5ayj - Revision history

OCA at 15:51, 8 November 2023

OCA — Wed, 08 Nov 2023 15:51:28 GMT

←Older revision		Revision as of 15:51, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ayj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._TB-90 Bacillus sp. TB-90]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AYJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ayj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._TB-90 Bacillus sp. TB-90]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AYJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MUA:9-METHYL+URIC+ACID'>MUA</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</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]] 2.05Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MUA:9-METHYL+URIC+ACID'>MUA</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ayj OCA], [https://pdbe.org/5ayj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ayj RCSB], [https://www.ebi.ac.uk/pdbsum/5ayj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ayj 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=5ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ayj OCA], [https://pdbe.org/5ayj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ayj RCSB], [https://www.ebi.ac.uk/pdbsum/5ayj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ayj ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:31, 31 May 2023

OCA — Wed, 31 May 2023 06:31:27 GMT

←Older revision		Revision as of 06:31, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5ayj' size='340' side='right'caption='[[5ayj]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5ayj' size='340' side='right'caption='[[5ayj]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ayj]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacsb Bacsb~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AYJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ayj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._TB-90 Bacillus sp. TB-90]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AYJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MUA:9-METHYL+URIC+ACID'>MUA</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</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=MUA:9-METHYL+URIC+ACID'>MUA</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</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">[[3wlv\|3wlv]], [[1j2g\|1j2g]]</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=5ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ayj OCA], [https://pdbe.org/5ayj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ayj RCSB], [https://www.ebi.ac.uk/pdbsum/5ayj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ayj ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uao ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36824 BACSB])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=5ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ayj OCA], [~~http~~://pdbe.org/5ayj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ayj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ayj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ayj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PUCL_BACSB PUCL_BACSB]] Catalyzes two steps in the degradation of uric acid, i.e. the oxidation of uric acid to 5-hydroxyisourate (HIU) and the stereoselective decarboxylation of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) to (S)-allantoin (By similarity).	+	[https://www.uniprot.org/uniprot/PUCL_BACSB PUCL_BACSB] Catalyzes two steps in the degradation of uric acid, i.e. the oxidation of uric acid to 5-hydroxyisourate (HIU) and the stereoselective decarboxylation of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) to (S)-allantoin (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacsb]]~~	+	[[Category: Bacillus sp. TB-90]]
-	~~[[Category: Factor independent urate hydroxylase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hibi, T]]	+	[[Category: Hibi T]]
-	[[Category: Itoh, T]]	+	[[Category: Itoh T]]
-	[[Category: Kawamura, A]]	+	[[Category: Kawamura A]]
-	[[Category: Kume, A]]	+	[[Category: Kume A]]
-	[[Category: Nishiya, Y]]	+	[[Category: Nishiya Y]]
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Oxidase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Protein engineering]]~~	+
-	~~[[Category: Subunit-subunit interaction]]~~	+
-	~~[[Category: Thermostability~~]]	+

OCA at 09:56, 26 February 2020

OCA — Wed, 26 Feb 2020 09:56:27 GMT

←Older revision		Revision as of 09:56, 26 February 2020
Line 1:		Line 1:

	==Hyperthermostable mutant of Bacillus sp. TB-90 Urate Oxidase - R298C==		==Hyperthermostable mutant of Bacillus sp. TB-90 Urate Oxidase - R298C==
-	<StructureSection load='5ayj' size='340' side='right' caption='[[5ayj]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5ayj' size='340' side='right'caption='[[5ayj]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ayj]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ayj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsb Bacsb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AYJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MUA:9-METHYL+URIC+ACID'>MUA</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</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"><scene name='pdbligand=MUA:9-METHYL+URIC+ACID'>MUA</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</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">[[3wlv\|3wlv]], [[1j2g\|1j2g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wlv\|3wlv]], [[1j2g\|1j2g]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uao ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36824 BACSB])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=5ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ayj OCA], [http://pdbe.org/5ayj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ayj RCSB], [http://www.ebi.ac.uk/pdbsum/5ayj PDBsum]</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=5ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ayj OCA], [http://pdbe.org/5ayj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ayj RCSB], [http://www.ebi.ac.uk/pdbsum/5ayj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ayj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsb]]
	[[Category: Factor independent urate hydroxylase]]		[[Category: Factor independent urate hydroxylase]]
		+	[[Category: Large Structures]]
	[[Category: Hibi, T]]		[[Category: Hibi, T]]
	[[Category: Itoh, T]]		[[Category: Itoh, T]]

OCA at 19:05, 20 February 2016

OCA — Sat, 20 Feb 2016 19:05:29 GMT

←Older revision		Revision as of 19:05, 20 February 2016
Line 1:		Line 1:
		+
	==Hyperthermostable mutant of Bacillus sp. TB-90 Urate Oxidase - R298C==		==Hyperthermostable mutant of Bacillus sp. TB-90 Urate Oxidase - R298C==
	<StructureSection load='5ayj' size='340' side='right' caption='[[5ayj]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5ayj' size='340' side='right' caption='[[5ayj]], [[Resolution\|resolution]] 2.05Å' scene=''>

