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X-ray analysis of bilirubin oxidase from Myrothecium verrucaria at 2.3 A resolution using a twinned crystal.

Mizutani K, Toyoda M, Sagara K, Takahashi N, Sato A, Kamitaka Y, Tsujimura S, Nakanishi Y, Sugiura T, Yamaguchi S, Kano K, Mikami B
Acta Crystallogr Sect F Struct Biol Cryst Commun 66 765-70 (2010)
Cited: 14 times
EuropePMC logo PMID: 20606269

Abstract

Bilirubin oxidase (BOD), a multicopper oxidase found in Myrothecium verrucaria, catalyzes the oxidation of bilirubin to biliverdin. Oxygen is the electron acceptor and is reduced to water. BOD is used for diagnostic analysis of bilirubin in serum and has attracted considerable attention as an enzymatic catalyst for the cathode of biofuel cells that work under neutral conditions. Here, the crystal structure of BOD is reported for the first time. Blue bipyramid-shaped crystals of BOD obtained in 2-methyl-2,4-pentanediol (MPD) and ammonium sulfate solution were merohedrally twinned in space group P6(3). Structure determination was achieved by the single anomalous diffraction (SAD) method using the anomalous diffraction of Cu atoms and synchrotron radiation and twin refinement was performed in the resolution range 33-2.3 A. The overall organization of BOD is almost the same as that of other multicopper oxidases: the protein is folded into three domains and a total of four copper-binding sites are found in domains 1 and 3. Although the four copper-binding sites were almost identical to those of other multicopper oxidases, the hydrophilic Asn residue (at the same position as a hydrophobic residue such as Leu in other multicopper oxidases) very close to the type I copper might contribute to the characteristically high redox potential of BOD.

Articles - 3abg mentioned but not cited (1)

  1. X-ray analysis of bilirubin oxidase from Myrothecium verrucaria at 2.3 A resolution using a twinned crystal. Mizutani K, Toyoda M, Sagara K, Takahashi N, Sato A, Kamitaka Y, Tsujimura S, Nakanishi Y, Sugiura T, Yamaguchi S, Kano K, Mikami B. Acta Crystallogr Sect F Struct Biol Cryst Commun 66 765-770 (2010)


Reviews citing this publication (4)

  1. Three-dimensional structures of laccases. Hakulinen N, Rouvinen J. Cell Mol Life Sci 72 857-868 (2015)
  2. Structural insights into the O2 reduction mechanism of multicopper oxidase. Komori H, Higuchi Y. J Biochem 158 293-298 (2015)
  3. Features and applications of bilirubin oxidases. Mano N. Appl Microbiol Biotechnol 96 301-307 (2012)
  4. High-throughput plasmid construction using homologous recombination in yeast: its mechanisms and application to protein production for X-ray crystallography. Mizutani K. Biosci Biotechnol Biochem 79 1-10 (2015)

Articles citing this publication (9)

  1. Bilirubin oxidase from Myrothecium verrucaria: X-ray determination of the complete crystal structure and a rational surface modification for enhanced electrocatalytic O2 reduction. Cracknell JA, McNamara TP, Lowe ED, Blanford CF. Dalton Trans 40 6668-6675 (2011)
  2. Spectroscopic and crystallographic characterization of "alternative resting" and "resting oxidized" enzyme forms of bilirubin oxidase: implications for activity and electrochemical behavior of multicopper oxidases. Kjaergaard CH, Durand F, Tasca F, Qayyum MF, Kauffmann B, Gounel S, Suraniti E, Hodgson KO, Hedman B, Mano N, Solomon EI. J Am Chem Soc 134 5548-5551 (2012)
  3. Optimization of a membraneless glucose/oxygen enzymatic fuel cell based on a bioanode with high coulombic efficiency and current density. Shao M, Zafar MN, Falk M, Ludwig R, Sygmund C, Peterbauer CK, Guschin DA, MacAodha D, Ó Conghaile P, Leech D, Toscano MD, Shleev S, Schuhmann W, Gorton L. Chemphyschem 14 2260-2269 (2013)
  4. Enzymatic polymerization of dihydroquercetin using bilirubin oxidase. Khlupova ME, Vasil'eva IS, Shumakovich GP, Morozova OV, Chertkov VA, Shestakova AK, Kisin AV, Yaropolov AI. Biochemistry (Mosc) 80 233-241 (2015)
  5. Redox Potential-Dependent Formation of an Unusual His-Trp Bond in Bilirubin Oxidase. Akter M, Tokiwa T, Shoji M, Nishikawa K, Shigeta Y, Sakurai T, Higuchi Y, Kataoka K, Shibata N. Chemistry 24 18052-18058 (2018)
  6. Putative role of conserved water molecules in the hydration and inter-domain recognition of mono nuclear copper centers in O2-bound human ceruloplasmin: A comparative study between X-ray and MD simulated structures. Mukhopadhyay BP. Bioinformation 15 402-411 (2019)
  7. Pyrenyl-carbon nanostructures for scalable enzyme electrocatalysis and biological fuel cells. Krishnan S, Frazis M, Premaratne G, Niroula J, Echeverria E, McIlroy DN. Analyst 143 2876-2882 (2018)
  8. Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction. Tokiwa T, Shoji M, Sladek V, Shibata N, Higuchi Y, Kataoka K, Sakurai T, Shigeta Y, Misaizu F. Molecules 24 E76 (2018)
  9. The Structure of Bilirubin Oxidase from Bacillus pumilus Reveals a Unique Disulfide Bond for Site-Specific Direct Electron Transfer. Gihaz S, Herzallh NS, Cohen Y, Bachar O, Fishman A, Yehezkeli O. Biosensors (Basel) 12 258 (2022)


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