3dk5 - Revision history

OCA at 08:24, 20 March 2024

OCA — Wed, 20 Mar 2024 08:24:08 GMT

←Older revision		Revision as of 08:24, 20 March 2024
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	<StructureSection load='3dk5' size='340' side='right'caption='[[3dk5]], [[Resolution\|resolution]] 2.23Å' scene=''>		<StructureSection load='3dk5' size='340' side='right'caption='[[3dk5]], [[Resolution\|resolution]] 2.23Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dk5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Mycta Mycta~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DK5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dk5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Ra Mycobacterium tuberculosis H37Ra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DK5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.23Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[3diu\|3diu]], [[3dj4\|3dj4]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">glmU, MRA_1026 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])~~</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=3dk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dk5 OCA], [https://pdbe.org/3dk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dk5 RCSB], [https://www.ebi.ac.uk/pdbsum/3dk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dk5 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=3dk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dk5 OCA], [https://pdbe.org/3dk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dk5 RCSB], [https://www.ebi.ac.uk/pdbsum/3dk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dk5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~GLMU_MYCTA GLMU_MYCTA]~~] Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain ~~(By similarity)~~.	+	[https://www.uniprot.org/uniprot/GLMU_MYCTU GLMU_MYCTU] Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain.<ref>PMID:19237750</ref> <ref>PMID:19121323</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=3dk5 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=3dk5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Identifying direct targets of kinases and determining how their activities are regulated are central to understanding how they generate biological responses. Genetic and biochemical studies have shown that Mycobacterium tuberculosis serine/threonine protein kinases PknA and PknB play a role in modulating cell shape and possibly cell division. In this report, we show that the enzyme N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) of M. tuberculosis is a novel substrate of PknB and is phosphorylated on threonine residues. GlmU carries out two important biochemical activities: a C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate to produce N-acetylglucosamine-1-phosphate, which is converted into UDP-N-acetylglucosamine by the transfer of uridine 5'-monophosphate (from uridine 5'-triphosphate), a reaction catalyzed by the N-terminal domain. We determined the crystal structures of GlmU in apo form and UDP-N-acetylglucosamine-bound form, and analyzed them to identify threonine residues that may be accessible to PknB. The structure shows a two-domain architecture, with an N-terminal domain having an alpha/beta-like fold and with a C-terminal domain that forms a left-handed parallel beta-helix structure. Kinase assays with PknB using the N- and C-terminal domains of GlmU as substrates illustrated that PknB phosphorylates GlmU in the C-terminal domain. Furthermore, mutational studies reveal one of the five threonines present in region 414-439 to be phosphorylated by PknB. Structural and biochemical analyses have shown the significance of a variable C-terminal tail in regulating acetyltransferase activity. Notably, we demonstrate that although PknB-mediated phosphorylation of GlmU does not affect its uridyltransferase activity, it significantly modulates the acetyltransferase activity. These findings imply a role for PknB in regulating peptidoglycan synthesis by modulating the acetyltransferase activity of GlmU.
-
-	PknB-mediated phosphorylation of a novel substrate, N-acetylglucosamine-1-phosphate uridyltransferase, modulates its acetyltransferase activity.,Parikh A, Verma SK, Khan S, Prakash B, Nandicoori VK J Mol Biol. 2009 Feb 20;386(2):451-64. Epub 2008 Dec 24. PMID:19121323<ref>PMID:19121323</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3dk5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mycta~~]]	+	[[Category: Mycobacterium tuberculosis H37Ra]]
-	[[Category: Prakash, B]]	+	[[Category: Prakash B]]
-	[[Category: Verma~~, S K]]~~	+	[[Category: Verma SK]]
-	~~[[Category: Acetyltransferase]]~~	+
-	~~[[Category: Bifunctional]]~~	+
-	~~[[Category: Cell shape]]~~	+
-	~~[[Category: Cell wall biogenesis/degradation]]~~	+
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Left-handed-beta-helix]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Multifunctional enzyme]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Peptidoglycan synthesis]]~~	+
-	~~[[Category: Pyrophosphorylase]]~~	+
-	~~[[Category: Rossmann-like fold]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Trimer~~]]	+

OCA at 08:00, 9 February 2022

OCA — Wed, 09 Feb 2022 08:00:28 GMT

←Older revision		Revision as of 08:00, 9 February 2022
Line 1:		Line 1:

	==Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis==		==Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis==
-	<StructureSection load='3dk5' size='340' side='right' caption='[[3dk5]], [[Resolution\|resolution]] 2.23Å' scene=''>	+	<StructureSection load='3dk5' size='340' side='right'caption='[[3dk5]], [[Resolution\|resolution]] 2.23Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dk5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mycta Mycta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DK5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DK5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dk5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycta Mycta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DK5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]], [[3dj4\|3dj4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3diu\|3diu]], [[3dj4\|3dj4]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, MRA_1026 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, MRA_1026 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</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=3dk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dk5 OCA], [~~http~~://pdbe.org/3dk5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dk5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dk5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dk5 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=3dk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dk5 OCA], [https://pdbe.org/3dk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dk5 RCSB], [https://www.ebi.ac.uk/pdbsum/3dk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dk5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GLMU_MYCTA GLMU_MYCTA]] Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain (By similarity).	+	[[https://www.uniprot.org/uniprot/GLMU_MYCTA GLMU_MYCTA]] Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mycta]]		[[Category: Mycta]]
	[[Category: Prakash, B]]		[[Category: Prakash, B]]

