5c7p - Revision history

OCA at 08:35, 27 September 2023

OCA — Wed, 27 Sep 2023 08:35:33 GMT

←Older revision		Revision as of 08:35, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5c7p]] is a 3 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=5C7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C7P FirstGlance]. <br>		<table><tr><td colspan='2'>[[5c7p]] is a 3 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=5C7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C7P 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=5c7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c7p OCA], [https://pdbe.org/5c7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c7p RCSB], [https://www.ebi.ac.uk/pdbsum/5c7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c7p 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]] 3.144Å</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=5c7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c7p OCA], [https://pdbe.org/5c7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c7p RCSB], [https://www.ebi.ac.uk/pdbsum/5c7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c7p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 06:23, 7 June 2023

OCA — Wed, 07 Jun 2023 06:23:13 GMT

←Older revision		Revision as of 06:23, 7 June 2023
Line 3:		Line 3:
	<StructureSection load='5c7p' size='340' side='right'caption='[[5c7p]], [[Resolution\|resolution]] 3.14Å' scene=''>		<StructureSection load='5c7p' size='340' side='right'caption='[[5c7p]], [[Resolution\|resolution]] 3.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5c7p]] is a 3 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=5C7P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5C7P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5c7p]] is a 3 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=5C7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C7P FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ngs\|3ngs]], [[5caa\|5caa]], [[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=5c7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c7p OCA], [https://pdbe.org/5c7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c7p RCSB], [https://www.ebi.ac.uk/pdbsum/5c7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c7p 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=5c7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c7p OCA], [~~http~~://pdbe.org/5c7p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5c7p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5c7p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5c7p 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 08:52, 1 January 2020

OCA — Wed, 01 Jan 2020 08:52:43 GMT

←Older revision		Revision as of 08:52, 1 January 2020
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	==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

OCA — Wed, 17 Apr 2019 06:19:22 GMT

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

	==Structure of Leishmania nucleoside diphostate kinase mutant P95S==		==Structure of Leishmania nucleoside diphostate kinase mutant P95S==
-	<StructureSection load='5c7p' size='340' side='right' caption='[[5c7p]], [[Resolution\|resolution]] 3.14Å' scene=''>	+	<StructureSection load='5c7p' size='340' side='right'caption='[[5c7p]], [[Resolution\|resolution]] 3.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5c7p]] is a 3 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=5C7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C7P FirstGlance]. <br>		<table><tr><td colspan='2'>[[5c7p]] is a 3 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=5C7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C7P FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5c7p" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5c7p" 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

OCA — Wed, 17 Jan 2018 08:03:02 GMT

←Older revision		Revision as of 08:03, 17 January 2018
Line 1:		Line 1:
		+
	==Structure of Leishmania nucleoside diphostate kinase mutant P95S==		==Structure of Leishmania nucleoside diphostate kinase mutant P95S==
	<StructureSection load='5c7p' size='340' side='right' caption='[[5c7p]], [[Resolution\|resolution]] 3.14Å' scene=''>		<StructureSection load='5c7p' size='340' side='right' caption='[[5c7p]], [[Resolution\|resolution]] 3.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5c7p]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C7P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5c7p]] is a 3 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=5C7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C7P FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ngs\|3ngs]], [[5caa\|5caa]], [[5cab\|5cab]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ngs\|3ngs]], [[5caa\|5caa]], [[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=5c7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c7p OCA], [http://pdbe.org/5c7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c7p RCSB], [http://www.ebi.ac.uk/pdbsum/5c7p 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=5c7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c7p OCA], [http://pdbe.org/5c7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c7p RCSB], [http://www.ebi.ac.uk/pdbsum/5c7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c7p 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 03:49, 16 October 2015

OCA — Fri, 16 Oct 2015 03:49:15 GMT

←Older revision		Revision as of 03:49, 16 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of Leishmania nucleoside diphostate kinase mutant P95S==
		+	<StructureSection load='5c7p' size='340' side='right' caption='[[5c7p]], [[Resolution\|resolution]] 3.14Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5c7p]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C7P FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ngs\|3ngs]], [[5caa\|5caa]], [[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=5c7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c7p OCA], [http://pdbe.org/5c7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c7p RCSB], [http://www.ebi.ac.uk/pdbsum/5c7p 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 5c7p 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 diphostate kinase mutant P95S~~	+	<div class="pdbe-citations 5c7p" 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 at 12:51, 22 July 2015

OCA — Wed, 22 Jul 2015 12:51:36 GMT

←Older revision		Revision as of 12:51, 22 July 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5c7p is ON HOLD	+	The entry 5c7p is ON HOLD until Paper Publication

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

OCA at 13:48, 8 July 2015

OCA — Wed, 08 Jul 2015 13:48:02 GMT

←Older revision		Revision as of 13:48, 8 July 2015
Line 5:		Line 5:
	Authors: Vieira, P.S., de Giuseppe, P.O., de Oliveira, A.H.C., Murakami, M.T.		Authors: Vieira, P.S., de Giuseppe, P.O., de Oliveira, A.H.C., Murakami, M.T.

-	Description: ~~The role of the C-terminus and Kpn-loop in the quaternary structure stability~~ of nucleoside ~~diphosphate kinases from Leishmania parasites~~	+	Description: Structure of Leishmania nucleoside diphostate kinase mutant P95S
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Vieira, P.S]]		[[Category: Vieira, P.S]]

OCA: Protected "5c7p" [edit=sysop:move=sysop]

OCA — Wed, 01 Jul 2015 11:15:45 GMT

Protected "5c7p" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:15, 1 July 2015

OCA: New page: '''Unreleased structure''' The entry 5c7p is ON HOLD Authors: Vieira, P.S., de Giuseppe, P.O., de Oliveira, A.H.C., Murakami, M.T. Description: The role of the C-terminus and Kpn-loop ...

OCA — Wed, 01 Jul 2015 11:15:44 GMT

New page: '''Unreleased structure''' The entry 5c7p is ON HOLD Authors: Vieira, P.S., de Giuseppe, P.O., de Oliveira, A.H.C., Murakami, M.T. Description: The role of the C-terminus and Kpn-loop ...

New page

'''Unreleased structure'''

The entry 5c7p is ON HOLD

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

Description: The role of the C-terminus and Kpn-loop in the quaternary structure stability of nucleoside diphosphate kinases from Leishmania parasites
[[Category: Unreleased Structures]]
[[Category: Vieira, P.S]]
[[Category: De Giuseppe, P.O]]
[[Category: Murakami, M.T]]
[[Category: De Oliveira, A.H.C]]