2dkd - Revision history

OCA at 13:47, 13 March 2024

OCA — Wed, 13 Mar 2024 13:47:39 GMT

←Older revision		Revision as of 13:47, 13 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candida_albicans Candida albicans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candida_albicans Candida albicans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NG1:N-ACETYL-ALPHA-D-GALACTOSAMINE+1-PHOSPHATE'>NG1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NG1:N-ACETYL-ALPHA-D-GALACTOSAMINE+1-PHOSPHATE'>NG1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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'>[https://proteopedia.org/fgij/fg.htm?mol=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [https://pdbe.org/2dkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [https://www.ebi.ac.uk/pdbsum/2dkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkd 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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [https://pdbe.org/2dkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [https://www.ebi.ac.uk/pdbsum/2dkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkd ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</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=2dkd 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=2dkd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	N-acetylglucosamine-phosphate mutase (AGM1) is an essential enzyme in the synthetic process of UDP-N-acetylglucosamine (UDP-GlcNAc). UDP-GlcNAc is a UDP sugar that serves as a biosynthetic precursor of glycoproteins, mucopolysaccharides, and the cell wall of bacteria. Thus, a specific inhibitor of AGM1 from pathogenetic fungi could be a new candidate for an antifungal reagent that inhibits cell wall synthesis. AGM1 catalyzes the conversion of N-acetylglucosamine 6-phosphate (GlcNAc-6-P) into N-acetylglucosamine 1-phosphate (GlcNAc-1-P). This enzyme is a member of the alpha-D-phosphohexomutase superfamily, which catalyzes the intramolecular phosphoryl transfer of sugar substrates. Here we report the crystal structures of AGM1 from Candida albicans for the first time, both in the apoform and in the complex forms with the substrate and the product, and discuss its catalytic mechanism. The structure of AGM1 consists of four domains, of which three domains have essentially the same fold. The overall structure is similar to those of phosphohexomutases; however, there are two additional beta-strands in domain 4, and a circular permutation occurs in domain 1. The catalytic cleft is formed by four loops from each domain. The N-acetyl group of the substrate is recognized by Val-370 and Asn-389 in domain 3, from which the substrate specificity arises. By comparing the substrate and product complexes, it is suggested that the substrate rotates about 180 degrees on the axis linking C-4 and the midpoint of the C-5-O-5 bond in the reaction.
-
-	Crystal structures of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, and its substrate and product complexes.,Nishitani Y, Maruyama D, Nonaka T, Kita A, Fukami TA, Mio T, Yamada-Okabe H, Yamada-Okabe T, Miki K J Biol Chem. 2006 Jul 14;281(28):19740-7. Epub 2006 May 1. PMID:16651269<ref>PMID:16651269</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2dkd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:29, 30 September 2022

OCA — Fri, 30 Sep 2022 04:29:01 GMT

←Older revision		Revision as of 04:29, 30 September 2022
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	<StructureSection load='2dkd' size='340' side='right'caption='[[2dkd]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2dkd' size='340' side='right'caption='[[2dkd]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_11006_[[monilia_stellatoidea]] Atcc 11006 [[monilia stellatoidea]]~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candida_albicans Candida albicans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NG1:N-ACETYL-ALPHA-D-GALACTOSAMINE+1-PHOSPHATE'>NG1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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" id="ligandDat"><scene name='pdbligand=NG1:N-ACETYL-ALPHA-D-GALACTOSAMINE+1-PHOSPHATE'>NG1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dka\|2dka]], [[2dkc\|2dkc]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphoacetylglucosamine_mutase Phosphoacetylglucosamine mutase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.3 5.4.2.3] </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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [https://pdbe.org/2dkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [https://www.ebi.ac.uk/pdbsum/2dkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkd 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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [https://pdbe.org/2dkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [https://www.ebi.ac.uk/pdbsum/2dkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AGM1_CANAX AGM1_CANAX]] Catalyzes the conversion of GlcNAc-6-P into GlcNAc-1-P during the synthesis of uridine diphosphate/UDP-GlcNAc, which is a biosynthetic precursor of chitin and also supplies the amino sugars for N-linked oligosaccharides of glycoproteins.<ref>PMID:11004509</ref>	+	[https://www.uniprot.org/uniprot/AGM1_CANAX AGM1_CANAX] Catalyzes the conversion of GlcNAc-6-P into GlcNAc-1-P during the synthesis of uridine diphosphate/UDP-GlcNAc, which is a biosynthetic precursor of chitin and also supplies the amino sugars for N-linked oligosaccharides of glycoproteins.<ref>PMID:11004509</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Candida albicans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Phosphoacetylglucosamine mutase]]~~	+	[[Category: Fukami TA]]
-	[[Category: Fukami~~, T A~~]]	+	[[Category: Kita A]]
-	[[Category: Kita, A]]	+	[[Category: Maruyama D]]
-	[[Category: Maruyama, D]]	+	[[Category: Miki K]]
-	[[Category: Miki, K]]	+	[[Category: Mio T]]
-	[[Category: Mio, T]]	+	[[Category: Nishitani Y]]
-	[[Category: Nishitani, Y]]	+	[[Category: Nonaka T]]
-	[[Category: Nonaka, T]]	+	[[Category: Yamada-Okabe H]]
-	[[Category: Yamada-Okabe, H]]	+	[[Category: Yamada-Okabe T]]
-	[[Category: Yamada-Okabe, T]]	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Mutase~~]]	+

