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PDBsum entry 1uw8

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protein ligands metals links
Lyase PDB id
1uw8
Jmol
Contents
Protein chain
377 a.a. *
Ligands
TRS
Metals
_MN ×2
Waters ×402
* Residue conservation analysis
PDB id:
1uw8
Name: Lyase
Title: Crystal structure of oxalate decarboxylase
Structure: Oxalate decarboxylase oxdc. Chain: a. Synonym: oxdc. Engineered: yes. Other_details: formerly known as yvrk
Source: Bacillus subtilis. Organism_taxid: 1423. Strain: 168. Atcc: 23857. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PDB file)
Resolution:
2.0Å     R-factor:   0.129     R-free:   0.158
Authors: V.J.Just,C.E.M.Stevenson,L.Bowater,A.Tanner,D.M.Lawson, S.Bornemann
Key ref:
V.J.Just et al. (2004). A closed conformation of Bacillus subtilis oxalate decarboxylase OxdC provides evidence for the true identity of the active site. J Biol Chem, 279, 19867-19874. PubMed id: 14871895 DOI: 10.1074/jbc.M313820200
Date:
02-Feb-04     Release date:   19-Feb-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O34714  (OXDC_BACSU) -  Oxalate decarboxylase OxdC
Seq:
Struc:
385 a.a.
377 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.2  - Oxalate decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Oxalate = formate + CO2
Oxalate
= formate
+ CO(2)
      Cofactor: Mn(2+)
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     metabolic process   1 term 
  Biochemical function     nutrient reservoir activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M313820200 J Biol Chem 279:19867-19874 (2004)
PubMed id: 14871895  
 
 
A closed conformation of Bacillus subtilis oxalate decarboxylase OxdC provides evidence for the true identity of the active site.
V.J.Just, C.E.Stevenson, L.Bowater, A.Tanner, D.M.Lawson, S.Bornemann.
 
