Copper site of the <i>met/deoxy</i> structure of catechol oxidase from <i>Aspergillus oryzae</i>.

<p>An <i>F</i>_<i>o</i><i>−F</i>_<i>c</i> omit map of oxygen species at the copper site is shown in green at the 3σ contour level. <b>A</b>: molecule A, the Cu-Cu distance was 4.3 Å, and the distance between water molecules was 2.5 Å. <b>B</b>: molecule B, Cu-Cu distance was 4.4 Å, and the distance between water molecules was 2.6 Å, <b>C</b>: molecule C, the Cu-Cu distance was 4.4 Å, and the distance from atom O2 of the peroxide moiety to water was 2.5 Å. <b>D</b>: molecule D, the Cu-Cu distance was 4.5 Å, and the distance between water molecules was 2.6 Å.</p

Copper sites in the crystal structures of catechol oxidase from <i>Aspergillus oryzae</i>.

<p>An <i>F</i>_<i>o</i><i>−F</i>_<i>c</i> omit map of oxygen species at the copper site is shown in green at the 3σ contour level. <b>A</b> 4J3P (now shown with a peroxide moiety) <b>B</b> <i>met/deoxy</i> (molecule B is shown) and <b>C</b> <i>deoxy</i> (molecule B is shown).</p

Different forms of coupled binuclear copper sites.

<p>Different forms of coupled binuclear copper sites.</p

A new crystal form of <i>Aspergillus oryzae</i> catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes

<div><p>Coupled binuclear copper (CBC) enzymes have a conserved type 3 copper site that binds molecular oxygen to oxidize various mono- and diphenolic compounds. In this study, we found a new crystal form of catechol oxidase from <i>Aspergillus oryzae</i> (<i>Ao</i>CO4) and solved two new structures from two different crystals at 1.8-Å and at 2.5-Å resolutions. These structures showed different copper site forms (<i>met/deoxy</i> and <i>deoxy</i>) and also differed from the copper site observed in the previously solved structure of <i>Ao</i>CO4. We also analysed the electron density maps of all of the 56 CBC enzyme structures available in the protein data bank (PDB) and found that many of the published structures have vague copper sites. Some of the copper sites were then re-refined to find a better fit to the observed electron density. General problems in the refinement of metalloproteins and metal centres are discussed.</p></div

Data collection and structure refinement statistics for <i>Ao</i>CO4 crystals.

<p>Data collection and structure refinement statistics for <i>Ao</i>CO4 crystals.</p

Re-evaluation of copper sites in CBC enzyme structures.

<p>Re-evaluation of copper sites in CBC enzyme structures.</p

Tyrosinase and catechol oxidase activity.

<p>Tyrosinase and catechol oxidase activity.</p

Re-refinement of publish CBC enzyme crystal structures.

<p><b>A</b> The copper site of the deposited 1BT3 (catechol oxidase from <i>Ipomoea batatas</i>) shows a positive peak of the <i>F</i>_<i>o</i><i>−F</i>_<i>c</i> electron density (in green) in PDB_REDO-calculated maps. The distance between copper ions was 2.9 Å, and the Cu-O distances were both 2.0 Å. <b>B</b> Calculated <i>F</i>_<i>o</i><i>−F</i>_<i>c</i> difference-Fourier omit map (in green) for oxygen in 1BT3. <b>C</b> Calculated <i>2F</i>_<i>o</i><i>−F</i>_<i>c</i> Fourier map (in blue, 1σ contour level) for the copper site in the re-refined structure of 1BT3. Two oxygen atoms were refined between the copper ions. The distance between copper ions was 3.0 Å, and all the Cu-O distances were 1.9 Å. <b>D</b> The copper site of the deposited 2AHL (tyrosinase from <i>Streptomyces castaneoglobisporus</i>) shows peaks of positive <i>F</i>_<i>o</i><i>−F</i>_<i>c</i> electron density (in green) around the water in the PDB_REDO-calculated maps. <b>E</b> Copper site of deposited 2P3X with the Cu-O-Cu unit shows a peak of <i>F</i>_<i>o</i><i>−F</i>_<i>c</i> difference electron density (in green) in PDB_REDO-calculated maps. <b>F</b> Copper site of deposited 4J6T (tyrosinase from <i>Bacillus megaterium)</i> with one water molecule shows a peak of <i>F</i>_<i>o</i><i>−F</i>_<i>c</i> difference electron density (in green) in PDB_REDO-calculated maps. Molecule A is shown. <b>G</b> The calculated <i>F</i>_<i>o</i><i>−F</i>_<i>c</i> difference-Fourier omit map (in green) for water in 4J6T. <b>H</b> Calculated <i>2F</i>_<i>o</i><i>−F</i>_<i>c</i> Fourier map (in blue) for the copper site in the re-refined structure of 4J6T. Peroxide ion was refined between the copper ions. The difference maps are all shown in 3σ contour level.</p

Physiological evaluation of the filamentous fungus in production processes by marker gene expression analysis-4

<p><b>Copyright information:</b></p><p>Taken from "Physiological evaluation of the filamentous fungus in production processes by marker gene expression analysis"</p><p>http://www.biomedcentral.com/1472-6750/7/28</p><p>BMC Biotechnology 2007;7():28-28.</p><p>Published online 30 May 2007</p><p>PMCID:PMC1899492.</p><p></p>se and laccase genes as logratio to maximal expression measured in the cultures (blue symbols). Expression of genes showing >2-fold increasing mRNA level relative to polyA RNA after exhaustion of lactose as logratio to the expression level in a sample taken before the observed increase (red symbols)

Physiological evaluation of the filamentous fungus in production processes by marker gene expression analysis-1

<p><b>Copyright information:</b></p><p>Taken from "Physiological evaluation of the filamentous fungus in production processes by marker gene expression analysis"</p><p>http://www.biomedcentral.com/1472-6750/7/28</p><p>BMC Biotechnology 2007;7():28-28.</p><p>Published online 30 May 2007</p><p>PMCID:PMC1899492.</p><p></p>pression level measured in the first sample (19.2 h). Expression levels were normalised using polyA RNA