OCA at 09:17, 14 November 2018

OCA — Wed, 14 Nov 2018 09:17:19 GMT

←Older revision		Revision as of 09:17, 14 November 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis==		==Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis==
	<StructureSection load='3dk5' size='340' side='right' caption='[[3dk5]], [[Resolution\|resolution]] 2.23Å' scene=''>		<StructureSection load='3dk5' size='340' side='right' caption='[[3dk5]], [[Resolution\|resolution]] 2.23Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]], [[3dj4\|3dj4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]], [[3dj4\|3dj4]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, MRA_1026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, MRA_1026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</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=3dk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dk5 OCA], [http://pdbe.org/3dk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dk5 RCSB], [http://www.ebi.ac.uk/pdbsum/3dk5 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=3dk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dk5 OCA], [http://pdbe.org/3dk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dk5 RCSB], [http://www.ebi.ac.uk/pdbsum/3dk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dk5 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/3dk5_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/3dk5_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 40:		Line 41:
	[[Category: Cell shape]]		[[Category: Cell shape]]
	[[Category: Cell wall biogenesis/degradation]]		[[Category: Cell wall biogenesis/degradation]]
		+	[[Category: Cytoplasm]]
	[[Category: Left-handed-beta-helix]]		[[Category: Left-handed-beta-helix]]
	[[Category: Magnesium]]		[[Category: Magnesium]]

OCA at 02:32, 10 February 2016

OCA — Wed, 10 Feb 2016 02:32:31 GMT

←Older revision		Revision as of 02:32, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='3dk5' size='340' side='right' caption='[[3dk5]], [[Resolution\|resolution]] 2.23Å' scene=''>		<StructureSection load='3dk5' size='340' side='right' caption='[[3dk5]], [[Resolution\|resolution]] 2.23Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dk5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium tuberculosis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DK5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DK5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dk5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycta Mycta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DK5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DK5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]], [[3dj4\|3dj4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]], [[3dj4\|3dj4]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, MRA_1026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1773 Mycobacterium tuberculosis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, MRA_1026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</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=3dk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dk5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dk5 RCSB], [http://www.ebi.ac.uk/pdbsum/3dk5 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=3dk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dk5 OCA], [http://pdbe.org/3dk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dk5 RCSB], [http://www.ebi.ac.uk/pdbsum/3dk5 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=3dk5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3dk5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mycobacterium tuberculosis~~]]	+	[[Category: Mycta]]
	[[Category: Prakash, B]]		[[Category: Prakash, B]]
	[[Category: Verma, S K]]		[[Category: Verma, S K]]

OCA at 11:10, 25 December 2014

OCA — Thu, 25 Dec 2014 11:10:26 GMT

←Older revision		Revision as of 11:10, 25 December 2014
Line 8:		Line 8:
	<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=3dk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dk5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dk5 RCSB], [http://www.ebi.ac.uk/pdbsum/3dk5 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=3dk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dk5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dk5 RCSB], [http://www.ebi.ac.uk/pdbsum/3dk5 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GLMU_MYCTA GLMU_MYCTA]] Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:58, 12 November 2014

OCA — Wed, 12 Nov 2014 07:58:18 GMT

←Older revision		Revision as of 07:58, 12 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3dk5.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis==
		+	<StructureSection load='3dk5' size='340' side='right' caption='[[3dk5]], [[Resolution\|resolution]] 2.23Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3dk5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DK5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DK5 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]], [[3dj4\|3dj4]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, MRA_1026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</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=3dk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dk5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dk5 RCSB], [http://www.ebi.ac.uk/pdbsum/3dk5 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/3dk5_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 ==
		+	Identifying direct targets of kinases and determining how their activities are regulated are central to understanding how they generate biological responses. Genetic and biochemical studies have shown that Mycobacterium tuberculosis serine/threonine protein kinases PknA and PknB play a role in modulating cell shape and possibly cell division. In this report, we show that the enzyme N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) of M. tuberculosis is a novel substrate of PknB and is phosphorylated on threonine residues. GlmU carries out two important biochemical activities: a C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate to produce N-acetylglucosamine-1-phosphate, which is converted into UDP-N-acetylglucosamine by the transfer of uridine 5'-monophosphate (from uridine 5'-triphosphate), a reaction catalyzed by the N-terminal domain. We determined the crystal structures of GlmU in apo form and UDP-N-acetylglucosamine-bound form, and analyzed them to identify threonine residues that may be accessible to PknB. The structure shows a two-domain architecture, with an N-terminal domain having an alpha/beta-like fold and with a C-terminal domain that forms a left-handed parallel beta-helix structure. Kinase assays with PknB using the N- and C-terminal domains of GlmU as substrates illustrated that PknB phosphorylates GlmU in the C-terminal domain. Furthermore, mutational studies reveal one of the five threonines present in region 414-439 to be phosphorylated by PknB. Structural and biochemical analyses have shown the significance of a variable C-terminal tail in regulating acetyltransferase activity. Notably, we demonstrate that although PknB-mediated phosphorylation of GlmU does not affect its uridyltransferase activity, it significantly modulates the acetyltransferase activity. These findings imply a role for PknB in regulating peptidoglycan synthesis by modulating the acetyltransferase activity of GlmU.