OCA at 10:32, 8 December 2021

OCA — Wed, 08 Dec 2021 10:32:19 GMT

←Older revision		Revision as of 10:32, 8 December 2021
Line 3:		Line 3:
	<StructureSection load='2dkd' size='340' side='right'caption='[[2dkd]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2dkd' size='340' side='right'caption='[[2dkd]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_11006_[[~~candida_stellatoidea~~]] Atcc 11006 [[~~candida~~ stellatoidea]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_11006_[[monilia_stellatoidea]] Atcc 11006 [[monilia stellatoidea]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NG1:N-ACETYL-ALPHA-D-GALACTOSAMINE+1-PHOSPHATE'>NG1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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" id="ligandDat"><scene name='pdbligand=NG1:N-ACETYL-ALPHA-D-GALACTOSAMINE+1-PHOSPHATE'>NG1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dka\|2dka]], [[2dkc\|2dkc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dka\|2dka]], [[2dkc\|2dkc]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Phosphoacetylglucosamine_mutase Phosphoacetylglucosamine mutase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.3 5.4.2.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphoacetylglucosamine_mutase Phosphoacetylglucosamine mutase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.3 5.4.2.3] </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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [~~http~~://pdbe.org/2dkd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dkd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkd 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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [https://pdbe.org/2dkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [https://www.ebi.ac.uk/pdbsum/2dkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AGM1_CANAX AGM1_CANAX]] Catalyzes the conversion of GlcNAc-6-P into GlcNAc-1-P during the synthesis of uridine diphosphate/UDP-GlcNAc, which is a biosynthetic precursor of chitin and also supplies the amino sugars for N-linked oligosaccharides of glycoproteins.<ref>PMID:11004509</ref>	+	[[https://www.uniprot.org/uniprot/AGM1_CANAX AGM1_CANAX]] Catalyzes the conversion of GlcNAc-6-P into GlcNAc-1-P during the synthesis of uridine diphosphate/UDP-GlcNAc, which is a biosynthetic precursor of chitin and also supplies the amino sugars for N-linked oligosaccharides of glycoproteins.<ref>PMID:11004509</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:35, 4 March 2020

OCA — Wed, 04 Mar 2020 07:35:54 GMT

←Older revision		Revision as of 07:35, 4 March 2020
Line 1:		Line 1:

	==Crystal structure of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, in the product complex==		==Crystal structure of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, in the product complex==
-	<StructureSection load='2dkd' size='340' side='right' caption='[[2dkd]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2dkd' size='340' side='right'caption='[[2dkd]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11006_[[candida_stellatoidea]] Atcc 11006 [[candida stellatoidea]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11006_[[candida_stellatoidea]] Atcc 11006 [[candida stellatoidea]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKD FirstGlance]. <br>
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Phosphoacetylglucosamine mutase]]		[[Category: Phosphoacetylglucosamine mutase]]
	[[Category: Fukami, T A]]		[[Category: Fukami, T A]]

