9vpf

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.

Structural highlights

9vpf is a 4 chain structure with sequence from Vanrija humicola. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4] ^[5]

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^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Takahashi S, Takahashi T, Kera Y, Matsunaga R, Shibuya H, Yamada RH. Cloning and expression in Escherichia coli of the D-aspartate oxidase gene from the yeast Cryptococcus humicola and characterization of the recombinant enzyme. J Biochem. 2004 Apr;135(4):533-40. PMID:15115779 doi:10.1093/jb/mvh068
↑ Takahashi S, Kakuichi T, Fujii K, Kera Y, Yamada RH. Physiological role of D-aspartate oxidase in the assimilation and detoxification of D-aspartate in the yeast Cryptococcus humicola. Yeast. 2005 Nov;22(15):1203-12. PMID:16278929 doi:10.1002/yea.1303
↑ Takahashi S, Shimada K, Nozawa S, Goto M, Abe K, Kera Y. Possible role of a histidine residue in the substrate specificity of yeast d-aspartate oxidase. J Biochem. 2016 Mar;159(3):371-8. PMID:26519738 doi:10.1093/jb/mvv108
↑ Yamada R, Ujiie H, Kera Y, Nakase T, Kitagawa K, Imasaka T, Arimoto K, Takahashi M, Matsumura Y. Purification and properties of D-aspartate oxidase from Cryptococcus humicolus UJ1. Biochim Biophys Acta. 1996 May 23;1294(2):153-8. PMID:8645733 doi:10.1016/0167-4838(96)00012-x
↑ Takahashi S, Kakuichi T, Fujii K, Kera Y, Yamada RH. Physiological role of D-aspartate oxidase in the assimilation and detoxification of D-aspartate in the yeast Cryptococcus humicola. Yeast. 2005 Nov;22(15):1203-12. PMID:16278929 doi:10.1002/yea.1303
↑ Goto M, Nonaka R, Mizobuchi T, Imanishi D, Takahashi S. Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1. Acta Crystallogr F Struct Biol Commun. 2025 Oct 1. PMID:40970329 doi:10.1107/S2053230X25008192

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/9vpf"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9vpf is ON HOLD  until Paper Publication
+==Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.==
+<StructureSection load='9vpf' size='340' side='right'caption='[[9vpf]], [[Resolution|resolution]] 1.70&Aring;' 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]] 1.7&#8491;</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.
-Authors: Goto, M., Nonaka, R., Mizobuchi, T., Imanishi, D., Takahashi, S.
+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>
-Description: Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Imanishi, D]]
+<div class="pdbe-citations 9vpf" style="background-color:#fffaf0;"></div>
-[[Category: Takahashi, S]]
+== References ==
-[[Category: Mizobuchi, T]]
+<references/>
-[[Category: Nonaka, R]]
+__TOC__
-[[Category: Goto, M]]
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Vanrija humicola]]
+[[Category: Goto M]]
+[[Category: Imanishi D]]
+[[Category: Mizobuchi T]]
+[[Category: Nonaka R]]
+[[Category: Takahashi S]]

9vpf

From Proteopedia

Current revision

Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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