-	~~{{STRUCTURE_3dk5\| PDB=3dk5 \| SCENE= }}~~	+	PknB-mediated phosphorylation of a novel substrate, N-acetylglucosamine-1-phosphate uridyltransferase, modulates its acetyltransferase activity.,Parikh A, Verma SK, Khan S, Prakash B, Nandicoori VK J Mol Biol. 2009 Feb 20;386(2):451-64. Epub 2008 Dec 24. PMID:19121323<ref>PMID:19121323</ref>

-	~~===Crystal Structure~~ of ~~Apo-GlmU from Mycobacterium tuberculosis===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19121323}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3dk5]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3DK5 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019121323<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Prakash, B.]]	+	[[Category: Prakash, B]]
-	[[Category: Verma, S K.]]	+	[[Category: Verma, S K]]
	[[Category: Acetyltransferase]]		[[Category: Acetyltransferase]]
	[[Category: Bifunctional]]		[[Category: Bifunctional]]

OCA: Protected "3dk5" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 17:47:02 GMT

Protected "3dk5" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:47, 7 January 2013

OCA at 17:46, 7 January 2013

OCA — Mon, 07 Jan 2013 17:46:57 GMT

←Older revision		Revision as of 17:46, 7 January 2013
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-	~~{{Seed}}~~	+	[[Image:3dk5.png\|left\|200px]]
-	[[Image:3dk5.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3dk5", 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_3dk5\| PDB=3dk5 \| SCENE= }}		{{STRUCTURE_3dk5\| PDB=3dk5 \| SCENE= }}

	===Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis===		===Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19121323}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19121323 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19121323}}		{{ABSTRACT_PUBMED_19121323}}

	==About this Structure==		==About this Structure==
-	~~3DK5~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DK5 OCA].	+	[[3dk5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DK5 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19121323~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019121323</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Prakash, B.]]		[[Category: Prakash, B.]]
Line 31:		Line 19:
	[[Category: Cell shape]]		[[Category: Cell shape]]
	[[Category: Cell wall biogenesis/degradation]]		[[Category: Cell wall biogenesis/degradation]]
-	[[Category: Cytoplasm]]
	[[Category: Left-handed-beta-helix]]		[[Category: Left-handed-beta-helix]]
	[[Category: Magnesium]]		[[Category: Magnesium]]
Line 42:		Line 29:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Trimer]]		[[Category: Trimer]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 17:06:03 2009''

OCA at 14:06, 20 May 2009

OCA — Wed, 20 May 2009 14:06:05 GMT

←Older revision		Revision as of 14:06, 20 May 2009
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3dk5.jpg\|left\|200px]]

-	The ~~entry 3dk5~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3dk5", 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_3dk5\| PDB=3dk5 \| SCENE= }}

-	~~Authors: Verma, S.K., Parikh, A., Nandicoori, V.K., Prakash, B.~~	+	===Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis===

-	Description: Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 23 12~~:14:~~18 2008~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19121323}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19121323 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19121323}}
		+
		+	==About this Structure==
		+	3DK5 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DK5 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19121323</ref><references group="xtra"/>
		+	[[Category: Mycobacterium tuberculosis]]
		+	[[Category: Prakash, B.]]
		+	[[Category: Verma, S K.]]
		+	[[Category: Acetyltransferase]]
		+	[[Category: Bifunctional]]
		+	[[Category: Cell shape]]
		+	[[Category: Cell wall biogenesis/degradation]]
		+	[[Category: Cytoplasm]]
		+	[[Category: Left-handed-beta-helix]]
		+	[[Category: Magnesium]]
		+	[[Category: Metal-binding]]
		+	[[Category: Multifunctional enzyme]]
		+	[[Category: Nucleotidyltransferase]]
		+	[[Category: Peptidoglycan synthesis]]
		+	[[Category: Pyrophosphorylase]]
		+	[[Category: Rossmann-like fold]]
		+	[[Category: Transferase]]
		+	[[Category: Trimer]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 17:06:03 2009''

OCA at 09:14, 23 July 2008

OCA — Wed, 23 Jul 2008 09:14:19 GMT

←Older revision		Revision as of 09:14, 23 July 2008
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3dk5 is ON HOLD	+	The entry 3dk5 is ON HOLD until Paper Publication

	Authors: Verma, S.K., Parikh, A., Nandicoori, V.K., Prakash, B.		Authors: Verma, S.K., Parikh, A., Nandicoori, V.K., Prakash, B.
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	Description: Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis		Description: Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri~~ Jul ~~11 13~~:08:15 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 12:14:18 2008''