  ABSTRACT  
 
Oxalate decarboxylase (EC 4.1.1.2) catalyzes the conversion of oxalate to formate and carbon dioxide and utilizes dioxygen as a cofactor. By contrast, the evolutionarily related oxalate oxidase (EC 1.2.3.4) converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. Divergent free radical catalytic mechanisms have been proposed for these enzymes that involve the requirement of an active site proton donor in the decarboxylase but not the oxidase reaction. The oxidase possesses only one domain and manganese binding site per subunit, while the decarboxylase has two domains and two manganese sites per subunit. A structure of the decarboxylase together with a limited mutagenesis study has recently been interpreted as evidence that the C-terminal domain manganese binding site (site 2) is the catalytic site and that Glu-333 is the crucial proton donor (Anand, R., Dorrestein, P. C., Kinsland, C., Begley, T. P., and Ealick, S. E. (2002) Biochemistry 41, 7659-7669). The N-terminal binding site (site 1) of this structure is solvent-exposed (open) and lacks a suitable proton donor for the decarboxylase reaction. We report a new structure of the decarboxylase that shows a loop containing a 3(10) helix near site 1 in an alternative conformation. This loop adopts a "closed" conformation forming a lid covering the entrance to site 1. This conformational change brings Glu-162 close to the manganese ion, making it a new candidate for the crucial proton donor. Site-directed mutagenesis of equivalent residues in each domain provides evidence that Glu-162 performs this vital role and that the N-terminal domain is either the sole or the dominant catalytically active domain.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. Closure of the lid in OxdC. Partial slab views of the open (A) (23) and closed (B) hexameric structures are shown. The solvent-accessible surface of the protein is shown in green (with a gray underside), the interior of the protein is shown in pale yellow, and bulk solvent is shown in pale blue. The surface shown at the top of the figure is that of the equator of the donut-shaped hexamer, while that at the bottom left is of the solvent channel along its 3-fold axis. The site 1 manganese ion is shown in blue space-filling mode. The Glu-162 side chain, the -carbons of amino acids 161-165, two of the metal ion ligands, His-97 and His-140, formate, and the water molecules are shown in Corey-Pauling-Koltun (CPK) colored ball-and-stick mode. The trajectory for substrate entry is indicated by a broken arrow. This figure was produced using the programs MSMS (www.scripps.edu/pub/olson-web/people/sanner/html/msms_home.html) and DINO (www.dino3d.org).
Figure 4.
FIG. 4. Comparison of the manganese ion binding sites of OxdC in the two structures and a model. The manganese binding sites of the closed structure (A = site 1 and B = site 2) are shown next to those of the open structure (C = site 1 and D = site 2) (23). A molecular model (E) of oxalate and dioxygen bound to site 1 manganese ion shows the need for Glu-162 to be displaced somewhat in comparison with the experimentally determined closed structure (A). Interatomic distances are shown in Å with dashed lines.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 19867-19874) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21264418 M.E.Moral, C.Tu, W.Imaram, A.Angerhofer, D.N.Silverman, and N.G.Richards (2011).
Nitric oxide reversibly inhibits Bacillus subtilis oxalate decarboxylase.
  Chem Commun (Camb), 47, 3111-3113.  
21277974 W.Imaram, B.T.Saylor, C.P.Centonze, N.G.Richards, and A.Angerhofer (2011).
EPR spin trapping of an oxalate-derived free radical in the oxalate decarboxylase reaction.
  Free Radic Biol Med, 50, 1009-1015.  
20464388 M.R.Mäkelä, K.Hildén, and T.K.Lundell (2010).
Oxalate decarboxylase: biotechnological update and prevalence of the enzyme in filamentous fungi.
  Appl Microbiol Biotechnol, 87, 801-814.  
18946701 A.Kolandaswamy, L.George, and S.Sadasivam (2009).
Heterologous expression of oxalate decarboxylase in Lactobacillus plantarum NC8.
  Curr Microbiol, 58, 117-121.  
19473032 E.W.Moomaw, A.Angerhofer, P.Moussatche, A.Ozarowski, I.García-Rubio, and N.G.Richards (2009).
Metal dependence of oxalate decarboxylase activity.
  Biochemistry, 48, 6116-6125.  
19066990 J.J.Stewart (2009).
Application of the PM6 method to modeling proteins.
  J Mol Model, 15, 765-805.  
19505123 L.C.Tabares, J.Gätjens, C.Hureau, M.R.Burrell, L.Bowater, V.L.Pecoraro, S.Bornemann, and S.Un (2009).
pH-dependent structures of the manganese binding sites in oxalate decarboxylase as revealed by high-field electron paramagnetic resonance.
  J Phys Chem B, 113, 9016-9025.  
18985279 M.Graz, A.Jarosz-Wilkołazka, and B.Pawlikowska-Pawlega (2009).
Abortiporus biennis tolerance to insoluble metal oxides: oxalate secretion, oxalate oxidase activity, and mycelial morphology.
  Biometals, 22, 401-410.  
18573182 S.R.MacLellan, T.Wecke, and J.D.Helmann (2008).
A previously unidentified sigma factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis.
  Mol Microbiol, 69, 954-967.  
17459326 D.Svedruzić, Y.Liu, L.A.Reinhardt, E.Wroclawska, W.W.Cleland, and N.G.Richards (2007).
Investigating the roles of putative active site residues in the oxalate decarboxylase from Bacillus subtilis.
  Arch Biochem Biophys, 464, 36-47.  
15909034 A.L.Fuller, R.W.Watkins, K.R.Dunbar, A.V.Prosvirin, A.M.Arif, and L.M.Berreau (2005).
Manganese(II) chemistry of a new N3O-donor chelate ligand: synthesis, X-ray structures, and magnetic properties of solvent- and oxalate-bound complexes.
  Dalton Trans, (), 1891-1896.  
16000768 M.R.Escutia, L.Bowater, A.Edwards, A.R.Bottrill, M.R.Burrell, R.Polanco, R.Vicuña, and S.Bornemann (2005).
Cloning and sequencing of two Ceriporiopsis subvermispora bicupin oxalate oxidase allelic isoforms: implications for the reaction specificity of oxalate oxidases and decarboxylases.
  Appl Environ Microbiol, 71, 3608-3616.  
16114032 S.Raymond, A.Tocilj, E.Ajamian, Y.Li, M.N.Hung, A.Matte, and M.Cygler (2005).
Crystal structure of ureidoglycolate hydrolase (AllA) from Escherichia coli O157:H7.
  Proteins, 61, 454-459.
PDB code: 1yqc
15583401 C.E.Stevenson, A.Tanner, L.Bowater, S.Bornemann, and D.M.Lawson (2004).
SAD at home: solving the structure of oxalate decarboxylase with the anomalous signal from manganese using X-ray data collected on a home source.
  Acta Crystallogr D Biol Crystallogr, 60, 2403-2406.  
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.