5OR4

Crystal structure of Aspergillus oryzae catechol oxidase in deoxy-form

Summary for 5OR4

• Entry DOI: 10.2210/pdb5or4/pdb
• Related: 5OR3
• Descriptor: catechol oxidase, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (7 entities in total)
• Functional Keywords: catechol oxidase, polyphenol oxidase, binuclear copper enzyme, type 3 copper center, oxidoreductase
• Biological source: Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)
• Total number of polymer chains: 4
• Total formula weight: 173765.57

Authors

Hakulinen, N.,Penttinen, L.,Rutanen, C.,Rouvinen, J. (deposition date: 2017-08-15, release date: 2018-05-09, Last modification date: 2024-10-09)

Primary citation

Penttinen, L.,Rutanen, C.,Saloheimo, M.,Kruus, K.,Rouvinen, J.,Hakulinen, N.
A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes.
PLoS ONE, 13:e0196691-e0196691, 2018

PubMed Abstract: 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 Aspergillus oryzae (AoCO4) 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 (met/deoxy and deoxy) and also differed from the copper site observed in the previously solved structure of AoCO4. 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.

PubMed: 29715329
DOI: 10.1371/journal.pone.0196691

Experimental method

X-RAY DIFFRACTION (2.445 Å)