5xr2 - Revision history

OCA at 10:07, 15 November 2023

OCA — Wed, 15 Nov 2023 10:07:42 GMT

←Older revision		Revision as of 10:07, 15 November 2023
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	==SAV0551==		==SAV0551==
-	<StructureSection load='5xr2' size='340' side='right' caption='[[5xr2]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5xr2' size='340' side='right'caption='[[5xr2]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xr2]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Staam Staam~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XR2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XR2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xr2]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus aureus subsp. aureus Mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XR2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XR2 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=LAC:LACTIC+ACID'>LAC</scene~~>, ~~<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]] 2.6Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~hchA, SAV0551 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=158878 STAAM])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LAC:LACTIC+ACID'>LAC</scene>, <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=5xr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xr2 OCA], [~~http~~://pdbe.org/5xr2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xr2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xr2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xr2 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=5xr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xr2 OCA], [https://pdbe.org/5xr2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xr2 RCSB], [https://www.ebi.ac.uk/pdbsum/5xr2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xr2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HCHA_STAAM HCHA_STAAM]] Protein and nucleotide deglycase that catalyzes the deglycation of the Maillard adducts formed between amino groups of proteins or nucleotides and reactive carbonyl groups of glyoxals. Thus, functions as a protein deglycase that repairs methylglyoxal- and glyoxal-glycated proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteine, arginine and lysine residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of Schiff bases and advanced glycation endproducts (AGE). Also functions as a nucleotide deglycase able to repair glycated guanine in the free nucleotide pool (GTP, GDP, GMP, dGTP) and in DNA and RNA. Is thus involved in a major nucleotide repair system named guanine glycation repair (GG repair), dedicated to reversing methylglyoxal and glyoxal damage via nucleotide sanitization and direct nucleic acid repair. Plays an important role in protecting cells from carbonyl stress.	+	[https://www.uniprot.org/uniprot/HCHA_STAAM HCHA_STAAM] Protein and nucleotide deglycase that catalyzes the deglycation of the Maillard adducts formed between amino groups of proteins or nucleotides and reactive carbonyl groups of glyoxals. Thus, functions as a protein deglycase that repairs methylglyoxal- and glyoxal-glycated proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteine, arginine and lysine residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of Schiff bases and advanced glycation endproducts (AGE). Also functions as a nucleotide deglycase able to repair glycated guanine in the free nucleotide pool (GTP, GDP, GMP, dGTP) and in DNA and RNA. Is thus involved in a major nucleotide repair system named guanine glycation repair (GG repair), dedicated to reversing methylglyoxal and glyoxal damage via nucleotide sanitization and direct nucleic acid repair. Plays an important role in protecting cells from carbonyl stress.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Staam~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kim, H J~~]]	+	[[Category: Staphylococcus aureus subsp. aureus Mu50]]
-	[[Category: ~~Kwon, A R~~]]	+	[[Category: Kim HJ]]
-	[[Category: ~~Lee, B J~~]]	+	[[Category: Kwon AR]]
-	[[Category: ~~Chaperone]]~~	+	[[Category: Lee BJ]]
-	~~[[Category: Glyoxalase iii]]~~	+
-	~~[[Category: Hsp31~~]]	+

OCA at 07:41, 29 November 2017

OCA — Wed, 29 Nov 2017 07:41:44 GMT

←Older revision		Revision as of 07:41, 29 November 2017
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	<StructureSection load='5xr2' size='340' side='right' caption='[[5xr2]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5xr2' size='340' side='right' caption='[[5xr2]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xr2]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XR2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XR2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xr2]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Staam Staam]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XR2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XR2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LAC:LACTIC+ACID'>LAC</scene>, <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=LAC:LACTIC+ACID'>LAC</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">hchA, SAV0551 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158878 STAAM])</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=5xr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xr2 OCA], [http://pdbe.org/5xr2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xr2 RCSB], [http://www.ebi.ac.uk/pdbsum/5xr2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xr2 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=5xr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xr2 OCA], [http://pdbe.org/5xr2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xr2 RCSB], [http://www.ebi.ac.uk/pdbsum/5xr2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xr2 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Staam]]
	[[Category: Kim, H J]]		[[Category: Kim, H J]]
	[[Category: Kwon, A R]]		[[Category: Kwon, A R]]

