5caa - Revision history

OCA at 08:36, 27 September 2023

2023-09-27T08:36:16Z

←Older revision		Revision as of 08:36, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5caa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CAA FirstGlance]. <br>		<table><tr><td colspan='2'>[[5caa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CAA FirstGlance]. <br>
-	</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=5caa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5caa OCA], [https://pdbe.org/5caa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5caa RCSB], [https://www.ebi.ac.uk/pdbsum/5caa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5caa ProSAT]</span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5caa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5caa OCA], [https://pdbe.org/5caa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5caa RCSB], [https://www.ebi.ac.uk/pdbsum/5caa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5caa ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 06:26, 7 June 2023

2023-06-07T06:26:11Z

←Older revision		Revision as of 06:26, 7 June 2023
Line 3:		Line 3:
	<StructureSection load='5caa' size='340' side='right'caption='[[5caa]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5caa' size='340' side='right'caption='[[5caa]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5caa]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Leima Leima~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CAA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CAA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5caa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CAA FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ngs\|3ngs]], [[5c7p\|5c7p]], [[5cab\|5cab]]</td></tr>~~	+	</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=5caa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5caa OCA], [https://pdbe.org/5caa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5caa RCSB], [https://www.ebi.ac.uk/pdbsum/5caa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5caa ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">L1648.07, LMJF_32_2950 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 LEIMA])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=5caa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5caa OCA], [~~http~~://pdbe.org/5caa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5caa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5caa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5caa ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9U1E1_LEIMA Q9U1E1_LEIMA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Leima]]
-	[[Category: Nucleoside-diphosphate kinase]]
-	[[Category: Giuseppe, P O.de]]
-	[[Category: Murakami, M T]]
-	[[Category: Oliveira, A H.C de]]
-	[[Category: Vieira, P S]]
-	[[Category: Conformational stability]]
	[[Category: Leishmania major]]		[[Category: Leishmania major]]
-	[[Category: ~~Nucleoside diphosphate kinase~~]]	+	[[Category: Murakami MT]]
-	[[Category: ~~Quaternary structure~~]]	+	[[Category: Vieira PS]]
-	[[Category: ~~Site directed-mutagenesis~~]]	+	[[Category: De Giuseppe PO]]
-	[[Category: ~~Transferase~~]]	+	[[Category: De Oliveira AHC]]

OCA at 08:53, 1 January 2020

2020-01-01T08:53:02Z

←Older revision		Revision as of 08:53, 1 January 2020
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]	+	*[[Nucleoside diphosphate kinase 3D structures\|Nucleoside diphosphate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:19, 17 April 2019

2019-04-17T06:19:26Z

←Older revision		Revision as of 06:19, 17 April 2019
Line 1:		Line 1:

	==Structure of Leishmania nucleoside diphosphate kinase mutant P100S/del5-Cterm==		==Structure of Leishmania nucleoside diphosphate kinase mutant P100S/del5-Cterm==
-	<StructureSection load='5caa' size='340' side='right' caption='[[5caa]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5caa' size='340' side='right'caption='[[5caa]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5caa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leima Leima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CAA FirstGlance]. <br>		<table><tr><td colspan='2'>[[5caa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leima Leima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CAA FirstGlance]. <br>
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5caa" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5caa" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Leima]]		[[Category: Leima]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]

OCA at 08:03, 17 January 2018

2018-01-17T08:03:05Z

←Older revision		Revision as of 08:03, 17 January 2018
Line 1:		Line 1:
		+
	==Structure of Leishmania nucleoside diphosphate kinase mutant P100S/del5-Cterm==		==Structure of Leishmania nucleoside diphosphate kinase mutant P100S/del5-Cterm==
	<StructureSection load='5caa' size='340' side='right' caption='[[5caa]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5caa' size='340' side='right' caption='[[5caa]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5caa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CAA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5caa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leima Leima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CAA FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ngs\|3ngs]], [[5c7p\|5c7p]], [[5cab\|5cab]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ngs\|3ngs]], [[5c7p\|5c7p]], [[5cab\|5cab]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">L1648.07, LMJF_32_2950 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 LEIMA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=5caa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5caa OCA], [http://pdbe.org/5caa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5caa RCSB], [http://www.ebi.ac.uk/pdbsum/5caa PDBsum]</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=5caa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5caa OCA], [http://pdbe.org/5caa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5caa RCSB], [http://www.ebi.ac.uk/pdbsum/5caa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5caa ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Leima]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Giuseppe, P O.de]]		[[Category: Giuseppe, P O.de]]

