9vpf: Difference between revisions
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==Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.== | |||
<StructureSection load='9vpf' size='340' side='right'caption='[[9vpf]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[9vpf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vanrija_humicola Vanrija humicola]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9VPF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9VPF FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9vpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9vpf OCA], [https://pdbe.org/9vpf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9vpf RCSB], [https://www.ebi.ac.uk/pdbsum/9vpf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9vpf ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/OXDD_VANHU OXDD_VANHU] Selectively catalyzes the oxidative deamination of acidic amino acids (PubMed:15115779, PubMed:26519738, PubMed:8645733, Ref.4). Protects the organism from the toxicity of D-amino acids (PubMed:16278929). Enables the organism to utilize D-amino acids as a source of nutrients (PubMed:16278929). Enables the organism to utilize D-aspartate as a source of nitrogen and carbon (PubMed:16278929).<ref>PMID:15115779</ref> <ref>PMID:16278929</ref> <ref>PMID:26519738</ref> <ref>PMID:8645733</ref> <ref>PMID:16278929</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The enzyme D-aspartate oxidase (DDO) oxidizes acidic D-amino acids using the coenzyme flavin adenine dinucleotide to generate the corresponding alpha-keto acids and ammonia. DDO differs from D-amino-acid oxidase (DAAO), which acts on neutral and basic D-amino acids. Although the enzymatic properties of DDO have been characterized in several species, the structure of DDO had remained unclear. The structure of DDO derived from Cryptococcus humicola strain UJ1 (chDDO) was determined by X-ray crystallography at 1.70 A resolution. While the three-dimensional structures of DAAOs are known to be homodimers, chDDO forms a homotetramer. This difference was found to be caused by the deletion of one loop and the insertion of two loops. | |||
Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.,Goto M, Nonaka R, Mizobuchi T, Imanishi D, Takahashi S Acta Crystallogr F Struct Biol Commun. 2025 Oct 1. doi: , 10.1107/S2053230X25008192. PMID:40970329<ref>PMID:40970329</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 9vpf" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Mizobuchi | <references/> | ||
[[Category: Nonaka | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Vanrija humicola]] | |||
[[Category: Goto M]] | |||
[[Category: Imanishi D]] | |||
[[Category: Mizobuchi T]] | |||
[[Category: Nonaka R]] | |||
[[Category: Takahashi S]] | |||
Latest revision as of 06:05, 1 October 2025
Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.
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