5xkt - Revision history

OCA at 08:05, 22 November 2023

OCA — Wed, 22 Nov 2023 08:05:30 GMT

←Older revision		Revision as of 08:05, 22 November 2023
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	==Klebsiella pneumoniae UreG in complex with GMPPNP and nickel==		==Klebsiella pneumoniae UreG in complex with GMPPNP and nickel==
-	<StructureSection load='5xkt' size='340' side='right' caption='[[5xkt]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5xkt' size='340' side='right'caption='[[5xkt]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xkt]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp.~~_rhinoscleromatis_sb3432~~ Klebsiella pneumoniae subsp. rhinoscleromatis ~~sb3432~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XKT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xkt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._rhinoscleromatis_SB3432 Klebsiella pneumoniae subsp. rhinoscleromatis SB3432]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XKT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID~~-~~GUANYLATE+ESTER'>GNP</scene>~~, ~~<scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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">~~ureG, KPR_4504 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=861365 Klebsiella pneumoniae subsp. rhinoscleromatis SB3432]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=5xkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkt OCA], [~~http~~://pdbe.org/5xkt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xkt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xkt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkt 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=5xkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkt OCA], [https://pdbe.org/5xkt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xkt RCSB], [https://www.ebi.ac.uk/pdbsum/5xkt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/R4YE37_KLEPR R4YE37_KLEPR]] Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.[HAMAP-Rule:MF_01389][SAAS:SAAS00098435]	+	[https://www.uniprot.org/uniprot/R4YE37_KLEPR R4YE37_KLEPR] Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.[HAMAP-Rule:MF_01389][SAAS:SAAS00098435]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5xkt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xkt" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Urease accessory protein\|Urease accessory protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Klebsiella pneumoniae subsp. rhinoscleromatis ~~sb3432~~]]	+	[[Category: Klebsiella pneumoniae subsp. rhinoscleromatis SB3432]]
-	[[Category: ~~Fong, Y H~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Lau, P H~~]]	+	[[Category: Fong YH]]
-	[[Category: ~~Nim, Y S~~]]	+	[[Category: Lau PH]]
-	[[Category: ~~Wong, K B~~]]	+	[[Category: Nim YS]]
-	[[Category: ~~Yuen, M H~~]]	+	[[Category: Wong KB]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Yuen MH]]
-	~~[[Category: Simibi class gtpase~~]]	+

OCA at 08:57, 27 December 2017

OCA — Wed, 27 Dec 2017 08:57:43 GMT

←Older revision		Revision as of 08:57, 27 December 2017
Line 3:		Line 3:
	<StructureSection load='5xkt' size='340' side='right' caption='[[5xkt]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5xkt' size='340' side='right' caption='[[5xkt]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xkt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XKT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xkt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._rhinoscleromatis_sb3432 Klebsiella pneumoniae subsp. rhinoscleromatis sb3432]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XKT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ureG, KPR_4504 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=861365 Klebsiella pneumoniae subsp. rhinoscleromatis SB3432])</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=5xkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkt OCA], [http://pdbe.org/5xkt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xkt RCSB], [http://www.ebi.ac.uk/pdbsum/5xkt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkt 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=5xkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkt OCA], [http://pdbe.org/5xkt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xkt RCSB], [http://www.ebi.ac.uk/pdbsum/5xkt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/R4YE37_KLEPR R4YE37_KLEPR]] Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.[HAMAP-Rule:MF_01389][SAAS:SAAS00098435]		[[http://www.uniprot.org/uniprot/R4YE37_KLEPR R4YE37_KLEPR]] Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.[HAMAP-Rule:MF_01389][SAAS:SAAS00098435]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The ability of metallochaperones to allosterically regulate the binding/release of metal ions and to switch protein-binding partners along the metal delivery pathway is essential to the metallation of the metalloenzymes. Urease, catalyzing the hydrolysis of urea into ammonia and carbon dioxide, contains two nickel ions bound by a carbamylated lysine in its active site. Delivery of nickel ions for urease maturation is dependent on GTP hydrolysis and is assisted by four urease accessory proteins UreE, UreF, UreG, and UreH(UreD). Here, we determined the crystal structure of the UreG dimer from Klebsiella pneumoniae in complex with nickel and GMPPNP, a nonhydrolyzable analog of GTP. Comparison with the structure of the GDP-bound Helicobacter pylori UreG (HpUreG) in the UreG2F2H2 complex reveals large conformational changes in the G2 region and residues near the 66CPH68 metal-binding motif. Upon GTP binding, the side chains of Cys66 and His68 from each of the UreG protomers rotate toward each other to coordinate a nickel ion in a square-planar geometry. Mutagenesis studies on HpUreG support the conformational changes induced by GTP binding as essential to dimerization of UreG, GTPase activity, in vitro urease activation, and the switching of UreG from the UreG2F2H2 complex to form the UreE2G2 complex with the UreE dimer. The nickel-charged UreE dimer, providing the sole source of nickel, and the UreG2F2H2 complex could activate urease in vitro in the presence of GTP. Based on our results, we propose a mechanism of how conformational changes of UreG during the GTP hydrolysis/binding cycle facilitate urease maturation.
		+
		+	Structural insights into how GTP-dependent conformational changes in a metallochaperone UreG facilitate urease maturation.,Yuen MH, Fong YH, Nim YS, Lau PH, Wong KB Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):E10890-E10898. doi:, 10.1073/pnas.1712658114. Epub 2017 Dec 4. PMID:29203664<ref>PMID:29203664</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xkt" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Klebsiella pneumoniae subsp. rhinoscleromatis sb3432]]
	[[Category: Fong, Y H]]		[[Category: Fong, Y H]]
	[[Category: Lau, P H]]		[[Category: Lau, P H]]

OCA at 07:00, 13 December 2017

OCA — Wed, 13 Dec 2017 07:00:57 GMT

←Older revision		Revision as of 07:00, 13 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xkt is ~~ON HOLD until Paper Publication~~	+	==Klebsiella pneumoniae UreG in complex with GMPPNP and nickel==
-		+	<StructureSection load='5xkt' size='340' side='right' caption='[[5xkt]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xkt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XKT FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5xkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkt OCA], [http://pdbe.org/5xkt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xkt RCSB], [http://www.ebi.ac.uk/pdbsum/5xkt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkt ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/R4YE37_KLEPR R4YE37_KLEPR]] Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.[HAMAP-Rule:MF_01389][SAAS:SAAS00098435]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fong, Y H]]
		+	[[Category: Lau, P H]]
		+	[[Category: Nim, Y S]]
		+	[[Category: Wong, K B]]
		+	[[Category: Yuen, M H]]
		+	[[Category: Hydrolase]]
		+	[[Category: Simibi class gtpase]]

OCA at 15:32, 27 September 2017

OCA — Wed, 27 Sep 2017 15:32:39 GMT

←Older revision		Revision as of 15:32, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 17 May 2017 14:54:31 GMT

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

←Older revision

Revision as of 14:54, 17 May 2017

OCA: New page: '''Unreleased structure''' The entry 5xkt is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 17 May 2017 14:54:30 GMT

New page: '''Unreleased structure''' The entry 5xkt is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xkt is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]