OCA at 03:55, 16 October 2015

2015-10-16T03:55:03Z

←Older revision		Revision as of 03:55, 16 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of Leishmania nucleoside diphosphate kinase mutant P100S/del5-Cterm==
		+	<StructureSection load='5caa' size='340' side='right' caption='[[5caa]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5caa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CAA FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ngs\|3ngs]], [[5c7p\|5c7p]], [[5cab\|5cab]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=5caa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5caa OCA], [http://pdbe.org/5caa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5caa RCSB], [http://www.ebi.ac.uk/pdbsum/5caa PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nucleoside diphosphate kinase (NDK) is a housekeeping enzyme that plays key roles in nucleotide recycling and homeostasis in trypanosomatids. Moreover, it is secreted by the intracellular parasite Leishmania to modulate the host response. These functions make NDK an attractive target for drug design and for studies aiming at a better understanding of the mechanisms mediating host-pathogen interactions. Here, we report the crystal structures of three mutants of the NDK from Leishmania major (LmNDK) that affects the stability of the hexameric biological assembly including P95S, Delta5Ct (lacking the last five residues) and the double mutant P100S/Delta5Ct. Although P95S and Delta5Ct variants conserve the hexameric structure of the wild-type protein, the double mutant becomes a dimer as shown by in solution studies. Free energy calculation of dimer-dimer interfaces and enzymatic assays indicate that P95S, Delta5Ct and P100S/Delta5Ct mutations progressively decrease the hexamer stability and enzyme activity. These results demonstrate that the mutated regions play a role in protein function through stabilizing the quaternary arrangement.

-	The ~~entry 5caa is ON HOLD until Paper Publication~~	+	The role of the C-terminus and Kpn loop in the quaternary structure stability of nucleoside diphosphate kinase from Leishmania parasites.,Vieira PS, de Giuseppe PO, de Oliveira AH, Murakami MT J Struct Biol. 2015 Sep 26. pii: S1047-8477(15)30064-2. doi:, 10.1016/j.jsb.2015.09.009. PMID:26410384<ref>PMID:26410384</ref>

-	~~Authors: Vieira~~, P.S.~~, de~~ Giuseppe, P.O., de Oliveira, A.H.C., ~~Murakami, M.T.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of Leishmania nucleoside diphosphate kinase mutant P100S/del5-Cterm~~	+	<div class="pdbe-citations 5caa" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: ~~Vieira, P.S~~]]	+	<references/>
-	[[Category: ~~De Giuseppe, P.O~~]]	+	__TOC__
-	[[Category: ~~Murakami, M.T~~]]	+	</StructureSection>
-	[[Category: ~~De Oliveira, A.H.C~~]]	+	[[Category: Nucleoside-diphosphate kinase]]
		+	[[Category: Giuseppe, P O.de]]
		+	[[Category: Murakami, M T]]
		+	[[Category: Oliveira, A H.C de]]
		+	[[Category: Vieira, P S]]
		+	[[Category: Conformational stability]]
		+	[[Category: Leishmania major]]
		+	[[Category: Nucleoside diphosphate kinase]]
		+	[[Category: Quaternary structure]]
		+	[[Category: Site directed-mutagenesis]]
		+	[[Category: Transferase]]

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

2015-07-08T13:54:01Z

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

←Older revision

Revision as of 13:54, 8 July 2015

OCA: New page: '''Unreleased structure''' The entry 5caa is ON HOLD until Paper Publication Authors: Vieira, P.S., de Giuseppe, P.O., de Oliveira, A.H.C., Murakami, M.T. Description: Structure of Lei...

2015-07-08T13:54:00Z

New page: '''Unreleased structure''' The entry 5caa is ON HOLD until Paper Publication Authors: Vieira, P.S., de Giuseppe, P.O., de Oliveira, A.H.C., Murakami, M.T. Description: Structure of Lei...

New page

'''Unreleased structure'''

The entry 5caa is ON HOLD until Paper Publication

Authors: Vieira, P.S., de Giuseppe, P.O., de Oliveira, A.H.C., Murakami, M.T.

Description: Structure of Leishmania nucleoside diphosphate kinase mutant P100S/del5-Cterm
[[Category: Unreleased Structures]]
[[Category: Vieira, P.S]]
[[Category: De Giuseppe, P.O]]
[[Category: Murakami, M.T]]
[[Category: De Oliveira, A.H.C]]