3dj4 - Revision history

OCA at 08:24, 20 March 2024

2024-03-20T08:24:06Z

←Older revision		Revision as of 08:24, 20 March 2024
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	<StructureSection load='3dj4' size='340' side='right'caption='[[3dj4]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='3dj4' size='340' side='right'caption='[[3dj4]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dj4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dj4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DJ4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</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]] 2.38Å</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]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">glmU, Rv1018c, MT1046 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])~~</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=3dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj4 OCA], [https://pdbe.org/3dj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dj4 RCSB], [https://www.ebi.ac.uk/pdbsum/3dj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dj4 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=3dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj4 OCA], [https://pdbe.org/3dj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dj4 RCSB], [https://www.ebi.ac.uk/pdbsum/3dj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dj4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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>	+	[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=3dj4 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=3dj4 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 3dj4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Prakash, B~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Verma, S K~~]]	+	[[Category: Prakash B]]
-	[[Category: ~~Acetyltransferase]]~~	+	[[Category: Verma SK]]
-	~~[[Category: Acyltransferase]]~~	+
-	~~[[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 07:59, 9 February 2022

2022-02-09T07:59:48Z

←Older revision		Revision as of 07:59, 9 February 2022
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	==Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.==		==Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.==
-	<StructureSection load='3dj4' size='340' side='right' caption='[[3dj4]], [[Resolution\|resolution]] 2.38Å' scene=''>	+	<StructureSection load='3dj4' size='340' side='right'caption='[[3dj4]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dj4]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DJ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dj4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DJ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]]</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]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, Rv1018c, MT1046 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, Rv1018c, MT1046 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=3dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj4 OCA], [~~http~~://pdbe.org/3dj4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dj4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dj4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dj4 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=3dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj4 OCA], [https://pdbe.org/3dj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dj4 RCSB], [https://www.ebi.ac.uk/pdbsum/3dj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dj4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://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>	+	[[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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	</div>		</div>
	<div class="pdbe-citations 3dj4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3dj4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[N-acetylglucosamine-1-phosphate uridyltransferase\|N-acetylglucosamine-1-phosphate uridyltransferase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Prakash, B]]		[[Category: Prakash, B]]
	[[Category: Verma, S K]]		[[Category: Verma, S K]]

OCA at 09:19, 14 November 2018

2018-11-14T09:19:25Z

←Older revision		Revision as of 09:19, 14 November 2018
Line 1:		Line 1:
		+
	==Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.==		==Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.==
	<StructureSection load='3dj4' size='340' side='right' caption='[[3dj4]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='3dj4' size='340' side='right' caption='[[3dj4]], [[Resolution\|resolution]] 2.38Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, Rv1018c, MT1046 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, Rv1018c, MT1046 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=3dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj4 OCA], [http://pdbe.org/3dj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dj4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dj4 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=3dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj4 OCA], [http://pdbe.org/3dj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dj4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dj4 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/dj/3dj4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dj/3dj4_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 16:17, 7 February 2016

2016-02-07T16:17:46Z

←Older revision		Revision as of 16:17, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3dj4' size='340' side='right' caption='[[3dj4]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='3dj4' size='340' side='right' caption='[[3dj4]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dj4]] 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=3DJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dj4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DJ4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, Rv1018c, MT1046 ([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, Rv1018c, MT1046 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=3dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dj4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dj4 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=3dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj4 OCA], [http://pdbe.org/3dj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dj4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dj4 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<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=3dj4 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 3dj4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Prakash, B]]		[[Category: Prakash, B]]
	[[Category: Verma, S K]]		[[Category: Verma, S K]]

OCA at 16:37, 24 December 2014

2014-12-24T16:37:22Z

←Older revision		Revision as of 16:37, 24 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=3dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dj4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dj4 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=3dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dj4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dj4 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://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]]

OCA at 08:01, 12 November 2014

2014-11-12T08:01:41Z

←Older revision		Revision as of 08:01, 12 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3dj4.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.==
		+	<StructureSection load='3dj4' size='340' side='right' caption='[[3dj4]], [[Resolution\|resolution]] 2.38Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3dj4]] 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=3DJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DJ4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3diu\|3diu]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glmU, Rv1018c, MT1046 ([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=3dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dj4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dj4 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/dj/3dj4_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_3dj4\| PDB=3dj4 \| 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 ~~GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19121323}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3dj4]] 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=3DJ4 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: Acyltransferase]]		[[Category: Acyltransferase]]

OCA: Protected "3dj4" [edit=sysop:move=sysop]

2013-01-07T22:45:00Z

Protected "3dj4" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:45, 7 January 2013

OCA at 22:44, 7 January 2013

2013-01-07T22:44:50Z

←Older revision		Revision as of 22:44, 7 January 2013
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3dj4.png\|left\|200px]]
-	[[Image:3dj4.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3dj4", 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_3dj4\| PDB=3dj4 \| SCENE= }}		{{STRUCTURE_3dj4\| PDB=3dj4 \| SCENE= }}

	===Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.===		===Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.===

-
-	<!--
-	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==
-	~~3DJ4~~ 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=3DJ4 OCA].	+	[[3dj4]] 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=3DJ4 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 32:		Line 20:
	[[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 43:		Line 30:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Trimer]]		[[Category: Trimer]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 17:10:38 2009''

OCA at 14:10, 20 May 2009

2009-05-20T14:10:40Z

←Older revision		Revision as of 14:10, 20 May 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3dj4.jpg\|left\|200px]]

-	The ~~entry 3dj4~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3dj4", 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_3dj4\| PDB=3dj4 \| SCENE= }}

-	~~Authors: Verma, S.K., Parikh, A., Nandicoori, V.K., Prakash, B~~.	+	===Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.===

-	Description: Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 23 12~~:14:~~06 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==
		+	3DJ4 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=3DJ4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19121323</ref><references group="xtra"/>
		+	[[Category: Mycobacterium tuberculosis]]
		+	[[Category: Prakash, B.]]
		+	[[Category: Verma, S K.]]
		+	[[Category: Acetyltransferase]]
		+	[[Category: Acyltransferase]]
		+	[[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 17:10:38 2009''

OCA at 09:14, 23 July 2008

2008-07-23T09:14:06Z

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

-	The entry 3dj4 is ON HOLD	+	The entry 3dj4 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.
Line 7:		Line 7:
	Description: Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.		Description: Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri~~ Jul ~~11 13~~:07:59 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 12:14:06 2008''