, 32, 1123-1129.  
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.  
19624733 F.Forneris, E.Battaglioli, A.Mattevi, and C.Binda (2009).
New roles of flavoproteins in molecular cell biology: histone demethylase LSD1 and chromatin.
  FEBS J, 276, 4304-4312.  
19199575 M.Henderson Pozzi, V.Gawandi, and P.F.Fitzpatrick (2009).
pH dependence of a mammalian polyamine oxidase: insights into substrate specificity and the role of lysine 315.
  Biochemistry, 48, 1508-1516.  
19088070 N.G.Leferink, M.W.Fraaije, H.J.Joosten, P.J.Schaap, A.Mattevi, and W.J.van Berkel (2009).
Identification of a gatekeeper residue that prevents dehydrogenases from acting as oxidases.
  J Biol Chem, 284, 4392-4397.  
19702312 P.R.Kommoju, R.C.Bruckner, P.Ferreira, C.J.Carrell, F.S.Mathews, and M.S.Jorns (2009).
Factors that affect oxygen activation and coupling of the two redox cycles in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase.
  Biochemistry, 48, 9542-9555.
PDB code: 3hzl
19530706 P.R.Kommoju, R.C.Bruckner, P.Ferreira, and M.S.Jorns (2009).
Probing the role of active site residues in NikD, an unusual amino acid oxidase that catalyzes an aromatization reaction important in nikkomycin biosynthesis.
  Biochemistry, 48, 6951-6962.  
19354202 R.C.Bruckner, and M.S.Jorns (2009).
Spectral and kinetic characterization of intermediates in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase.
  Biochemistry, 48, 4455-4465.  
18186483 A.Ilari, A.Bonamore, S.Franceschini, A.Fiorillo, A.Boffi, and G.Colotti (2008).
The X-ray structure of N-methyltryptophan oxidase reveals the structural determinants of substrate specificity.
  Proteins, 71, 2065-2075.
PDB code: 2uzz
18667417 F.Collard, J.Zhang, I.Nemet, K.R.Qanungo, V.M.Monnier, and V.C.Yee (2008).
Crystal Structure of the Deglycating Enzyme Fructosamine Oxidase (Amadoriase II).
  J Biol Chem, 283, 27007-27016.  
18693755 G.Zhao, R.C.Bruckner, and M.S.Jorns (2008).
Identification of the oxygen activation site in monomeric sarcosine oxidase: role of Lys265 in catalysis.
  Biochemistry, 47, 9124-9135.  
18793324 J.Jin, H.Mazon, R.H.van den Heuvel, A.J.Heck, D.B.Janssen, and M.W.Fraaije (2008).
Covalent flavinylation of vanillyl-alcohol oxidase is an autocatalytic process.
  FEBS J, 275, 5191-5200.  
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
17542620 E.C.Ralph, J.S.Hirschi, M.A.Anderson, W.W.Cleland, D.A.Singleton, and P.F.Fitzpatrick (2007).
Insights into the mechanism of flavoprotein-catalyzed amine oxidation from nitrogen isotope effects on the reaction of N-methyltryptophan oxidase.
  Biochemistry, 46, 7655-7664.  
17364200 G.Sindelar, and V.F.Wendisch (2007).
Improving lysine production by Corynebacterium glutamicum through DNA microarray-based identification of novel target genes.
  Appl Microbiol Biotechnol, 76, 677-689.  
17419730 J.Jin, H.Mazon, R.H.van den Heuvel, D.B.Janssen, and M.W.Fraaije (2007).
Discovery of a eugenol oxidase from Rhodococcus sp. strain RHA1.
  FEBS J, 274, 2311-2321.  
17160532 M.Fujiwara, J.Sumitani, S.Koga, I.Yoshioka, T.Kouzuma, S.Imamura, T.Kawaguchi, and M.Arai (2007).
Alteration of substrate specificity of fructosyl-amino acid oxidase from Fusarium oxysporum.
  Appl Microbiol Biotechnol, 74, 813-819.  
