5hxu - Revision history

OCA at 10:59, 16 August 2023

OCA — Wed, 16 Aug 2023 10:59:00 GMT

←Older revision		Revision as of 10:59, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='5hxu' size='340' side='right'caption='[[5hxu]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='5hxu' size='340' side='right'caption='[[5hxu]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hxu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HXU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HXU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hxu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HXU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MHA:(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC+ACID'>MHA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.83Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hwe\|5hwe]], [[5hxz\|5hxz]], [[5hy0\|5hy0]], [[5hy1\|5hy1]], [[5hy2\|5hy2]], [[5hy4\|5hy4]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MHA:(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC+ACID'>MHA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Barbiturase Barbiturase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.1 3.5.2.1] </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=5hxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hxu OCA], [https://pdbe.org/5hxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hxu RCSB], [https://www.ebi.ac.uk/pdbsum/5hxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hxu ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5hxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hxu OCA], [~~http~~://pdbe.org/5hxu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hxu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hxu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hxu ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~BAR_RHOER BAR_RHOER~~]~~] Cleaves~~ the barbituric acid ring to yield ureidomalonic acid.<ref>PMID:11485332</ref> <ref>PMID:11748240</ref>	+	[https://www.uniprot.org/uniprot/BAH_RHOER BAH_RHOER] Responsible for the hydrolysis of barbituric acid (2,4,6-trihydroxy-1,3-pyrimidine), an intermediate in the oxidative catabolism of pyrimidines. Catalyzes the hydrolytic opening of the pyrimidine ring of barbituric acid to yield ureidomalonic acid.[HAMAP-Rule:MF_01989]<ref>PMID:11485332</ref> <ref>PMID:11748240</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Barbiturase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Balotra, S]]	+	[[Category: Rhodococcus erythropolis]]
-	[[Category: Newman, J]]	+	[[Category: Balotra S]]
-	[[Category: Peat~~, T S~~]]	+	[[Category: Newman J]]
-	[[Category: Scott, C]]	+	[[Category: Peat TS]]
-	[[Category: Wilding, M]]	+	[[Category: Scott C]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Wilding M]]
-	~~[[Category: Pyrimidine catabolism]]~~	+
-	~~[[Category: Toblerone fold~~]]	+

OCA at 08:36, 27 May 2020

OCA — Wed, 27 May 2020 08:36:06 GMT

←Older revision		Revision as of 08:36, 27 May 2020
Line 1:		Line 1:

	==Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes==		==Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes==
-	<StructureSection load='5hxu' size='340' side='right' caption='[[5hxu]], [[Resolution\|resolution]] 1.83Å' scene=''>	+	<StructureSection load='5hxu' size='340' side='right'caption='[[5hxu]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hxu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HXU OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HXU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hxu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HXU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HXU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MHA:(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC+ACID'>MHA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MHA:(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC+ACID'>MHA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hwe\|5hwe]], [[5hxz\|5hxz]], [[5hy0\|5hy0]], [[5hy1\|5hy1]], [[5hy2\|5hy2]], [[5hy4\|5hy4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hwe\|5hwe]], [[5hxz\|5hxz]], [[5hy0\|5hy0]], [[5hy1\|5hy1]], [[5hy2\|5hy2]], [[5hy4\|5hy4]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Barbiturase Barbiturase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.1 3.5.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Barbiturase Barbiturase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.1 3.5.2.1] </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=5hxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hxu OCA], [http://pdbe.org/5hxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hxu RCSB], [http://www.ebi.ac.uk/pdbsum/5hxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hxu ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5hxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hxu OCA], [http://pdbe.org/5hxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hxu RCSB], [http://www.ebi.ac.uk/pdbsum/5hxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hxu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Barbiturase]]		[[Category: Barbiturase]]
		+	[[Category: Large Structures]]
	[[Category: Balotra, S]]		[[Category: Balotra, S]]
	[[Category: Newman, J]]		[[Category: Newman, J]]

