2z7b - Revision history

OCA at 13:56, 13 March 2024

OCA — Wed, 13 Mar 2024 13:56:28 GMT

←Older revision		Revision as of 13:56, 13 March 2024
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	<StructureSection load='2z7b' size='340' side='right'caption='[[2z7b]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2z7b' size='340' side='right'caption='[[2z7b]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z7b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Mesorhizobium_loti~~ Mesorhizobium ~~loti~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z7b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_japonicum_MAFF_303099 Mesorhizobium japonicum MAFF 303099]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z7B FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.9Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">5335 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266835 Mesorhizobium loti])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridine-4,5-dicarboxylate_4-decarboxylase 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.51 4.1.1.51] </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=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [https://pdbe.org/2z7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [https://www.ebi.ac.uk/pdbsum/2z7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7b 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=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [https://pdbe.org/2z7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [https://www.ebi.ac.uk/pdbsum/2z7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7b ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/HMPD_RHILO HMPD_RHILO] Involved in the catabolism of pyridoxal 5-phosphate (Vitamin B6). Catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to yield 3-hydroxy-2-methylpyridine-5-carboxylate. The decarboxylation proceeds by an aldolase-like mechanism in which the binding of the substrate frees Glu-73 residue from its interaction with manganese ion replacing it by an interaction with the hydroxyl group from the substrate. Glu-73 residue then provides the proton for the keto-enol tautomerization. The decarboxylation reaction is analogous to the retroaldol reaction except that it does not need a base as the carboxylate is likely to be deprotonated under the reaction conditions.<ref>PMID:17973403</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z7b ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z7b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The function of the mlr6791 gene from Mesorhizobium loti MAFF303099 has been identified. This gene encodes 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase (HMPDdc), an enzyme involved in the catabolism of pyridoxal 5'-phosphate (Vitamin B6). This enzyme was overexpressed in Escherichia coli and characterized. HMPDdc is a 26 kDa protein that catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to 3-hydroxy-2-methylpyridine-5-carboxylate. The KM and kcat were found to be 366 microM and 0.6 s-1, respectively. The structure of this enzyme was determined at 1.9 A resolution using SAD phasing and belongs to the class II aldolase/adducin superfamily. While the decarboxylation of hydroxy-substituted benzene rings is a common motif in biosynthesis, the mechanism of this reaction is still poorly characterized. The structural studies described here suggest that catalysis of such decarboxylations proceeds by an aldolase-like mechanism.
-
-	Gene identification and structural characterization of the pyridoxal 5'-phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from mesorhizobium loti MAFF303099.,Mukherjee T, McCulloch KM, Ealick SE, Begley TP Biochemistry. 2007 Nov 27;46(47):13606-15. Epub 2007 Oct 31. PMID:17973403<ref>PMID:17973403</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2z7b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mesorhizobium ~~loti~~]]	+	[[Category: Mesorhizobium japonicum MAFF 303099]]
-	[[Category: Begley~~, T P~~]]	+	[[Category: Begley TP]]
-	[[Category: Ealick~~, S E~~]]	+	[[Category: Ealick SE]]
-	[[Category: McCulloch~~, K M~~]]	+	[[Category: McCulloch KM]]
-	[[Category: Mukherjee, T]]	+	[[Category: Mukherjee T]]
-	~~[[Category: Class ii aldolase superfamily]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 10:47, 8 December 2021

OCA — Wed, 08 Dec 2021 10:47:34 GMT

←Older revision		Revision as of 10:47, 8 December 2021
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	==Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase==		==Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase==
-	<StructureSection load='2z7b' size='340' side='right' caption='[[2z7b]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='2z7b' size='340' side='right'caption='[[2z7b]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z7b]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z7b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z7B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">5335 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266835 Mesorhizobium loti])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">5335 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266835 Mesorhizobium loti])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridine-4,5-dicarboxylate_4-decarboxylase 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.51 4.1.1.51] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridine-4,5-dicarboxylate_4-decarboxylase 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.51 4.1.1.51] </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=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [~~http~~://pdbe.org/2z7b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z7b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7b 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=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [https://pdbe.org/2z7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [https://www.ebi.ac.uk/pdbsum/2z7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7b ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/2z7b_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/2z7b_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]		[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]
		+	[[Category: Large Structures]]
	[[Category: Mesorhizobium loti]]		[[Category: Mesorhizobium loti]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]