  19890477 P.F.Fitzpatrick (2007).
Insights into the mechanisms of flavoprotein oxidases from kinetic isotope effects.
  J Labelled Comp Radiopharm, 50, 1016-1025.  
17176107 E.C.Ralph, M.A.Anderson, W.W.Cleland, and P.F.Fitzpatrick (2006).
Mechanistic studies of the flavoenzyme tryptophan 2-monooxygenase: deuterium and 15N kinetic isotope effects on alanine oxidation by an L-amino acid oxidase.
  Biochemistry, 45, 15844-15852.  
16681370 G.Zhao, and M.S.Jorns (2006).
Spectral and kinetic characterization of the michaelis charge transfer complex in monomeric sarcosine oxidase.
  Biochemistry, 45, 5985-5992.  
16977470 K.Guo, X.Ma, G.Sun, Y.Zhao, X.Li, W.Zhao, and L.Kai (2006).
Expression and characterization of a thermostable sarcosine oxidase (SOX) from Bacillus sp. in Escherichia coli.
  Appl Microbiol Biotechnol, 73, 559-566.  
16934831 R.M.Hynson, F.S.Mathews, and M.Schuman Jorns (2006).
Identification of a stable flavin-thiolate adduct in heterotetrameric sarcosine oxidase.
  J Mol Biol, 362, 656-663.  
17043907 S.Miura, S.Ferri, W.Tsugawa, S.Kim, and K.Sode (2006).
Active site analysis of fructosyl amine oxidase using homology modeling and site-directed mutagenesis.
  Biotechnol Lett, 28, 1895-1900.  
15922624 A.Hassan-Abdallah, G.Zhao, M.Eschenbrenner, Z.W.Chen, F.S.Mathews, and M.S.Jorns (2005).
Cloning, expression and crystallization of heterotetrameric sarcosine oxidase from Pseudomonas maltophilia.
  Protein Expr Purif, 43, 33-43.  
15850379 A.Hassan-Abdallah, R.C.Bruckner, G.Zhao, and M.S.Jorns (2005).
Biosynthesis of covalently bound flavin: isolation and in vitro flavinylation of the monomeric sarcosine oxidase apoprotein.
  Biochemistry, 44, 6452-6462.  
15723552 E.C.Ralph, and P.F.Fitzpatrick (2005).
pH and kinetic isotope effects on sarcosine oxidation by N-methyltryptophan oxidase.
  Biochemistry, 44, 3074-3081.  
16363800 G.Zhao, and M.S.Jorns (2005).
Ionization of zwitterionic amine substrates bound to monomeric sarcosine oxidase.
  Biochemistry, 44, 16866-16874.  
16027125 H.Tsuge, R.Kawakami, H.Sakuraba, H.Ago, M.Miyano, K.Aki, N.Katunuma, and T.Ohshima (2005).
Crystal structure of a novel FAD-, FMN-, and ATP-containing L-proline dehydrogenase complex from Pyrococcus horikoshii.
  J Biol Chem, 280, 31045-31049.
PDB code: 1y56
14766747 A.Goyer, T.L.Johnson, L.J.Olsen, E.Collakova, Y.Shachar-Hill, D.Rhodes, and A.D.Hanson (2004).
Characterization and metabolic function of a peroxisomal sarcosine and pipecolate oxidase from Arabidopsis.
  J Biol Chem, 279, 16947-16953.  
15105420 M.Mörtl, K.Diederichs, W.Welte, G.Molla, L.Motteran, G.Andriolo, M.S.Pilone, and L.Pollegioni (2004).
Structure-function correlation in glycine oxidase from Bacillus subtilis.
  J Biol Chem, 279, 29718-29727.
PDB code: 1ryi
12912903 D.Leys, J.Basran, and N.S.Scrutton (2003).
Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase.
  EMBO J, 22, 4038-4048.
PDB codes: 1pj5 1pj6 1pj7
12654003 G.Molla, L.Motteran, V.Job, M.S.Pilone, and L.Pollegioni (2003).
Kinetic mechanisms of glycine oxidase from Bacillus subtilis.