OCA at 06:12, 1 November 2017

OCA — Wed, 01 Nov 2017 06:12:45 GMT

←Older revision		Revision as of 06:12, 1 November 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5xr2 is ~~ON HOLD until Paper~~ Publication	+	==SAV0551==
		+	<StructureSection load='5xr2' size='340' side='right' caption='[[5xr2]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xr2]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XR2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XR2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LAC:LACTIC+ACID'>LAC</scene>, <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=5xr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xr2 OCA], [http://pdbe.org/5xr2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xr2 RCSB], [http://www.ebi.ac.uk/pdbsum/5xr2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xr2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HCHA_STAAM HCHA_STAAM]] Protein and nucleotide deglycase that catalyzes the deglycation of the Maillard adducts formed between amino groups of proteins or nucleotides and reactive carbonyl groups of glyoxals. Thus, functions as a protein deglycase that repairs methylglyoxal- and glyoxal-glycated proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteine, arginine and lysine residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of Schiff bases and advanced glycation endproducts (AGE). Also functions as a nucleotide deglycase able to repair glycated guanine in the free nucleotide pool (GTP, GDP, GMP, dGTP) and in DNA and RNA. Is thus involved in a major nucleotide repair system named guanine glycation repair (GG repair), dedicated to reversing methylglyoxal and glyoxal damage via nucleotide sanitization and direct nucleic acid repair. Plays an important role in protecting cells from carbonyl stress.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The DJ-1/ThiJ/PfpI superfamily of proteins is highly conserved across all biological kingdoms showing divergent multi-functions, such as chaperone, catalase, protease, and kinase. The common theme of these functions is responding to and managing various cellular stresses. DJ-1/ThiJ/PfpI superfamily members are classified into three subfamilies according to their quaternary structure (DJ-1-, YhbO-, and Hsp-types). The Hsp-type subfamily includes Hsp31, a chaperone and glyoxalase III. SAV0551, an Hsp-type subfamily member from Staphylococcus aureus, is a hypothetical protein that is predicted as Hsp31. Thus, to reveal the function and reaction mechanism of SAV0551, the crystal structure of SAV0551 was determined. The overall folds in SAV0551 are similar to other members of the Hsp-type subfamily. We have shown that SAV0551 functions as a chaperone and that the surface structure is crucial for holding unfolded substrates. As many DJ-1/ThiJ/PfpI superfamily proteins have been characterized as glyoxalase III, our study also demonstrates SAV0551 as a glyoxalase III that is independent of any cofactors. The reaction mechanism was evaluated via a glyoxylate-bound structure that mimics the hemithioacetal reaction intermediate. We have confirmed that the components required for reaction are present in the structure, including a catalytic triad for a catalytic action, His78 as a base, and a water molecule for hydrolysis. Our functional studies based on the crystal structures of native and glyoxylate-bound SAV0551 will provide a better understanding of the reaction mechanism of a chaperone and glyoxalase III.

-	~~Authors~~:	+	Structural and functional studies of SAV0551 from Staphylococcus aureus as a chaperone and glyoxalase III.,Kim HJ, Lee KY, Kwon AR, Lee BJ Biosci Rep. 2017 Oct 18. pii: BSR20171106. doi: 10.1042/BSR20171106. PMID:29046369<ref>PMID:29046369</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xr2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kim, H J]]
		+	[[Category: Kwon, A R]]
		+	[[Category: Lee, B J]]
		+	[[Category: Chaperone]]
		+	[[Category: Glyoxalase iii]]
		+	[[Category: Hsp31]]

OCA at 05:20, 11 October 2017

OCA — Wed, 11 Oct 2017 05:20:44 GMT

←Older revision		Revision as of 05:20, 11 October 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xr2 is ON HOLD	+	The entry 5xr2 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5xr2" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 15:42:06 GMT

Protected "5xr2" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:42, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xr2 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 15:42:04 GMT

New page: '''Unreleased structure''' The entry 5xr2 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xr2 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]