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6ajd

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Crystal structure of a monometallic dihydropyrimidinase from Pseudomonas aeruginosa PAO1 reveals no lysine carbamylation within the active site

Structural highlights

6ajd is a 2 chain structure with sequence from Pseudomonas aeruginosa PAO1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.223Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HYDA_PSEAE Catalyzes the hydrolysis of dihydropyrimidines and of the structurally related DL-5-mono-substituted hydantoins, to produce N-carbamoyl-D-amino acids.

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 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6ajd"

Categories: Large Structures | Pseudomonas aeruginosa PAO1 | Huang CY | Huang YH

@@ Line 1: / Line 1: @@
 ==Crystal structure of a monometallic dihydropyrimidinase from Pseudomonas aeruginosa PAO1 reveals no lysine carbamylation within the active site==
-<StructureSection load='6ajd' size='340' side='right' caption='[[6ajd]], [[Resolution|resolution]] 2.22&Aring;' scene=''>
+<StructureSection load='6ajd' size='340' side='right'caption='[[6ajd]], [[Resolution|resolution]] 2.22&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ajd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AJD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AJD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ajd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AJD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AJD 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]] 2.223&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydropyrimidinase Dihydropyrimidinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.2 3.5.2.2] </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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ajd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ajd OCA], [http://pdbe.org/6ajd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ajd RCSB], [http://www.ebi.ac.uk/pdbsum/6ajd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ajd ProSAT]</span></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=6ajd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ajd OCA], [https://pdbe.org/6ajd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ajd RCSB], [https://www.ebi.ac.uk/pdbsum/6ajd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ajd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HYDA_PSEAE HYDA_PSEAE]] Catalyzes the hydrolysis of dihydropyrimidines and of the structurally related DL-5-mono-substituted hydantoins, to produce N-carbamoyl-D-amino acids.
+[https://www.uniprot.org/uniprot/HYDA_PSEAE HYDA_PSEAE] Catalyzes the hydrolysis of dihydropyrimidines and of the structurally related DL-5-mono-substituted hydantoins, to produce N-carbamoyl-D-amino acids.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Dihydropyrimidinase]]
+[[Category: Large Structures]]
-[[Category: Huang, C Y]]
+[[Category: Pseudomonas aeruginosa PAO1]]
-[[Category: Huang, Y H]]
+[[Category: Huang CY]]
-[[Category: Hydrolase]]
+[[Category: Huang YH]]

6ajd

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Crystal structure of a monometallic dihydropyrimidinase from Pseudomonas aeruginosa PAO1 reveals no lysine carbamylation within the active site

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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