OCA at 09:26, 12 October 2017

OCA — Thu, 12 Oct 2017 09:26:34 GMT

←Older revision		Revision as of 09:26, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase==		==Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase==
	<StructureSection load='2z7b' size='340' side='right' caption='[[2z7b]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2z7b' size='340' side='right' caption='[[2z7b]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">5335 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266835 Mesorhizobium loti])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">5335 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266835 Mesorhizobium loti])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridine-4,5-dicarboxylate_4-decarboxylase 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.51 4.1.1.51] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridine-4,5-dicarboxylate_4-decarboxylase 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.51 4.1.1.51] </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=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [http://pdbe.org/2z7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [http://www.ebi.ac.uk/pdbsum/2z7b 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=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [http://pdbe.org/2z7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [http://www.ebi.ac.uk/pdbsum/2z7b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7b ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 13:47, 9 February 2016

OCA — Tue, 09 Feb 2016 13:47:08 GMT

←Older revision		Revision as of 13:47, 9 February 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">5335 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~381~~ Mesorhizobium loti])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">5335 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266835 Mesorhizobium loti])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridine-4,5-dicarboxylate_4-decarboxylase 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.51 4.1.1.51] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridine-4,5-dicarboxylate_4-decarboxylase 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.51 4.1.1.51] </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=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [http://www.ebi.ac.uk/pdbsum/2z7b 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=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [http://pdbe.org/2z7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [http://www.ebi.ac.uk/pdbsum/2z7b PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z7b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2z7b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:26, 20 January 2015

OCA — Tue, 20 Jan 2015 08:26:32 GMT

←Older revision		Revision as of 08:26, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z7b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z7B FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z7b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z7B FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">5335 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381 Mesorhizobium loti])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">5335 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381 Mesorhizobium loti])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridine-4,5-dicarboxylate_4-decarboxylase 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.51 4.1.1.51] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridine-4,5-dicarboxylate_4-decarboxylase 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.51 4.1.1.51] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [http://www.ebi.ac.uk/pdbsum/2z7b 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=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [http://www.ebi.ac.uk/pdbsum/2z7b PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]		[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]
	[[Category: Mesorhizobium loti]]		[[Category: Mesorhizobium loti]]
-	[[Category: Begley, T P.]]	+	[[Category: Begley, T P]]
-	[[Category: Ealick, S E.]]	+	[[Category: Ealick, S E]]
-	[[Category: McCulloch, K M.]]	+	[[Category: McCulloch, K M]]
-	[[Category: Mukherjee, T.]]	+	[[Category: Mukherjee, T]]
	[[Category: Class ii aldolase superfamily]]		[[Category: Class ii aldolase superfamily]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 05:07, 2 October 2014

OCA — Thu, 02 Oct 2014 05:07:04 GMT

←Older revision		Revision as of 05:07, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2z7b.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase==
		+	<StructureSection load='2z7b' size='340' side='right' caption='[[2z7b]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2z7b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z7B FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">5335 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381 Mesorhizobium loti])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridine-4,5-dicarboxylate_4-decarboxylase 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.51 4.1.1.51] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [http://www.ebi.ac.uk/pdbsum/2z7b PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/2z7b_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The function of the mlr6791 gene from Mesorhizobium loti MAFF303099 has been identified. This gene encodes 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase (HMPDdc), an enzyme involved in the catabolism of pyridoxal 5'-phosphate (Vitamin B6). This enzyme was overexpressed in Escherichia coli and characterized. HMPDdc is a 26 kDa protein that catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to 3-hydroxy-2-methylpyridine-5-carboxylate. The KM and kcat were found to be 366 microM and 0.6 s-1, respectively. The structure of this enzyme was determined at 1.9 A resolution using SAD phasing and belongs to the class II aldolase/adducin superfamily. While the decarboxylation of hydroxy-substituted benzene rings is a common motif in biosynthesis, the mechanism of this reaction is still poorly characterized. The structural studies described here suggest that catalysis of such decarboxylations proceeds by an aldolase-like mechanism.