  Eur J Biochem, 270, 1474-1482.  
12015330 C.Binda, A.Mattevi, and D.E.Edmondson (2002).
Structure-function relationships in flavoenzyme-dependent amine oxidations: a comparison of polyamine oxidase and monoamine oxidase.
  J Biol Chem, 277, 23973-23976.  
11842205 G.Fritz, A.Roth, A.Schiffer, T.Büchert, G.Bourenkov, H.D.Bartunik, H.Huber, K.O.Stetter, P.M.Kroneck, and U.Ermler (2002).
Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6-A resolution.
  Proc Natl Acad Sci U S A, 99, 1836-1841.
PDB codes: 1jnr 1jnz
12146941 G.Zhao, H.Song, Z.W.Chen, F.S.Mathews, and M.S.Jorns (2002).
Monomeric sarcosine oxidase: role of histidine 269 in catalysis.
  Biochemistry, 41, 9751-9764.
PDB codes: 1l9c 1l9d 1l9e
12146940 G.Zhao, and M.S.Jorns (2002).
Monomeric sarcosine oxidase: evidence for an ionizable group in the E.S complex.
  Biochemistry, 41, 9747-9750.  
12400161 K.Ito (2002).
[Structural and functional analysis of enzymes and their application to clinical analysis--study on Pseudomonas putida formaldehyde dehydrogenase]
  Yakugaku Zasshi, 122, 805-811.  
11744710 V.Job, G.L.Marcone, M.S.Pilone, and L.Pollegioni (2002).
Glycine oxidase from Bacillus subtilis. Characterization of a new flavoprotein.
  J Biol Chem, 277, 6985-6993.  
11874460 V.Job, G.Molla, M.S.Pilone, and L.Pollegioni (2002).
Overexpression of a recombinant wild-type and His-tagged Bacillus subtilis glycine oxidase in Escherichia coli.
  Eur J Biochem, 269, 1456-1463.  
11761328 D.E.Edmondson, and P.Newton-Vinson (2001).
The covalent FAD of monoamine oxidase: structural and functional role and mechanism of the flavinylation reaction.
  Antioxid Redox Signal, 3, 789-806.  
11705372 J.J.Hollenbeck, D.G.Gurnon, G.C.Fazio, J.J.Carlson, and M.G.Oakley (2001).
A GCN4 variant with a C-terminal basic region binds to DNA with wild-type affinity.
  Biochemistry, 40, 13833-13839.  
11330998 M.Eschenbrenner, L.J.Chlumsky, P.Khanna, F.Strasser, and M.S.Jorns (2001).
Organization of the multiple coenzymes and subunits and role of the covalent flavin link in the complex heterotetrameric sarcosine oxidase.
  Biochemistry, 40, 5352-5367.  
11514662 O.Dym, and D.Eisenberg (2001).
Sequence-structure analysis of FAD-containing proteins.
  Protein Sci, 10, 1712-1728.  
11157233 Y.Liu, T.M.Louie, J.Payne, J.Bohuslavek, H.Bolton, and L.Xun (2001).
Identification, purification, and characterization of iminodiacetate oxidase from the EDTA-degrading bacterium BNC1.
  Appl Environ Microbiol, 67, 696-701.  
10880957 C.Brizio, A.Otto, R.Brandsch, S.Passarella, and M.Barile (2000).
A protein factor of rat liver mitochondrial matrix involved in flavinylation of dimethylglycine dehydrogenase.
  Eur J Biochem, 267, 4346-4354.  
10809721 R.H.van den Heuvel, M.W.Fraaije, A.Mattevi, and W.J.van Berkel (2000).
Asp-170 is crucial for the redox properties of vanillyl-alcohol oxidase.
  J Biol Chem, 275, 14799-14808.
PDB code: 1dzn
10684633 X.Wu, M.Takahashi, S.G.Chen, and V.M.Monnier (2000).
Cloning of amadoriase I isoenzyme from Aspergillus sp.: evidence of FAD covalently linked to Cys342.
  Biochemistry, 39, 1515-1521.  
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.