OCA at 06:15, 30 May 2018

OCA — Wed, 30 May 2018 06:15:22 GMT

←Older revision		Revision as of 06:15, 30 May 2018
Line 1:		Line 1:
		+
	==Crystal structure of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, in the product complex==		==Crystal structure of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, in the product complex==
	<StructureSection load='2dkd' size='340' side='right' caption='[[2dkd]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2dkd' size='340' side='right' caption='[[2dkd]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dka\|2dka]], [[2dkc\|2dkc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dka\|2dka]], [[2dkc\|2dkc]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoacetylglucosamine_mutase Phosphoacetylglucosamine mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.3 5.4.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoacetylglucosamine_mutase Phosphoacetylglucosamine mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.3 5.4.2.3] </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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [http://pdbe.org/2dkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [http://www.ebi.ac.uk/pdbsum/2dkd 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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [http://pdbe.org/2dkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [http://www.ebi.ac.uk/pdbsum/2dkd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkd_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>

OCA at 22:20, 7 February 2016

OCA — Sun, 07 Feb 2016 22:20:12 GMT

←Older revision		Revision as of 22:20, 7 February 2016
Line 18:		Line 18:
	<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=2dkd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:25, 10 September 2015

OCA — Thu, 10 Sep 2015 05:25:51 GMT

←Older revision		Revision as of 05:25, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2dkd' size='340' side='right' caption='[[2dkd]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2dkd' size='340' side='right' caption='[[2dkd]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Candida_albicans Candida albicans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11006_[[candida_stellatoidea]] Atcc 11006 [[candida stellatoidea]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NG1:N-ACETYL-ALPHA-D-GALACTOSAMINE+1-PHOSPHATE'>NG1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=NG1:N-ACETYL-ALPHA-D-GALACTOSAMINE+1-PHOSPHATE'>NG1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dka\|2dka]], [[2dkc\|2dkc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dka\|2dka]], [[2dkc\|2dkc]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoacetylglucosamine_mutase Phosphoacetylglucosamine mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.3 5.4.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoacetylglucosamine_mutase Phosphoacetylglucosamine mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.3 5.4.2.3] </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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [http://www.ebi.ac.uk/pdbsum/2dkd 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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [http://pdbe.org/2dkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [http://www.ebi.ac.uk/pdbsum/2dkd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~AGM1_CANAL AGM1_CANAL~~]] ~~Interconverts~~ GlcNAc-6-P ~~and~~ GlcNAc-1-P.	+	[[http://www.uniprot.org/uniprot/AGM1_CANAX AGM1_CANAX]] Catalyzes the conversion of GlcNAc-6-P into GlcNAc-1-P during the synthesis of uridine diphosphate/UDP-GlcNAc, which is a biosynthetic precursor of chitin and also supplies the amino sugars for N-linked oligosaccharides of glycoproteins.<ref>PMID:11004509</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 28:
	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 2dkd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Candida albicans]]
	[[Category: Phosphoacetylglucosamine mutase]]		[[Category: Phosphoacetylglucosamine mutase]]
	[[Category: Fukami, T A]]		[[Category: Fukami, T A]]

OCA at 18:35, 24 December 2014

OCA — Wed, 24 Dec 2014 18:35:09 GMT

←Older revision		Revision as of 18:35, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Candida_albicans Candida albicans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Candida_albicans Candida albicans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NG1:N-ACETYL-ALPHA-D-GALACTOSAMINE+1-PHOSPHATE'>NG1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NG1:N-ACETYL-ALPHA-D-GALACTOSAMINE+1-PHOSPHATE'>NG1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dka\|2dka]], [[2dkc\|2dkc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dka\|2dka]], [[2dkc\|2dkc]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoacetylglucosamine_mutase Phosphoacetylglucosamine mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.3 5.4.2.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoacetylglucosamine_mutase Phosphoacetylglucosamine mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.3 5.4.2.3] </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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [http://www.ebi.ac.uk/pdbsum/2dkd 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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [http://www.ebi.ac.uk/pdbsum/2dkd PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AGM1_CANAL AGM1_CANAL]] Interconverts GlcNAc-6-P and GlcNAc-1-P.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Candida albicans]]		[[Category: Candida albicans]]
	[[Category: Phosphoacetylglucosamine mutase]]		[[Category: Phosphoacetylglucosamine mutase]]
-	[[Category: Fukami, T A.]]	+	[[Category: Fukami, T A]]
-	[[Category: Kita, A.]]	+	[[Category: Kita, A]]
-	[[Category: Maruyama, D.]]	+	[[Category: Maruyama, D]]
-	[[Category: Miki, K.]]	+	[[Category: Miki, K]]
-	[[Category: Mio, T.]]	+	[[Category: Mio, T]]
-	[[Category: Nishitani, Y.]]	+	[[Category: Nishitani, Y]]
-	[[Category: Nonaka, T.]]	+	[[Category: Nonaka, T]]
-	[[Category: Yamada-Okabe, H.]]	+	[[Category: Yamada-Okabe, H]]
-	[[Category: Yamada-Okabe, T.]]	+	[[Category: Yamada-Okabe, T]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Mutase]]		[[Category: Mutase]]

