5unn - Revision history

OCA at 13:30, 4 October 2023

OCA — Wed, 04 Oct 2023 13:30:49 GMT

←Older revision		Revision as of 13:30, 4 October 2023
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	<StructureSection load='5unn' size='340' side='right'caption='[[5unn]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5unn' size='340' side='right'caption='[[5unn]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5unn]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ensifer_meliloti Ensifer~~ meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UNN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5unn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti_1021 Sinorhizobium meliloti 1021]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UNN 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=GOL:GLYCEROL'>GOL</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[4z0p\|4z0p]], [[4weq\|4weq]], [[5uog\|5uog]]~~<~~/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=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">SMc02828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266834 Ensifer meliloti])~~</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=5unn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5unn OCA], [https://pdbe.org/5unn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5unn RCSB], [https://www.ebi.ac.uk/pdbsum/5unn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5unn 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=5unn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5unn OCA], [~~http~~://pdbe.org/5unn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5unn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5unn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5unn ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q92T34_RHIME Q92T34_RHIME]
	<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: Ensifer meliloti]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Sinorhizobium meliloti 1021]]
-	[[Category: Bonanno, J]]	+	[[Category: Almo SC]]
-	[[Category: Gasiorowska~~, O A~~]]	+	[[Category: Bonanno J]]
-	[[Category: Handing~~, K B~~]]	+	[[Category: Gasiorowska OA]]
-	[[Category: Kutner, J]]	+	[[Category: Handing KB]]
-	[[Category: LaRowe, C]]	+	[[Category: Kutner J]]
-	[[Category: Minor, W]]	+	[[Category: LaRowe C]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Minor W]]
-	[[Category: Shabalin~~, I G]]~~	+	[[Category: Shabalin IG]]
-	~~[[Category: Nadp-dependent dehydrogenase]]~~	+
-	~~[[Category: Nysgrc]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Psi-biology]]~~	+
-	~~[[Category: Sinorhizobium meliloti~~]]	+

OCA at 09:31, 4 December 2019

OCA — Wed, 04 Dec 2019 09:31:18 GMT

←Older revision		Revision as of 09:31, 4 December 2019
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	==Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in apo form==		==Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in apo form==
-	<StructureSection load='5unn' size='340' side='right' caption='[[5unn]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5unn' size='340' side='right'caption='[[5unn]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5unn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UNN FirstGlance]. <br>		<table><tr><td colspan='2'>[[5unn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UNN FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Ensifer meliloti]]		[[Category: Ensifer meliloti]]
		+	[[Category: Large Structures]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Bonanno, J]]		[[Category: Bonanno, J]]

OCA at 05:52, 16 May 2018

OCA — Wed, 16 May 2018 05:52:28 GMT

←Older revision		Revision as of 05:52, 16 May 2018
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	<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=5unn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5unn OCA], [http://pdbe.org/5unn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5unn RCSB], [http://www.ebi.ac.uk/pdbsum/5unn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5unn 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=5unn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5unn OCA], [http://pdbe.org/5unn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5unn RCSB], [http://www.ebi.ac.uk/pdbsum/5unn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5unn ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The d-2-hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGhrA reduces pyruvate (with low efficiency). We present nine crystal structures of both enzymes in apo forms and in complexes with cofactors and substrates/substrate analogues. In particular, we determined a crystal structure of SmGhrB with 2-keto-d-gluconate, which is the biggest substrate cocrystallized with a 2HADH member. The structures reveal significant differences between SmGhrA and SmGhrB, both in the overall structure and within the substrate-binding pocket, offering insight into the molecular basis for the observed substrate preferences and subfamily differences. In addition, we provide an overview of all GHRA and GHRB structures complexed with a ligand in the active site.
		+
		+	Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.,Kutner J, Shabalin IG, Matelska D, Handing KB, Gasiorowska O, Sroka P, Gorna MW, Ginalski K, Wozniak K, Minor W Biochemistry. 2018 Jan 26. doi: 10.1021/acs.biochem.7b01137. PMID:29309127<ref>PMID:29309127</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5unn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:35, 6 November 2017

OCA — Mon, 06 Nov 2017 14:35:28 GMT

←Older revision		Revision as of 14:35, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5unn' size='340' side='right' caption='[[5unn]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5unn' size='340' side='right' caption='[[5unn]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5unn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UNN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5unn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UNN 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=GOL:GLYCEROL'>GOL</scene></td></tr>		</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=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4z0p\|4z0p]], [[4weq\|4weq]], [[5uog\|5uog]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4z0p\|4z0p]], [[4weq\|4weq]], [[5uog\|5uog]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SMc02828 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266834 Ensifer meliloti])</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=5unn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5unn OCA], [http://pdbe.org/5unn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5unn RCSB], [http://www.ebi.ac.uk/pdbsum/5unn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5unn 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=5unn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5unn OCA], [http://pdbe.org/5unn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5unn RCSB], [http://www.ebi.ac.uk/pdbsum/5unn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5unn ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ensifer meliloti]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Bonanno, J]]		[[Category: Bonanno, J]]

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

OCA — Sat, 11 Mar 2017 01:45:03 GMT

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

←Older revision

Revision as of 01:45, 11 March 2017

OCA: New page: ==Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in apo form== == Structural highlights ==
<table><tr><td colspan='2'>[[5unn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNN OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UNN FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[4z0p|4z0p]], [[4weq|4weq]], [[5uog|5uog]]</td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5unn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5unn OCA], [http://pdbe.org/5unn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5unn RCSB], [http://www.ebi.ac.uk/pdbsum/5unn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5unn ProSAT]</td></tr>
</table>
TOC
</StructureSection>
[[Category: Almo, S C]]
[[Category: Bonanno, J]]
[[Category: Gasiorowska, O A]]
[[Category: Handing, K B]]
[[Category: Kutner, J]]
[[Category: LaRowe, C]]
[[Category: Minor, W]]
[[Category: Structural genomic]]
[[Category: Shabalin, I G]]
[[Category: Nadp-dependent dehydrogenase]]
[[Category: Nysgrc]]
[[Category: Oxidoreductase]]
[[Category: Psi-biology]]
[[Category: Sinorhizobium meliloti]]