5i0j - Revision history

OCA at 08:19, 23 August 2023

OCA — Wed, 23 Aug 2023 08:19:19 GMT

←Older revision		Revision as of 08:19, 23 August 2023
Line 1:		Line 1:

	==Crystal structure of DR2231_E47A mutant in complex with dUMP==		==Crystal structure of DR2231_E47A mutant in complex with dUMP==
-	<StructureSection load='5i0j' size='340' side='right' caption='[[5i0j]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5i0j' size='340' side='right'caption='[[5i0j]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i0j]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus~~ radiodurans~~" raj et al. 1960~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I0J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I0J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i0j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I0J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I0J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=UMP:2~~-~~DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</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]] 1.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DR_2231 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1299~~ "~~Micrococcus radiodurans~~" ~~Raj et al. 1960])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></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=5i0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i0j OCA], [~~http~~://pdbe.org/5i0j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i0j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i0j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i0j 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=5i0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i0j OCA], [https://pdbe.org/5i0j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i0j RCSB], [https://www.ebi.ac.uk/pdbsum/5i0j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i0j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9RS96_DEIRA Q9RS96_DEIRA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Micrococcus~~ radiodurans ~~raj et al. 1960~~]]	+	[[Category: Deinococcus radiodurans]]
-	[[Category: ~~Goncalves, A M.D~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Mota, C S~~]]	+	[[Category: Goncalves AMD]]
-	[[Category: ~~Sanctis, D de~~]]	+	[[Category: Mota CS]]
-	[[Category: ~~Alpha helix]]~~	+	[[Category: De Sanctis D]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:47, 4 April 2018

OCA — Wed, 04 Apr 2018 06:47:20 GMT

←Older revision		Revision as of 06:47, 4 April 2018
Line 3:		Line 3:
	<StructureSection load='5i0j' size='340' side='right' caption='[[5i0j]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5i0j' size='340' side='right' caption='[[5i0j]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i0j]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I0J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i0j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I0J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR_2231 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=5i0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i0j OCA], [http://pdbe.org/5i0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i0j RCSB], [http://www.ebi.ac.uk/pdbsum/5i0j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i0j 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=5i0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i0j OCA], [http://pdbe.org/5i0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i0j RCSB], [http://www.ebi.ac.uk/pdbsum/5i0j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i0j ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Micrococcus radiodurans raj et al. 1960]]
	[[Category: Goncalves, A M.D]]		[[Category: Goncalves, A M.D]]
	[[Category: Mota, C S]]		[[Category: Mota, C S]]
-	[[Category: Sanctis, D De]]	+	[[Category: Sanctis, D de]]
	[[Category: Alpha helix]]		[[Category: Alpha helix]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 18:32, 26 October 2016

OCA — Wed, 26 Oct 2016 18:32:37 GMT

←Older revision		Revision as of 18:32, 26 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i0j is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of DR2231_E47A mutant in complex with dUMP==
		+	<StructureSection load='5i0j' size='340' side='right' caption='[[5i0j]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5i0j]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I0J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></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=5i0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i0j OCA], [http://pdbe.org/5i0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i0j RCSB], [http://www.ebi.ac.uk/pdbsum/5i0j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i0j ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DR2231 from Deinococcus radiodurans was previously functionally and structurally characterized as an all-alpha NTP pyrophosphohydrolase with specific dUTPase activity. dUTPases have a central role in the regulation of dUTP intracellular levels and dTTP nucleotide metabolism. DR2231 presents a conserved di-metal catalytic site, similar to the all-alpha dimeric dUTPases, but contrary to these enzymes, it is unable to process dUDP. In this article we present functional and structural evidence of single-point mutations that affect directly or indirectly the enzyme catalysis and provide a complete description of the all-alpha NTP pyrophosphohydrolase mechanism. Activity assays, isothermal titration calorimetry and the crystal structures of these mutants obtained in complex with dUMP or a dUTP analogue aid in probing the reaction mechanism. Our results demonstrate that the two metals are necessary for enzyme processing and also important to modulate the substrate binding affinity. Single-point mutations located in a structurally mobile lid-like loop show that the interactions with the nucleoside monophosphate are essential for induction of the closed conformation and ultimately for substrate processing. beta and gamma-phosphates are held in place through coordination with the second metal, which is responsible for the substrate "gauche" orientation in the catalytic position. The lack of sufficient contacts to orient the dUDP beta-phosphate for hydrolysis explains DR2231 preference towards dUTP. Sequence and structural similarities with MazG proteins suggest that a similar mechanism might be conserved within the protein family. This article is protected by copyright. All rights reserved.

-	~~Authors:~~ Mota~~, C.S.~~, Goncalves, A.M.D.~~, De Sanctis, D~~.	+	Deinococcus radiodurans DR2231 is a two-metal-ion mechanism hydrolase with exclusive activity on dUTP.,Mota CS, Goncalves AM, de Sanctis D FEBS J. 2016 Oct 14. doi: 10.1111/febs.13923. PMID:27739259<ref>PMID:27739259</ref>

-	~~Description: Crystal structure~~ of ~~DR2231_E47A mutant in complex with dUMP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~De Sanctis~~, D]]	+	<div class="pdbe-citations 5i0j" style="background-color:#fffaf0;"></div>
-	[[Category: Mota, C.S]]	+	== References ==
-	[[Category: ~~Goncalves~~, ~~A.M.~~D]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Goncalves, A M.D]]
		+	[[Category: Mota, C S]]
		+	[[Category: Sanctis, D De]]
		+	[[Category: Alpha helix]]
		+	[[Category: Hydrolase]]

OCA at 01:23, 21 February 2016

OCA — Sun, 21 Feb 2016 01:23:57 GMT

←Older revision		Revision as of 01:23, 21 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i0j is ON HOLD	+	The entry 5i0j is ON HOLD until Paper Publication

	Authors: Mota, C.S., Goncalves, A.M.D., De Sanctis, D.		Authors: Mota, C.S., Goncalves, A.M.D., De Sanctis, D.

OCA: Protected "5i0j" [edit=sysop:move=sysop]

OCA — Wed, 10 Feb 2016 16:01:30 GMT

Protected "5i0j" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:01, 10 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i0j is ON HOLD Authors: Mota, C.S., Goncalves, A.M.D., De Sanctis, D. Description: Crystal structure of DR2231_E47A mutant in complex with dUMP [[...

OCA — Wed, 10 Feb 2016 16:01:29 GMT

New page: '''Unreleased structure''' The entry 5i0j is ON HOLD Authors: Mota, C.S., Goncalves, A.M.D., De Sanctis, D. Description: Crystal structure of DR2231_E47A mutant in complex with dUMP [[...

New page

'''Unreleased structure'''

The entry 5i0j is ON HOLD

Authors: Mota, C.S., Goncalves, A.M.D., De Sanctis, D.

Description: Crystal structure of DR2231_E47A mutant in complex with dUMP
[[Category: Unreleased Structures]]
[[Category: De Sanctis, D]]
[[Category: Mota, C.S]]
[[Category: Goncalves, A.M.D]]