5yh7 - Revision history

OCA at 08:29, 22 November 2023

OCA — Wed, 22 Nov 2023 08:29:49 GMT

←Older revision		Revision as of 08:29, 22 November 2023
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	<StructureSection load='5yh7' size='340' side='right'caption='[[5yh7]], [[Resolution\|resolution]] 2.03Å' scene=''>		<StructureSection load='5yh7' size='340' side='right'caption='[[5yh7]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yh7]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Acibc Acibc~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YH7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YH7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yh7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii_ACICU Acinetobacter baumannii ACICU]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YH7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YH7 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=COA:COENZYME+A'>COA</scene~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.03Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>coaD, ACICU_00798 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~405416 ACIBC])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[http://en.wikipedia.org/wiki/Pantetheine-phosphate_adenylyltransferase Pantetheine-phosphate adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.3 2.7.7.3] </~~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=5yh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yh7 OCA], [https://pdbe.org/5yh7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yh7 RCSB], [https://www.ebi.ac.uk/pdbsum/5yh7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yh7 ProSAT]</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=5yh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yh7 OCA], [~~http~~://pdbe.org/5yh7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yh7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yh7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yh7 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/COAD_ACIBC COAD_ACIBC]] Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate.[HAMAP-Rule:MF_00151]	+	[https://www.uniprot.org/uniprot/COAD_ACIBC COAD_ACIBC] Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate.[HAMAP-Rule:MF_00151]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acibc~~]]	+	[[Category: Acinetobacter baumannii ACICU]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Pantetheine-phosphate adenylyltransferase]]~~	+	[[Category: Gupta A]]
-	[[Category: Gupta, A]]	+	[[Category: Kaur P]]
-	[[Category: Kaur, P]]	+	[[Category: Sharma S]]
-	[[Category: Sharma, S]]	+	[[Category: Singh PK]]
-	[[Category: Singh~~, P K~~]]	+	[[Category: Singh TP]]
-	[[Category: Singh~~, T P]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:32, 17 April 2019

OCA — Wed, 17 Apr 2019 06:32:55 GMT

←Older revision		Revision as of 06:32, 17 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yh7 is ~~ON HOLD~~	+	==Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Coenzyme A at 2.0 A resolution==
		+	<StructureSection load='5yh7' size='340' side='right'caption='[[5yh7]], [[Resolution\|resolution]] 2.03Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yh7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acibc Acibc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YH7 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">coaD, ACICU_00798 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=405416 ACIBC])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pantetheine-phosphate_adenylyltransferase Pantetheine-phosphate adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.3 2.7.7.3] </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=5yh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yh7 OCA], [http://pdbe.org/5yh7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yh7 RCSB], [http://www.ebi.ac.uk/pdbsum/5yh7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yh7 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/COAD_ACIBC COAD_ACIBC]] Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate.[HAMAP-Rule:MF_00151]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phosphopantetheine adenylyltransferase (PPAT, EC. 2.7.7.3) catalyzes an essential step in the reaction that transfers an adenylyl group from adenosine tri phosphate (ATP) to 4'-phosphopantetheine (pPant) yielding 3'- dephospho-coenzyme A (dPCoA) and pyrophosphate (PP) in the coenzyme A (CoA) biosynthesis pathway. The enzyme PPAT from Acinetobacter baumannii (AbPPAT) was cloned, expressed and purified. The binding studies of AbPPAT were carried out with two compounds, trisodium citrate (TSC) and l-ascorbic acid (LAA, vitamin-C) using fluorescence spectroscopic (FS) and surface Plasmon resonance (SPR) methods. Both methods provided similar values of dissociation constants for TSC and LAA which were of the order of 10(-8)M and 10(-5)M respectively. The computer aided docking studies indicated fewer interactions of LAA with AbPPAT as compared to those of TSC. The freshly purified samples of AbPPAT were crystallized. The crystals of AbPPAT were soaked in the solutions containing TSC and LAA. However, the crystals of the complex of AbPPAT with LAA did not diffract well and hence the structure of the complex of AbPPAT with LAA could not be determined. On the other hand, the crystals of the complex of AbPPAT with TSC diffracted well and the structure was determined at 1.76A resolution. It showed that TSC bound to AbPPAT at the ATP binding site and formed several intermolecular contacts including 12 hydrogen bonds. The results of binding studies for both TSC and LAA and the structure of the complex of AbPPAT with TSC clearly indicated a potential role of TSC and LAA as antibacterial agents.

-	~~Authors: Singh, P.K~~., Gupta, A., ~~Kaur~~, P., Sharma, S., Singh, T.P.	+	Structural and binding studies of phosphopantetheine adenylyl transferase from Acinetobacter baumannii.,Gupta A, Singh PK, Iqbal N, Sharma P, Baraigya HR, Kaur P, Umar MS, Ahmad F, Sharma A, Owais M, Sharma S, Singh TP Biochim Biophys Acta Proteins Proteom. 2019 Mar 15;1867(6):537-547. doi:, 10.1016/j.bbapap.2019.03.002. PMID:30885618<ref>PMID:30885618</ref>

-	~~Description: Crystal structure~~ of the ~~complex~~ of ~~Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Coenzyme A at 2~~.~~0 A resolution~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Singh, P.K~~]]	+	<div class="pdbe-citations 5yh7" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Sharma, S~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Acibc]]
		+	[[Category: Large Structures]]
		+	[[Category: Pantetheine-phosphate adenylyltransferase]]
	[[Category: Gupta, A]]		[[Category: Gupta, A]]
-	[[Category: Singh, T.P]]
	[[Category: Kaur, P]]		[[Category: Kaur, P]]
		+	[[Category: Sharma, S]]
		+	[[Category: Singh, P K]]
		+	[[Category: Singh, T P]]
		+	[[Category: Transferase]]

OCA: Protected "5yh7" [edit=sysop:move=sysop]

OCA — Wed, 04 Oct 2017 08:06:25 GMT

Protected "5yh7" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:06, 4 October 2017

OCA: New page: '''Unreleased structure''' The entry 5yh7 is ON HOLD Authors: Singh, P.K., Gupta, A., Kaur, P., Sharma, S., Singh, T.P. Description: Crystal structure of the complex of Phosphopantethe...

OCA — Wed, 04 Oct 2017 08:06:23 GMT

New page: '''Unreleased structure''' The entry 5yh7 is ON HOLD Authors: Singh, P.K., Gupta, A., Kaur, P., Sharma, S., Singh, T.P. Description: Crystal structure of the complex of Phosphopantethe...

New page

'''Unreleased structure'''

The entry 5yh7 is ON HOLD

Authors: Singh, P.K., Gupta, A., Kaur, P., Sharma, S., Singh, T.P.

Description: Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Coenzyme A at 2.0 A resolution
[[Category: Unreleased Structures]]
[[Category: Singh, P.K]]
[[Category: Sharma, S]]
[[Category: Gupta, A]]
[[Category: Singh, T.P]]
[[Category: Kaur, P]]