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5zu3

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<StructureSection load='5zu3' size='340' side='right'caption='[[5zu3]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='5zu3' size='340' side='right'caption='[[5zu3]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5zu3]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZU3 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5zu3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae_RIB40 Aspergillus oryzae RIB40]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZU3 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAY:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+(2R,3S,4S)-5-(8-formyl-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl+dihydrogen+diphosphate'>FAY</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zu3 OCA], [http://pdbe.org/5zu3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zu3 RCSB], [http://www.ebi.ac.uk/pdbsum/5zu3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zu3 ProSAT]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAY:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+(2R,3S,4S)-5-(8-formyl-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl+dihydrogen+diphosphate'>FAY</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5zu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zu3 OCA], [https://pdbe.org/5zu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zu3 RCSB], [https://www.ebi.ac.uk/pdbsum/5zu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zu3 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q2UD26_ASPOR Q2UD26_ASPOR]
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Aspergillus oryzae RIB40 formate oxidase has Arg87 and Arg554 near the formyl group and O(4) atom of 8-formyl-flavin adenine dinucleotide (FAD), respectively, with Asp396 neighboring Arg554. Herein, we probed the roles of these three residues in modification of FAD to 8-formyl-FAD. Replacement of Arg87 or Arg554 with Lys or Ala decreased and abolished the modification, respectively. Replacement of Asp396 with Ala or Asn lowered the modification rate. The observation of unusual effects of maintaining pH 7.0 on the modification in R87K, R554K, and D396 variants indicates initial and subsequent processes with different pH dependencies. Comparison of the initial process at pH 4.5 and 7.0 suggests that the microenvironment around Arg87 and the protonation state of Asp396 affect the initial process in the native enzyme. Comparison of the crystal structures of native and R554 variants showed that the replacements had minimal effect on catalytic site structure. The positively charged Arg87 might contribute to the formation of an anionic quinone-methide tautomer intermediate, while the positively charged Arg554, in collaboration with the negatively charged Asp396, might stabilize this intermediate and form a hydrogen bonding network with the N(5)/O(4) region, thereby facilitating efficient FAD modification.
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The microenvironment surrounding FAD mediates its conversion to 8-formyl-FAD in Aspergillus oryzae RIB40 formate oxidase.,Doubayashi D, Oki M, Mikami B, Uchida H J Biochem. 2019 Feb 1. pii: 5305892. doi: 10.1093/jb/mvz009. PMID:30715389<ref>PMID:30715389</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5zu3" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Aspergillus oryzae RIB40]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Doubayashi, D]]
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[[Category: Doubayashi D]]
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[[Category: Mikami, B]]
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[[Category: Mikami B]]
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[[Category: Uchida, H]]
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[[Category: Uchida H]]
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[[Category: 8-formyl-fad]]
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[[Category: Effect of mutation]]
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[[Category: Formate oxidase]]
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[[Category: Oxidoreductase]]
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Current revision

Effect of mutation (R554K) on FAD modification in Aspergillus oryzae RIB40formate oxidase

PDB ID 5zu3

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