OCA at 17:01, 20 January 2016

OCA — Wed, 20 Jan 2016 17:01:20 GMT

←Older revision		Revision as of 17:01, 20 January 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Hyperthermostable mutant of Bacillus sp. TB-90 Urate Oxidase - R298C==
		+	<StructureSection load='5ayj' size='340' side='right' caption='[[5ayj]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ayj]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AYJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MUA:9-METHYL+URIC+ACID'>MUA</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</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">[[3wlv\|3wlv]], [[1j2g\|1j2g]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=5ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ayj OCA], [http://pdbe.org/5ayj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ayj RCSB], [http://www.ebi.ac.uk/pdbsum/5ayj PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PUCL_BACSB PUCL_BACSB]] Catalyzes two steps in the degradation of uric acid, i.e. the oxidation of uric acid to 5-hydroxyisourate (HIU) and the stereoselective decarboxylation of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) to (S)-allantoin (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacillus sp. TB-90 urate oxidase (BTUO) is one of the most thermostable homotetrameric enzymes. We previously reported [Hibi, T., et al. (2014) Biochemistry 53, 3879-3888] that specific binding of a sulfate anion induced thermostabilization of the enzyme, because the bound sulfate formed a salt bridge with two Arg298 residues, which stabilized the packing between two beta-barrel dimers. To extensively characterize the sulfate-binding site, Arg298 was substituted with cysteine by site-directed mutagenesis. This substitution markedly increased the protein melting temperature by approximately 20 degrees C compared with that of the wild-type enzyme, which was canceled by reduction with dithiothreitol. Calorimetric analysis of the thermal denaturation suggested that the hyperstabilization resulted from suppression of the dissociation of the tetramer into the two homodimers. The crystal structure of R298C at 2.05 A resolution revealed distinct disulfide bond formation between the symmetrically related subunits via Cys298, although the Cbeta distance between Arg298 residues of the wild-type enzyme (5.4 A apart) was too large to predict stable formation of an engineered disulfide cross-link. Disulfide bonding was associated with local disordering of interface loop II (residues 277-300), which suggested that the structural plasticity of the loop allowed hyperstabilization by disulfide formation. Another conformational change in the C-terminal region led to intersubunit hydrogen bonding between Arg7 and Asp312, which probably promoted mutant thermostability. Knowledge of the disulfide linkage of flexible loops at the subunit interface will help in the development of new strategies for enhancing the thermostabilization of multimeric proteins.

-	~~The entry 5ayj is ON HOLD until Paper Publication~~	+	Hyperstabilization of Tetrameric Bacillus sp. TB-90 Urate Oxidase by Introducing Disulfide Bonds through Structural Plasticity.,Hibi T, Kume A, Kawamura A, Itoh T, Fukada H, Nishiya Y Biochemistry. 2016 Jan 15. PMID:26739254<ref>PMID:26739254</ref>

-	~~Authors: Hibi~~, T.~~, Kume, A~~.~~, Kawamura, A., Itoh, T., Nishiya, Y~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Hyperthermostable mutant of Bacillus sp. TB~~-~~90 Urate Oxidase~~ -~~R298C~~	+	<div class="pdbe-citations 5ayj" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: ~~Nishiya~~, Y]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Factor independent urate hydroxylase]]
		+	[[Category: Hibi, T]]
		+	[[Category: Itoh, T]]
	[[Category: Kawamura, A]]		[[Category: Kawamura, A]]
-	[[Category: Itoh, T]]
-	[[Category: Hibi, T]]
	[[Category: Kume, A]]		[[Category: Kume, A]]
		+	[[Category: Nishiya, Y]]
		+	[[Category: Disulfide bond]]
		+	[[Category: Oxidase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Protein engineering]]
		+	[[Category: Subunit-subunit interaction]]
		+	[[Category: Thermostability]]

OCA at 09:53, 9 December 2015

OCA — Wed, 09 Dec 2015 09:53:42 GMT

←Older revision		Revision as of 09:53, 9 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Hibi, T., Kume, A., Kawamura, A., Itoh, T., Nishiya, Y.		Authors: Hibi, T., Kume, A., Kawamura, A., Itoh, T., Nishiya, Y.

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

OCA — Wed, 02 Sep 2015 10:01:03 GMT

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

←Older revision

Revision as of 10:01, 2 September 2015

OCA: New page: '''Unreleased structure''' The entry 5ayj is ON HOLD Authors: Hibi, T., Kume, A., Kawamura, A., Itoh, T., Nishiya, Y. Description: Hyperthermostable mutant of Bacillus sp. TB-90 Urate ...

OCA — Wed, 02 Sep 2015 10:01:02 GMT

New page: '''Unreleased structure''' The entry 5ayj is ON HOLD Authors: Hibi, T., Kume, A., Kawamura, A., Itoh, T., Nishiya, Y. Description: Hyperthermostable mutant of Bacillus sp. TB-90 Urate ...

New page

'''Unreleased structure'''

The entry 5ayj is ON HOLD

Authors: Hibi, T., Kume, A., Kawamura, A., Itoh, T., Nishiya, Y.

Description: Hyperthermostable mutant of Bacillus sp. TB-90 Urate Oxidase -R298C
[[Category: Unreleased Structures]]
[[Category: Nishiya, Y]]
[[Category: Kawamura, A]]
[[Category: Itoh, T]]
[[Category: Hibi, T]]
[[Category: Kume, A]]