6kv3 - Revision history

OCA at 10:44, 22 November 2023

OCA — Wed, 22 Nov 2023 10:44:16 GMT

←Older revision		Revision as of 10:44, 22 November 2023
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	<StructureSection load='6kv3' size='340' side='right'caption='[[6kv3]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6kv3' size='340' side='right'caption='[[6kv3]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kv3]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Staac Staac~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KV3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KV3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kv3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_COL Staphylococcus aureus subsp. aureus COL]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KV3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KV3 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>nadE, SACOL1974 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=93062 STAAC])</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]] 2.3Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~http://en.wikipedia.org/wiki/NAD(+)_synthase NAD(+) synthase~~]~~, with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6~~.3~~.1.5 6.3.1.5] </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=6kv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kv3 OCA], [https://pdbe.org/6kv3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kv3 RCSB], [https://www.ebi.ac.uk/pdbsum/6kv3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kv3 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6kv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kv3 OCA], [~~http~~://pdbe.org/6kv3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kv3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kv3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kv3 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NADE_STAAC NADE_STAAC]] Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses ammonia as a nitrogen source.	+	[https://www.uniprot.org/uniprot/NADE_STAAC NADE_STAAC] Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses ammonia as a nitrogen source.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6kv3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6kv3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[NAD synthase\|NAD synthase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Staac~~]]	+	[[Category: Staphylococcus aureus subsp. aureus COL]]
-	[[Category: Nasrin~~, S K~~]]	+	[[Category: Nasrin SK]]
-	[[Category: Sandeep~~, S K]]~~	+	[[Category: Sandeep SK]]
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Nad pathway]]~~	+
-	~~[[Category: Nad synthetase nucleotide-binding protein]]~~	+
-	~~[[Category: Staphylococcus aureus~~]]	+

OCA at 08:06, 11 November 2020

OCA — Wed, 11 Nov 2020 08:06:04 GMT

←Older revision		Revision as of 08:06, 11 November 2020
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	==Crystal Structure of NAD+ Synthetase from Staphylococcus aureus==		==Crystal Structure of NAD+ Synthetase from Staphylococcus aureus==
-	<StructureSection load='6kv3' size='340' side='right'caption='[[6kv3]]' scene=''>	+	<StructureSection load='6kv3' size='340' side='right'caption='[[6kv3]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KV3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KV3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kv3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staac Staac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KV3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KV3 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kv3 OCA], [http://pdbe.org/6kv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kv3 RCSB], [http://www.ebi.ac.uk/pdbsum/6kv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kv3 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nadE, SACOL1974 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93062 STAAC])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_synthase NAD(+) synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.1.5 6.3.1.5] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kv3 OCA], [http://pdbe.org/6kv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kv3 RCSB], [http://www.ebi.ac.uk/pdbsum/6kv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kv3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NADE_STAAC NADE_STAAC]] Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses ammonia as a nitrogen source.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	NAD synthetase (NadE) catalyzes the last step in NAD biosynthesis, transforming deamido-NAD(+) into NAD(+) by a two-step reaction with co-substrates ATP and amide donor ammonia. In this study, we report the crystal structure of Staphylococcus aureus NAD synthetase enzyme (saNadE) at 2.3 A resolution. We used this structure to perform molecular dynamics simulations of apo-enzyme, enzyme-substrate (NadE with ATP and NaAD) and enzyme-intermediate complexes (NadE with NaAD-AMP) to investigate key binding interactions and explore the conformational transitions and flexibility of the binding pocket. Our results show large shift of N-terminal region in substrate bound form which is important for ATP binding. Substrates drive the correlated movement of loop regions surrounding it as well as some regions distal to the active site and stabilize them at complex state. Principal component analysis of atomic projections distinguish feasible trajectories to delineate distinct motions in enzyme-substrate to enzyme-intermediate states. Our results suggest mixed binding involving dominant induced fit and conformational selection. MD simulation extracted ensembles of NadE could potentially be utilized for in silico screening and structure based design of more effective Methicillin Resistant Staphylococcus aureus (MRSA) inhibitors.
		+
		+	Crystallographic and molecular dynamics simulation analysis of NAD synthetase from methicillin resistant Staphylococcus aureus (MRSA).,Sultana KN, Kuldeep J, Siddiqi MI, Srivastava SK Int J Biol Macromol. 2020 Oct 21;165(Pt B):2349-2362. doi:, 10.1016/j.ijbiomac.2020.10.096. PMID:33098904<ref>PMID:33098904</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kv3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Nasrin SK]]	+	[[Category: Staac]]
-	[[Category: Sandeep SK]]	+	[[Category: Nasrin, S K]]
		+	[[Category: Sandeep, S K]]
		+	[[Category: Ligase]]
		+	[[Category: Nad pathway]]
		+	[[Category: Nad synthetase nucleotide-binding protein]]
		+	[[Category: Staphylococcus aureus]]

OCA at 09:28, 9 September 2020

OCA — Wed, 09 Sep 2020 09:28:51 GMT

←Older revision		Revision as of 09:28, 9 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6kv3 ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of NAD+ Synthetase from Staphylococcus aureus==
-		+	<StructureSection load='6kv3' size='340' side='right'caption='[[6kv3]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KV3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KV3 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kv3 OCA], [http://pdbe.org/6kv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kv3 RCSB], [http://www.ebi.ac.uk/pdbsum/6kv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kv3 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Nasrin SK]]
		+	[[Category: Sandeep SK]]

OCA: Protected "6kv3" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2019 06:49:12 GMT

Protected "6kv3" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:49, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6kv3 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Oct 2019 06:49:10 GMT

New page: '''Unreleased structure''' The entry 6kv3 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6kv3 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]