OCA at 13:14, 15 March 2017

OCA — Wed, 15 Mar 2017 13:14:44 GMT

←Older revision		Revision as of 13:14, 15 March 2017
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BAR_RHOER BAR_RHOER]] Cleaves the barbituric acid ring to yield ureidomalonic acid.<ref>PMID:11485332</ref> <ref>PMID:11748240</ref>		[[http://www.uniprot.org/uniprot/BAR_RHOER BAR_RHOER]] Cleaves the barbituric acid ring to yield ureidomalonic acid.<ref>PMID:11485332</ref> <ref>PMID:11748240</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Toblerone-fold was discovered recently when the first structure of the cyclic amide hydrolase, AtzD (a cyanuric acid hydrolase), was elucidated. We surveyed the cyclic amide hydrolase family finding a strong correlation between phylogenetic distribution and specificity for either cyanuric acid or barbituric acid; albeit, one of six classes (IV) could not be tested due to lack of expression of the proteins from it, and another class (V) had neither cyanuric acid nor barbituric acid hydrolase activity. High resolution X-ray structures were obtained for a class VI barbituric acid hydrolase (1.7 A) from a Rhodococcus sp. and a class V cyclic amide hydrolase (2.4 A) from a Frankia sp. for which we were unable to identify a substrate. Both structures were homologous with the tetrameric Toblerone-fold enzyme AtzD, demonstrating a high degree of structural conservation within the cyclic amide hydrolase family. The barbituric acid hydrolase structure did not contain zinc, in contrast with early reports of zinc-dependent activity for this enzyme. Instead, each barbituric acid hydrolase monomer contained either a Na+ or a Mg2+, analogous to the structural metal found in cyanuric acid hydrolase. The Frankia cyclic amide hydrolase contained no metal, but instead formed unusual, reversible, intermolecular vicinal disulfide bonds that contributed to the thermal stability of the protein. The active sites were largely conserved between the three enzymes, differing at six positions, which likely determine substrate specificity.Importance The 'Toblerone-fold' enzymes catalyze an unusual ring-opening hydrolysis with cyclic amide substrates. A survey of these enzymes shows that there is a good correlation between physiological function and phylogenetic distribution within this family of enzymes, and provide insights into the evolutionary relationships between the cyanuric acid and barbituric acid hydrolases.This family of enzymes is structurally and mechanistically distinct from other enzyme families; however, to date the structure of just two, physiologically identical, enzymes from this family have been described. We present two new structures: a barbituric acid hydrolase and an enzyme of unknown function. These structures confirm that the CyAH family share the unusual Toblerone fold, albeit with some significant differences.
		+
		+	High resolution X-ray structures of two functionally distinct members of the cyclic amide hydrolase (CyAH) family of Toblerone fold enzymes.,Peat TS, Balotra S, Wilding M, Hartley CJ, Newman J, Scott C Appl Environ Microbiol. 2017 Feb 24. pii: AEM.03365-16. doi:, 10.1128/AEM.03365-16. PMID:28235873<ref>PMID:28235873</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5hxu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:05, 1 February 2017

OCA — Wed, 01 Feb 2017 18:05:52 GMT

←Older revision		Revision as of 18:05, 1 February 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5hxu is ~~ON HOLD until Paper Publication~~	+	==Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes==
-		+	<StructureSection load='5hxu' size='340' side='right' caption='[[5hxu]], [[Resolution\|resolution]] 1.83Å' scene=''>
-	~~Authors~~: ~~Peat~~, T.S., ~~Balotra~~, S., ~~Wilding~~, M., ~~Newman, J~~., ~~Scott, C~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5hxu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HXU FirstGlance]. <br>
-	~~Description~~: ~~Structure-function analysis of functionally diverse members of~~ the ~~cyclic amide hydrolase family of Toblerone fold enzymes~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MHA:(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC+ACID'>MHA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hwe\|5hwe]], [[5hxz\|5hxz]], [[5hy0\|5hy0]], [[5hy1\|5hy1]], [[5hy2\|5hy2]], [[5hy4\|5hy4]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Barbiturase Barbiturase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.1 3.5.2.1] </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=5hxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hxu OCA], [http://pdbe.org/5hxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hxu RCSB], [http://www.ebi.ac.uk/pdbsum/5hxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hxu ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BAR_RHOER BAR_RHOER]] Cleaves the barbituric acid ring to yield ureidomalonic acid.<ref>PMID:11485332</ref> <ref>PMID:11748240</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Barbiturase]]
		+	[[Category: Balotra, S]]
		+	[[Category: Newman, J]]
		+	[[Category: Peat, T S]]
	[[Category: Scott, C]]		[[Category: Scott, C]]
-	[[Category: Peat, T.S]]
-	[[Category: Newman, J]]
	[[Category: Wilding, M]]		[[Category: Wilding, M]]
-	[[Category: ~~Balotra, S~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Pyrimidine catabolism]]
		+	[[Category: Toblerone fold]]

OCA at 00:01, 11 May 2016

OCA — Wed, 11 May 2016 00:01:45 GMT

←Older revision		Revision as of 00:01, 11 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hxu is ON HOLD	+	The entry 5hxu is ON HOLD until Paper Publication

	Authors: Peat, T.S., Balotra, S., Wilding, M., Newman, J., Scott, C.		Authors: Peat, T.S., Balotra, S., Wilding, M., Newman, J., Scott, C.

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

OCA — Wed, 10 Feb 2016 15:52:13 GMT

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

←Older revision

Revision as of 15:52, 10 February 2016

OCA: New page: '''Unreleased structure''' The entry 5hxu is ON HOLD Authors: Peat, T.S., Balotra, S., Wilding, M., Newman, J., Scott, C. Description: Structure-function analysis of functionally diver...

OCA — Wed, 10 Feb 2016 15:52:12 GMT

New page: '''Unreleased structure''' The entry 5hxu is ON HOLD Authors: Peat, T.S., Balotra, S., Wilding, M., Newman, J., Scott, C. Description: Structure-function analysis of functionally diver...

New page

'''Unreleased structure'''

The entry 5hxu is ON HOLD

Authors: Peat, T.S., Balotra, S., Wilding, M., Newman, J., Scott, C.

Description: Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes
[[Category: Unreleased Structures]]
[[Category: Scott, C]]
[[Category: Peat, T.S]]
[[Category: Newman, J]]
[[Category: Wilding, M]]
[[Category: Balotra, S]]