OCA at 01:38, 30 September 2014

OCA — Tue, 30 Sep 2014 01:38:01 GMT

←Older revision		Revision as of 01:38, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2dkd.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, in the product complex==
		+	<StructureSection load='2dkd' size='340' side='right' caption='[[2dkd]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2dkd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Candida_albicans Candida albicans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NG1:N-ACETYL-ALPHA-D-GALACTOSAMINE+1-PHOSPHATE'>NG1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dka\|2dka]], [[2dkc\|2dkc]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoacetylglucosamine_mutase Phosphoacetylglucosamine mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.3 5.4.2.3] </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=2dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkd RCSB], [http://www.ebi.ac.uk/pdbsum/2dkd 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/dk/2dkd_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 ==
		+	N-acetylglucosamine-phosphate mutase (AGM1) is an essential enzyme in the synthetic process of UDP-N-acetylglucosamine (UDP-GlcNAc). UDP-GlcNAc is a UDP sugar that serves as a biosynthetic precursor of glycoproteins, mucopolysaccharides, and the cell wall of bacteria. Thus, a specific inhibitor of AGM1 from pathogenetic fungi could be a new candidate for an antifungal reagent that inhibits cell wall synthesis. AGM1 catalyzes the conversion of N-acetylglucosamine 6-phosphate (GlcNAc-6-P) into N-acetylglucosamine 1-phosphate (GlcNAc-1-P). This enzyme is a member of the alpha-D-phosphohexomutase superfamily, which catalyzes the intramolecular phosphoryl transfer of sugar substrates. Here we report the crystal structures of AGM1 from Candida albicans for the first time, both in the apoform and in the complex forms with the substrate and the product, and discuss its catalytic mechanism. The structure of AGM1 consists of four domains, of which three domains have essentially the same fold. The overall structure is similar to those of phosphohexomutases; however, there are two additional beta-strands in domain 4, and a circular permutation occurs in domain 1. The catalytic cleft is formed by four loops from each domain. The N-acetyl group of the substrate is recognized by Val-370 and Asn-389 in domain 3, from which the substrate specificity arises. By comparing the substrate and product complexes, it is suggested that the substrate rotates about 180 degrees on the axis linking C-4 and the midpoint of the C-5-O-5 bond in the reaction.

-	~~{{STRUCTURE_2dkd\| PDB=2dkd \| SCENE= }}~~	+	Crystal structures of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, and its substrate and product complexes.,Nishitani Y, Maruyama D, Nonaka T, Kita A, Fukami TA, Mio T, Yamada-Okabe H, Yamada-Okabe T, Miki K J Biol Chem. 2006 Jul 14;281(28):19740-7. Epub 2006 May 1. PMID:16651269<ref>PMID:16651269</ref>

-	~~===Crystal structure of N-acetylglucosamine-phosphate mutase~~, a ~~member~~ of the ~~alpha-D-phosphohexomutase superfamily, in the product complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16651269}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2dkd]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Candida_albicans Candida albicans]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DKD OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016651269<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Candida albicans]]		[[Category: Candida albicans]]
	[[Category: Phosphoacetylglucosamine mutase]]		[[Category: Phosphoacetylglucosamine mutase]]

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

OCA — Sun, 06 Jan 2013 10:52:47 GMT

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

←Older revision

Revision as of 10:52, 6 January 2013