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5ynz

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Crystal structure of the dihydroorotase domain (K1556A) of human CAD

Structural highlights

5ynz is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.774Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYR1_HUMAN This protein is a "fusion" protein encoding four enzymatic activities of the pyrimidine pathway (GATase, CPSase, ATCase and DHOase).

Publication Abstract from PubMed

Dihydropyrimidinase (DHPase) is a member of the cyclic amidohydrolase family, which also includes allantoinase, dihydroorotase (DHOase), hydantoinase, and imidase. Almost all of these zinc metalloenzymes possess a binuclear metal center in which two metal ions are bridged by a post-translational carbamylated Lys. Crystal structure of Tetraodon nigroviridis DHPase reveals that one zinc ion is sufficient to stabilize Lys carbamylation. In this study, we found that one metal coordination was not sufficient to fix CO2 to the Lys in bacterial DHPase. We prepared and characterized mono-Zn DHPase from Pseudomonas aeruginosa (PaDHPase), and the catalytic activity of mono-Zn PaDHPase was not detected. The crystal structure of mono-Zn PaDHPase determined at 2.23A resolution (PDB entry 6AJD) revealed that Lys150 was no longer carbamylated. This finding indicated the decarbamylation of the Lys during the metal chelating process. To confirm the state of Lys carbamylation in mono-Zn PaDHPase in solution, mass spectrometric (MS) analysis was carried out. The MS result was in agreement with the theoretical value for uncarbamylated PaDHPase. Crystal structure of the human DHOase domain (huDHOase) K1556A mutant was also determined (PDB entry 5YNZ), and the structure revealed that the active site of huDHOase K1556A mutant contained one metal ion. Like mono-Zn PaDHPase, oxygen ligands of the carbamylated Lys were not required for Znalpha binding. Considering the collective data from X-ray crystal structure and MS analysis, mono-Zn PaDHPase in both crystalline state and solution was not carbamylated. In addition, structural evidences indicated that post-translational carbamylated Lys was not required for Znalpha binding in PaDHPase and in huDHOase.

Crystal structures of monometallic dihydropyrimidinase and the human dihydroorotase domain K1556A mutant reveal no lysine carbamylation within the active site.,Cheng JH, Huang YH, Lin JJ, Huang CY Biochem Biophys Res Commun. 2018 Oct 28;505(2):439-444. doi:, 10.1016/j.bbrc.2018.09.153. Epub 2018 Sep 27. PMID:30268498^[1]

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

References

↑ Cheng JH, Huang YH, Lin JJ, Huang CY. Crystal structures of monometallic dihydropyrimidinase and the human dihydroorotase domain K1556A mutant reveal no lysine carbamylation within the active site. Biochem Biophys Res Commun. 2018 Oct 28;505(2):439-444. doi:, 10.1016/j.bbrc.2018.09.153. Epub 2018 Sep 27. PMID:30268498 doi:http://dx.doi.org/10.1016/j.bbrc.2018.09.153

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ynz"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the dihydroorotase domain (K1556A) of human CAD==
-<StructureSection load='5ynz' size='340' side='right' caption='[[5ynz]], [[Resolution|resolution]] 2.77&Aring;' scene=''>
+<StructureSection load='5ynz' size='340' side='right'caption='[[5ynz]], [[Resolution|resolution]] 2.77&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ynz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YNZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YNZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ynz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YNZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.774&#8491;</td></tr>
-<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=5ynz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynz OCA], [http://pdbe.org/5ynz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ynz RCSB], [http://www.ebi.ac.uk/pdbsum/5ynz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynz ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5ynz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynz OCA], [https://pdbe.org/5ynz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ynz RCSB], [https://www.ebi.ac.uk/pdbsum/5ynz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynz ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PYR1_HUMAN PYR1_HUMAN]] This protein is a "fusion" protein encoding four enzymatic activities of the pyrimidine pathway (GATase, CPSase, ATCase and DHOase).
+[https://www.uniprot.org/uniprot/PYR1_HUMAN PYR1_HUMAN] This protein is a "fusion" protein encoding four enzymatic activities of the pyrimidine pathway (GATase, CPSase, ATCase and DHOase).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 5ynz" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[CAD protein 3D structures|CAD protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Chen, K L]]
+[[Category: Homo sapiens]]
-[[Category: Cheng, J H]]
+[[Category: Large Structures]]
-[[Category: Huang, C Y]]
+[[Category: Chen KL]]
-[[Category: Huang, Y H]]
+[[Category: Cheng JH]]
-[[Category: Dihydroorotase]]
+[[Category: Huang CY]]
-[[Category: Human cad]]
+[[Category: Huang YH]]
-[[Category: Hydrolase]]
-[[Category: Zn]]

5ynz

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Current revision

Crystal structure of the dihydroorotase domain (K1556A) of human CAD

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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