-	~~{{STRUCTURE_2z7b\| PDB=2z7b \| SCENE= }}~~	+	Gene identification and structural characterization of the pyridoxal 5'-phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from mesorhizobium loti MAFF303099.,Mukherjee T, McCulloch KM, Ealick SE, Begley TP Biochemistry. 2007 Nov 27;46(47):13606-15. Epub 2007 Oct 31. PMID:17973403<ref>PMID:17973403</ref>

-	~~===Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4~~,~~5-dicarboxylate decarboxylase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17973403}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2z7b]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mesorhizobium_loti Mesorhizobium loti]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017973403<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]		[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]
	[[Category: Mesorhizobium loti]]		[[Category: Mesorhizobium loti]]

OCA: Protected "2z7b" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 18:15:49 GMT

Protected "2z7b" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:15, 7 January 2013

OCA at 18:15, 7 January 2013

OCA — Mon, 07 Jan 2013 18:15:48 GMT

←Older revision		Revision as of 18:15, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2z7b.png\|left\|200px]]		[[Image:2z7b.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2z7b", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2z7b\| PDB=2z7b \| SCENE= }}		{{STRUCTURE_2z7b\| PDB=2z7b \| SCENE= }}

	===Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase===		===Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17973403}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17973403 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17973403}}		{{ABSTRACT_PUBMED_17973403}}

	==About this Structure==		==About this Structure==
-	~~2Z7B~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA].	+	[[2z7b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17973403~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017973403</ref><references group="xtra"/>
	[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]		[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]
	[[Category: Mesorhizobium loti]]		[[Category: Mesorhizobium loti]]
Line 32:		Line 20:
	[[Category: Class ii aldolase superfamily]]		[[Category: Class ii aldolase superfamily]]
	[[Category: Lyase]]		[[Category: Lyase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:14:24 2009''

OCA at 08:14, 17 February 2009

OCA — Tue, 17 Feb 2009 08:14:27 GMT

←Older revision		Revision as of 08:14, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2Z7B is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA].	+	2Z7B is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA].

	==Reference==		==Reference==
-	Gene identification and structural characterization of the pyridoxal 5'-phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from mesorhizobium loti MAFF303099., Mukherjee T, McCulloch KM, Ealick SE, Begley TP, Biochemistry. 2007 Nov 27;46(47):13606-15. Epub 2007 Oct 31. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17973403 17973403]~~	+	<ref group="xtra">PMID:17973403</ref><references group="xtra"/>
	[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]		[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]
	[[Category: Mesorhizobium loti]]		[[Category: Mesorhizobium loti]]
-	[[Category: Single protein]]
	[[Category: Begley, T P.]]		[[Category: Begley, T P.]]
	[[Category: Ealick, S E.]]		[[Category: Ealick, S E.]]
Line 34:		Line 33:
	[[Category: Lyase]]		[[Category: Lyase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 14~~:02:~~08 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:14:24 2009''

OCA at 11:02, 28 July 2008

OCA — Mon, 28 Jul 2008 11:02:16 GMT

←Older revision		Revision as of 11:02, 28 July 2008
Line 1:		Line 1:
-	[[Image:2z7b.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2z7b.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2z7b\| PDB=2z7b \| SCENE= }}		{{STRUCTURE_2z7b\| PDB=2z7b \| SCENE= }}

-	~~'''~~Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase~~'''~~	+	===Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase===


-	~~==Overview==~~	+	<!--
-	The ~~function of the mlr6791 gene from Mesorhizobium loti MAFF303099 has been identified. This gene encodes 3-hydroxy-2-methylpyridine-4~~,~~5-dicarboxylate decarboxylase (HMPDdc)~~, ~~an enzyme involved in~~ the ~~catabolism of pyridoxal 5'-phosphate~~ (~~Vitamin B6)~~. ~~This enzyme was overexpressed in Escherichia coli and characterized~~. ~~HMPDdc~~ is ~~a 26 kDa protein that catalyzes~~ the ~~decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to 3-hydroxy-2-methylpyridine-5-carboxylate~~. ~~The KM and kcat were found to be 366 microM and 0.6 s~~-~~1, respectively. The structure of this enzyme was determined at 1.9 A resolution using SAD phasing and belongs to the class II aldolase/adducin superfamily. While the decarboxylation of hydroxy~~-substituted benzene rings is a common motif in biosynthesis, the mechanism of this reaction is still poorly characterized. The structural studies described here suggest that catalysis of such decarboxylations proceeds by an aldolase-like mechanism.	+	The line below this paragraph, {{ABSTRACT_PUBMED_17973403}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17973403 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17973403}}

	==About this Structure==		==About this Structure==
Line 29:		Line 33:
	[[Category: Class ii aldolase superfamily]]		[[Category: Class ii aldolase superfamily]]
	[[Category: Lyase]]		[[Category: Lyase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 20~~:01:26 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 14:02:08 2008''