8jfs - Revision history

OCA at 19:55, 29 May 2024

OCA — Wed, 29 May 2024 19:55:37 GMT

←Older revision		Revision as of 19:55, 29 May 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/ACYP_DEIRA ACYP_DEIRA]		[https://www.uniprot.org/uniprot/ACYP_DEIRA ACYP_DEIRA]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Acylphosphatase (Acp) is a hydrolase which specifically cleaves carboxyl-phosphate bond of intermediates of metabolic pathways. It is a small cytosolic enzyme found in both prokaryotic and eukaryotic organisms. Previous crystal structures of acylphosphatase from different organisms have provided insights into the active site but the complete understanding of substrate binding and catalytic mechanisms in acylphosphatase remain elusive. Here we report the crystal structure of phosphate bound acylphosphatase from a mesothermic bacterium, Deinococcus radiodurans (drAcp) at resolution of 1.0 A. Our structural analysis shows how the terminal phosphate group of substrates is bound to the active site, highlighting the importance of arginine in substrate recognition, role of asparagine in mode of catalysis and shedding light on the reaction mechanism. Additionally, the protein can refold after thermal melting by gradually lowering the temperature. To further explore the dynamics of drAcp, molecular dynamics simulation of drAcp and homologs from thermophilic organisms were carried out which revealed similar root mean square fluctuation profile but drAcp showed comparatively higher fluctuations.
		+
		+	Crystal structure of phosphate bound Acyl phosphatase mini-enzyme from Deinococcus radiodurans at 1A resolution.,Khakerwala Z, Kumar A, Makde RD Biochem Biophys Res Commun. 2023 Sep 3;671:153-159. doi: , 10.1016/j.bbrc.2023.06.003. Epub 2023 Jun 5. PMID:37302289<ref>PMID:37302289</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 8jfs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:27, 28 June 2023

OCA — Wed, 28 Jun 2023 21:27:15 GMT

←Older revision		Revision as of 21:27, 28 June 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8jfs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8JFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8JFS FirstGlance]. <br>		<table><tr><td colspan='2'>[[8jfs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8JFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8JFS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8jfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8jfs OCA], [https://pdbe.org/8jfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8jfs RCSB], [https://www.ebi.ac.uk/pdbsum/8jfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8jfs 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=8jfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8jfs OCA], [https://pdbe.org/8jfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8jfs RCSB], [https://www.ebi.ac.uk/pdbsum/8jfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8jfs ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:21, 14 June 2023

OCA — Wed, 14 Jun 2023 08:21:23 GMT

←Older revision		Revision as of 08:21, 14 June 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8jfs is ~~ON HOLD~~	+	==Phosphate bound acylphosphatase from Deinococcus radiodurans at 1 Angstrom resolution==
-		+	<StructureSection load='8jfs' size='340' side='right'caption='[[8jfs]], [[Resolution\|resolution]] 1.00Å' scene=''>
-	~~Authors~~: ~~Khakerwala~~, Z., ~~Kumar~~, A., ~~Makde~~, R.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[8jfs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8JFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8JFS FirstGlance]. <br>
-	~~Description~~: ~~Phosphate bound acylphosphatase from~~ Deinococcus radiodurans ~~at 1 Angstrom resolution~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8jfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8jfs OCA], [https://pdbe.org/8jfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8jfs RCSB], [https://www.ebi.ac.uk/pdbsum/8jfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8jfs ProSAT]</span></td></tr>
-	[[Category: ~~Makde, R.D~~]]	+	</table>
-	[[Category: Kumar, A]]	+	== Function ==
-	[[Category: ~~Khakerwala, Z~~]]	+	[https://www.uniprot.org/uniprot/ACYP_DEIRA ACYP_DEIRA]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Deinococcus radiodurans R1]]
		+	[[Category: Large Structures]]
		+	[[Category: Khakerwala Z]]
		+	[[Category: Kumar A]]
		+	[[Category: Makde RD]]

OCA: Protected "8jfs" [edit=sysop:move=sysop]

OCA — Thu, 25 May 2023 02:30:28 GMT

Protected "8jfs" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:30, 25 May 2023

OCA: New page: '''Unreleased structure''' The entry 8jfs is ON HOLD Authors: Khakerwala, Z., Kumar, A., Makde, R.D. Description: Phosphate bound acylphosphatase from Deinococcus radiodurans at 1 Angs...

OCA — Thu, 25 May 2023 02:30:26 GMT

New page: '''Unreleased structure''' The entry 8jfs is ON HOLD Authors: Khakerwala, Z., Kumar, A., Makde, R.D. Description: Phosphate bound acylphosphatase from Deinococcus radiodurans at 1 Angs...

New page

'''Unreleased structure'''

The entry 8jfs is ON HOLD

Authors: Khakerwala, Z., Kumar, A., Makde, R.D.

Description: Phosphate bound acylphosphatase from Deinococcus radiodurans at 1 Angstrom resolution
[[Category: Unreleased Structures]]
[[Category: Makde, R.D]]
[[Category: Kumar, A]]
[[Category: Khakerwala, Z]]