5o5z - Revision history

OCA at 19:09, 29 November 2023

OCA — Wed, 29 Nov 2023 19:09:16 GMT

←Older revision		Revision as of 19:09, 29 November 2023
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	<StructureSection load='5o5z' size='340' side='right'caption='[[5o5z]], [[Resolution\|resolution]] 2.44Å' scene=''>		<StructureSection load='5o5z' size='340' side='right'caption='[[5o5z]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o5z]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~'caldococcus_litoralis'_z-1301 'caldococcus~~ litoralis~~' z-1301~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O5Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o5z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_litoralis Thermococcus litoralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O5Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AT4:5-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE'>AT4</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.441Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glkA, OCC_09701 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2265 'Caldococcus litoralis' Z-1301])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AT4:5-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE'>AT4</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5z OCA], [~~http~~://pdbe.org/5o5z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o5z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o5z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5z 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=5o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5z OCA], [https://pdbe.org/5o5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o5z RCSB], [https://www.ebi.ac.uk/pdbsum/5o5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GLKA_THELN GLKA_THELN]] Catalyzes the phosphorylation of D-glucose to D-glucose 6-phosphate using ADP as the phosphate donor. Can also use CDP as the phosphoryl group donor and D-glucosamine and D-1,5-anhydroglucitol as the phosphoryl group acceptor.<ref>PMID:11098152</ref>	+	[https://www.uniprot.org/uniprot/GLKA_THELN GLKA_THELN] Catalyzes the phosphorylation of D-glucose to D-glucose 6-phosphate using ADP as the phosphate donor. Can also use CDP as the phosphoryl group donor and D-glucosamine and D-1,5-anhydroglucitol as the phosphoryl group acceptor.<ref>PMID:11098152</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Caldococcus litoralis z-1301]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Castro-Fernandez, V]]	+	[[Category: Thermococcus litoralis]]
-	[[Category: Fernandez~~, F J~~]]	+	[[Category: Castro-Fernandez V]]
-	[[Category: Guixe, V]]	+	[[Category: Fernandez FJ]]
-	[[Category: Herrera-Morande, A]]	+	[[Category: Guixe V]]
-	[[Category: Merino, F]]	+	[[Category: Herrera-Morande A]]
-	[[Category: Ramirez-Sarmiento~~, C A~~]]	+	[[Category: Merino F]]
-	[[Category: Vega~~, M C]]~~	+	[[Category: Ramirez-Sarmiento CA]]
-	~~[[Category: Adp-dependent]]~~	+	[[Category: Vega MC]]
-	~~[[Category: Glucokinase]]~~	+
-	~~[[Category: Ribokinase superfamily]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 13:16, 10 May 2019

OCA — Fri, 10 May 2019 13:16:50 GMT

←Older revision		Revision as of 13:16, 10 May 2019
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	==CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS ADP-DEPENDENT GLUCOKINASE (GK)==		==CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS ADP-DEPENDENT GLUCOKINASE (GK)==
-	<StructureSection load='5o5z' size='340' side='right' caption='[[5o5z]], [[Resolution\|resolution]] 2.44Å' scene=''>	+	<StructureSection load='5o5z' size='340' side='right'caption='[[5o5z]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O5Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o5z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'caldococcus_litoralis'_z-1301 'caldococcus litoralis' z-1301]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O5Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AT4:5-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE'>AT4</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AT4:5-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE'>AT4</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glkA, OCC_09701 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2265 'Caldococcus litoralis' Z-1301])</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=5o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5z OCA], [http://pdbe.org/5o5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5z RCSB], [http://www.ebi.ac.uk/pdbsum/5o5z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5z 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=5o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5z OCA], [http://pdbe.org/5o5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5z RCSB], [http://www.ebi.ac.uk/pdbsum/5o5z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5z ProSAT]</span></td></tr>
	</table>		</table>
Line 11:		Line 12:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~ADP~~-~~dependent glucokinases represent~~ a ~~unique family of kinases that belong~~ to the ribokinase superfamily, ~~being present mainly in hyperthermophilic archaea~~. ~~For these enzymes there~~ is ~~no agreement about~~ the ~~magnitude~~ of the ~~structural transitions associated with ligand binding and whether they are meaningful to the function~~ of the ~~enzyme~~. ~~We used~~ the ADP-dependent ~~glucokinase from Termococcus~~ litoralis ~~as a model to investigate~~ the ~~conformational changes observed in X-ray crystallographic structures upon~~ substrate binding ~~and to compare them with those determined in solution in~~ order ~~to understand their interplay with~~ the ~~glucokinase function~~. ~~Initial velocity studies indicate~~ that ~~catalysis follows a sequential ordered mechanism that correlates with~~ the ~~structural transitions experienced by~~ the enzyme ~~in solution and~~ in the ~~crystal state~~. ~~The combined data allowed us to resolve~~ the ~~open-closed conformational transition that accounts for~~ the ~~complete reaction cycle and to identify~~ the ~~corresponding clusters~~ of ~~aminoacids residues responsible for it. These results provide molecular bases for a general mechanism conserved across~~ the ~~ADP~~-~~dependent kinase family~~.	+	During evolution, some homologs proteins appear with different connectivity between secondary structures (different topology) but conserving the tridimensional arrangement of them (same architecture). These events can produce two types of arrangements; circular permutation or non-cyclic permutations. The first one results in the N and C terminus transferring to a different position on a protein sequence while the second refers to a more complex arrangement of the structural elements. In ribokinase superfamily, two different topologies can be identified, which are related to each other as a non-cyclic permutation occurred during the evolution. Interestingly, this change in topology is correlated with the nucleotide specificity of its members. Thereby, the connectivity of the secondary elements allows us to distinguish an ATP-dependent and an ADP-dependent topology. Here we address the impact of introducing the topology of a homologous ATP-dependent kinase in an ADP-dependent kinase (Thermococcus litoralis glucokinase) in the structure, nucleotide specificity, and substrate binding order of the engineered enzyme. Structural evidence demonstrates that rewiring the topology of TlGK leads to an active and soluble enzyme without modifications on its three-dimensional architecture. The permuted enzyme (PerGK) retains the nucleotide preference of the parent TlGK enzyme but shows a change in the substrate binding order. Our results illustrate how the rearrangement of the protein folding topology during the evolution of the ribokinase superfamily enzymes may have dictated the substrate-binding order in homologous enzymes of this superfamily.

