5ykd - Revision history

OCA at 08:32, 22 November 2023

OCA — Wed, 22 Nov 2023 08:32:23 GMT

←Older revision		Revision as of 08:32, 22 November 2023
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	==Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 at 2.17 angstrom resolution==		==Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 at 2.17 angstrom resolution==
-	<StructureSection load='5ykd' size='340' side='right' caption='[[5ykd]], [[Resolution\|resolution]] 2.17Å' scene=''>	+	<StructureSection load='5ykd' size='340' side='right'caption='[[5ykd]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ykd]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ykd]] is a 4 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=5YKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YKD 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]] 2.17Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dht~~, ~~PA0441 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])~~<~~/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=5ykd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykd OCA], [https://pdbe.org/5ykd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ykd RCSB], [https://www.ebi.ac.uk/pdbsum/5ykd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykd ProSAT]</span></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='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=5ykd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykd OCA], [~~http~~://pdbe.org/5ykd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ykd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ykd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykd ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dihydropyrimidinase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Huang~~, C Y~~]]	+	[[Category: Huang CY]]
-	[[Category: Huang~~, Y H]]~~	+	[[Category: Huang YH]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 08:27, 2 May 2018

OCA — Wed, 02 May 2018 08:27:46 GMT

←Older revision		Revision as of 08:27, 2 May 2018
Line 3:		Line 3:
	<StructureSection load='5ykd' size='340' side='right' caption='[[5ykd]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='5ykd' size='340' side='right' caption='[[5ykd]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ykd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ykd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YKD 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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dht, PA0441 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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='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='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=5ykd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykd OCA], [http://pdbe.org/5ykd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ykd RCSB], [http://www.ebi.ac.uk/pdbsum/5ykd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykd ProSAT]</span></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=5ykd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykd OCA], [http://pdbe.org/5ykd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ykd RCSB], [http://www.ebi.ac.uk/pdbsum/5ykd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykd ProSAT]</span></td></tr>
Line 11:		Line 12:
	== Function ==		== 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.		[[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.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dihydropyrimidinase, a dimetalloenzyme containing a carboxylated lysine within the active site, is a member of the cyclic amidohydrolase family, which also includes allantoinase, dihydroorotase, hydantoinase, and imidase. Unlike all known dihydropyrimidinases, which are tetrameric, pseudomonal dihydropyrimidinase forms a dimer at neutral pH. In this paper, we report the crystal structure of P. aeruginosa dihydropyrimidinase at pH 5.9 (PDB entry 5YKD). The crystals of P. aeruginosa dihydropyrimidinase belonged to space group C2221 with cell dimensions of a = 108.9, b = 155.7, and c = 235.6 A. The structure of P. aeruginosa dihydropyrimidinase was solved at 2.17 A resolution. An asymmetric unit of the crystal contained four crystallographically independent P. aeruginosa dihydropyrimidinase monomers. Gel filtration chromatographic analysis of purified P. aeruginosa dihydropyrimidinase revealed a mixture of dimers and tetramers at pH 5.9. Thus, P. aeruginosa dihydropyrimidinase can form a stable tetramer both in the crystalline state and in the solution. Based on sequence analysis and structural comparison of the dimer-dimer interface between P. aeruginosa dihydropyrimidinase and Thermus sp. dihydropyrimidinase, different oligomerization mechanisms are proposed.
		+
		+	Structural Basis for pH-Dependent Oligomerization of Dihydropyrimidinase from Pseudomonas aeruginosa PAO1.,Cheng JH, Huang CC, Huang YH, Huang CY Bioinorg Chem Appl. 2018 Jan 30;2018:9564391. doi: 10.1155/2018/9564391., eCollection 2018. PMID:29666631<ref>PMID:29666631</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ykd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Dihydropyrimidinase]]		[[Category: Dihydropyrimidinase]]
		+	[[Category: Pseae]]
	[[Category: Huang, C Y]]		[[Category: Huang, C Y]]
	[[Category: Huang, Y H]]		[[Category: Huang, Y H]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 07:21, 22 February 2018

OCA — Thu, 22 Feb 2018 07:21:39 GMT

←Older revision		Revision as of 07:21, 22 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ykd is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 at 2.17 angstrom resolution==
-		+	<StructureSection load='5ykd' size='340' side='right' caption='[[5ykd]], [[Resolution\|resolution]] 2.17Å' scene=''>
-	~~Authors~~: ~~Huang~~, Y.H., ~~Huang~~, C.Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ykd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YKD FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~dihydropyrimidinase from Pseudomonas aeruginosa PAO1 at 2~~.~~17 angstrom resolution~~	+	</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>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	[[Category: Huang, Y.H]]	+	<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>
-	[[Category: Huang, C.Y]]	+	<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=5ykd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykd OCA], [http://pdbe.org/5ykd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ykd RCSB], [http://www.ebi.ac.uk/pdbsum/5ykd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykd 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.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dihydropyrimidinase]]
		+	[[Category: Huang, C Y]]
		+	[[Category: Huang, Y H]]
		+	[[Category: Hydrolase]]

OCA: Protected "5ykd" [edit=sysop:move=sysop]

OCA — Wed, 25 Oct 2017 05:37:38 GMT

Protected "5ykd" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:37, 25 October 2017

OCA: New page: '''Unreleased structure''' The entry 5ykd is ON HOLD until Paper Publication Authors: Huang, Y.H., Huang, C.Y. Description: Crystal structure of dihydropyrimidinase from Pseudomonas ae...

OCA — Wed, 25 Oct 2017 05:37:37 GMT

New page: '''Unreleased structure''' The entry 5ykd is ON HOLD until Paper Publication Authors: Huang, Y.H., Huang, C.Y. Description: Crystal structure of dihydropyrimidinase from Pseudomonas ae...

New page

'''Unreleased structure'''

The entry 5ykd is ON HOLD until Paper Publication

Authors: Huang, Y.H., Huang, C.Y.

Description: Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 at 2.17 angstrom resolution
[[Category: Unreleased Structures]]
[[Category: Huang, Y.H]]
[[Category: Huang, C.Y]]