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The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations.

Just VJ, Burrell MR, Bowater L, McRobbie I, Stevenson CE, Lawson DM, Bornemann S
Biochem J 407 397-406 (2007)
Related entries: 2uy9, 2uya, 2uyb

Cited: 22 times
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Abstract

Oxalate decarboxylase (EC 4.1.1.2) catalyses the conversion of oxalate into carbon dioxide and formate. It requires manganese and, uniquely, dioxygen for catalysis. It forms a homohexamer and each subunit contains two similar, but distinct, manganese sites termed sites 1 and 2. There is kinetic evidence that only site 1 is catalytically active and that site 2 is purely structural. However, the kinetics of enzymes with mutations in site 2 are often ambiguous and all mutant kinetics have been interpreted without structural information. Nine new site-directed mutants have been generated and four mutant crystal structures have now been solved. Most mutants targeted (i) the flexibility (T165P), (ii) favoured conformation (S161A, S164A, D297A or H299A) or (iii) presence (Delta162-163 or Delta162-164) of a lid associated with site 1. The kinetics of these mutants were consistent with only site 1 being catalytically active. This was particularly striking with D297A and H299A because they disrupted hydrogen bonds between the lid and a neighbouring subunit only when in the open conformation and were distant from site 2. These observations also provided the first evidence that the flexibility and stability of lid conformations are important in catalysis. The deletion of the lid to mimic the plant oxalate oxidase led to a loss of decarboxylase activity, but only a slight elevation in the oxalate oxidase side reaction, implying other changes are required to afford a reaction specificity switch. The four mutant crystal structures (R92A, E162A, Delta162-163 and S161A) strongly support the hypothesis that site 2 is purely structural.

Articles - 2uy8 mentioned but not cited (2)

  1. Structural and immunologic characterization of Ara h 1, a major peanut allergen. Chruszcz M, Maleki SJ, Majorek KA, Demas M, Bublin M, Solberg R, Hurlburt BK, Ruan S, Mattison CP, Breiteneder H, Minor W. J Biol Chem 286 39318-39327 (2011)
  2. The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations. Just VJ, Burrell MR, Bowater L, McRobbie I, Stevenson CE, Lawson DM, Bornemann S. Biochem J 407 397-406 (2007)


Reviews citing this publication (2)

  1. Oxalate decarboxylase: biotechnological update and prevalence of the enzyme in filamentous fungi. Mäkelä MR, Hildén K, Lundell TK. Appl Microbiol Biotechnol 87 801-814 (2010)
  2. Oxygen activation by mononuclear Mn, Co, and Ni centers in biology and synthetic complexes. Fiedler AT, Fischer AA. J Biol Inorg Chem 22 407-424 (2017)

Articles citing this publication (18)

  1. Structural insight into the Clostridium difficile ethanolamine utilisation microcompartment. Pitts AC, Tuck LR, Faulds-Pain A, Lewis RJ, Marles-Wright J. PLoS One 7 e48360 (2012)
  2. A previously unidentified sigma factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis. MacLellan SR, Wecke T, Helmann JD. Mol Microbiol 69 954-967 (2008)
  3. Metal dependence of oxalate decarboxylase activity. Moomaw EW, Angerhofer A, Moussatche P, Ozarowski A, García-Rubio I, Richards NG. Biochemistry 48 6116-6125 (2009)
  4. pH-dependent structures of the manganese binding sites in oxalate decarboxylase as revealed by high-field electron paramagnetic resonance. Tabares LC, Gätjens J, Hureau C, Burrell MR, Bowater L, Pecoraro VL, Bornemann S, Un S. J Phys Chem B 113 9016-9025 (2009)
  5. Oxalate decarboxylase of the white-rot fungus Dichomitus squalens demonstrates a novel enzyme primary structure and non-induced expression on wood and in liquid cultures. Mäkelä MR, Hildén K, Hatakka A, Lundell TK. Microbiology (Reading) 155 2726-2738 (2009)
  6. A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase. Saylor BT, Reinhardt LA, Lu Z, Shukla MS, Nguyen L, Cleland WW, Angerhofer A, Allen KN, Richards NG. Biochemistry 51 2911-2920 (2012)
  7. EPR spin trapping of an oxalate-derived free radical in the oxalate decarboxylase reaction. Imaram W, Saylor BT, Centonze CP, Richards NG, Angerhofer A. Free Radic Biol Med 50 1009-1015 (2011)
  8. Formation of Hexacoordinate Mn(III) in Bacillus subtilis Oxalate Decarboxylase Requires Catalytic Turnover. Zhu W, Wilcoxen J, Britt RD, Richards NG. Biochemistry 55 429-434 (2016)
  9. Membrane inlet for mass spectrometric measurement of catalysis by enzymatic decarboxylases. Moral ME, Tu C, Richards NG, Silverman DN. Anal Biochem 418 73-77 (2011)
  10. Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase. Zhu W, Easthon LM, Reinhardt LA, Tu C, Cohen SE, Silverman DN, Allen KN, Richards NG. Biochemistry 55 2163-2173 (2016)
  11. Observation of superoxide production during catalysis of Bacillus subtilis oxalate decarboxylase at pH 4. Twahir UT, Stedwell CN, Lee CT, Richards NG, Polfer NC, Angerhofer A. Free Radic Biol Med 80 59-66 (2015)
  12. Assigning the EPR fine structure parameters of the Mn(II) centers in Bacillus subtilis oxalate decarboxylase by site-directed mutagenesis and DFT/MM calculations. Campomanes P, Kellett WF, Easthon LM, Ozarowski A, Allen KN, Angerhofer A, Rothlisberger U, Richards NG. J Am Chem Soc 136 2313-2323 (2014)
  13. Kinetic and spectroscopic studies of bicupin oxalate oxidase and putative active site mutants. Moomaw EW, Hoffer E, Moussatche P, Salerno JC, Grant M, Immelman B, Uberto R, Ozarowski A, Angerhofer A. PLoS One 8 e57933 (2013)
  14. The effects of Oxazyme on oxalate degradation: results and implications of in vitro experiments. Mufarrij PW, Lange JN, Knight J, Assimos DG, Holmes RP. J Endourol 27 284-287 (2013)
  15. Oxalate decarboxylase uses electron hole hopping for catalysis. Pastore AJ, Teo RD, Montoya A, Burg MJ, Twahir UT, Bruner SD, Beratan DN, Angerhofer A. J Biol Chem 297 100857 (2021)
  16. Biochemical properties and oxalate-degrading activity of oxalate decarboxylase from bacillus subtilis at neutral pH. Conter C, Oppici E, Dindo M, Rossi L, Magnani M, Cellini B. IUBMB Life 71 917-927 (2019)
  17. Immobilization of Bacillus subtilis oxalate decarboxylase on a Zn-IMAC resin. Twahir U, Molina L, Ozarowski A, Angerhofer A. Biochem Biophys Rep 4 98-103 (2015)
  18. Optimization of monomethoxy polyethyleneglycol-modified oxalate decarboxylase by response surface methodology. Long H, Cai X, Yang H, He J, Wu J, Lin R. J Biol Phys 43 445-459 (2017)


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