-	~~Crystal Structure, SAXS and Kinetic Mechanism of Hyperthermophilic ADP~~-~~Dependent Glucokinase from Thermococcus litoralis Reveal a Conserved Mechanism for Catalysis~~.~~,Rivas-Pardo JA~~, Herrera-Morande A, Castro-Fernandez V, Fernandez FJ, Vega MC, Guixe V ~~PLoS One~~. ~~2013 Jun 20~~;8(6):~~e66687~~. doi: 10.~~1371~~/~~journal~~.~~pone~~.~~0066687~~. ~~Print 2013~~. PMID:~~23818958~~<ref>PMID:~~23818958~~</ref>	+	Protein topology determines substrate-binding mechanism in homologous enzymes.,Herrera-Morande A, Castro-Fernandez V, Merino F, Ramirez-Sarmiento CA, Fernandez FJ, Vega MC, Guixe V Biochim Biophys Acta Gen Subj. 2018 Dec;1862(12):2869-2878. doi:, 10.1016/j.bbagen.2018.09.007. Epub 2018 Sep 12. PMID:30251675<ref>PMID:30251675</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Caldococcus litoralis z-1301]]
		+	[[Category: Large Structures]]
	[[Category: Castro-Fernandez, V]]		[[Category: Castro-Fernandez, V]]
	[[Category: Fernandez, F J]]		[[Category: Fernandez, F J]]

OCA at 05:43, 24 October 2018

OCA — Wed, 24 Oct 2018 05:43:21 GMT

←Older revision		Revision as of 05:43, 24 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5o5z is ~~ON HOLD~~	+	==CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS ADP-DEPENDENT GLUCOKINASE (GK)==
		+	<StructureSection load='5o5z' size='340' side='right' caption='[[5o5z]], [[Resolution\|resolution]] 2.44Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O5Z FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AT4:5-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE'>AT4</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5z OCA], [http://pdbe.org/5o5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5z RCSB], [http://www.ebi.ac.uk/pdbsum/5o5z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5z ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GLKA_THELN GLKA_THELN]] Catalyzes the phosphorylation of D-glucose to D-glucose 6-phosphate using ADP as the phosphate donor. Can also use CDP as the phosphoryl group donor and D-glucosamine and D-1,5-anhydroglucitol as the phosphoryl group acceptor.<ref>PMID:11098152</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	ADP-dependent glucokinases represent a unique family of kinases that belong to the ribokinase superfamily, being present mainly in hyperthermophilic archaea. For these enzymes there is no agreement about the magnitude of the structural transitions associated with ligand binding and whether they are meaningful to the function of the enzyme. We used the ADP-dependent glucokinase from Termococcus litoralis as a model to investigate the conformational changes observed in X-ray crystallographic structures upon substrate binding and to compare them with those determined in solution in order to understand their interplay with the glucokinase function. Initial velocity studies indicate that catalysis follows a sequential ordered mechanism that correlates with the structural transitions experienced by the enzyme in solution and in the crystal state. The combined data allowed us to resolve the open-closed conformational transition that accounts for the complete reaction cycle and to identify the corresponding clusters of aminoacids residues responsible for it. These results provide molecular bases for a general mechanism conserved across the ADP-dependent kinase family.

-	~~Authors~~:	+	Crystal Structure, SAXS and Kinetic Mechanism of Hyperthermophilic ADP-Dependent Glucokinase from Thermococcus litoralis Reveal a Conserved Mechanism for Catalysis.,Rivas-Pardo JA, Herrera-Morande A, Castro-Fernandez V, Fernandez FJ, Vega MC, Guixe V PLoS One. 2013 Jun 20;8(6):e66687. doi: 10.1371/journal.pone.0066687. Print 2013. PMID:23818958<ref>PMID:23818958</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5o5z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Castro-Fernandez, V]]
		+	[[Category: Fernandez, F J]]
		+	[[Category: Guixe, V]]
		+	[[Category: Herrera-Morande, A]]
		+	[[Category: Merino, F]]
		+	[[Category: Ramirez-Sarmiento, C A]]
		+	[[Category: Vega, M C]]
		+	[[Category: Adp-dependent]]
		+	[[Category: Glucokinase]]
		+	[[Category: Ribokinase superfamily]]
		+	[[Category: Transferase]]

OCA: Protected "5o5z" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:04:17 GMT

Protected "5o5z" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:04, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5o5z is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 12:04:16 GMT

New page: '''Unreleased structure''' The entry 5o5z is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5o5z is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]