5htr - Revision history

OCA at 09:16, 20 March 2024

2024-03-20T09:16:08Z

←Older revision		Revision as of 09:16, 20 March 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/XK1_ARATH XK1_ARATH] Exhibits ATP hydrolysis without substrate. Can phosphorylate D-ribulose with low efficiency.<ref>PMID:27223615</ref>		[https://www.uniprot.org/uniprot/XK1_ARATH XK1_ARATH] Exhibits ATP hydrolysis without substrate. Can phosphorylate D-ribulose with low efficiency.<ref>PMID:27223615</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The genome of the Synechococcus elongatus strain PCC 7942 encodes a putative sugar kinase (SePSK), which shares 44.9% sequence identity with the xylulose kinase-1 (AtXK-1) from Arabidopsis thaliana. Sequence alignment suggests that both kinases belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. However, their exact physiological function and real substrates remain unknown. Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. The two kinases exhibit nearly identical overall architecture, with both kinases possessing ATP hydrolysis activity in the absence of substrates. In addition, our enzymatic assays suggested that SePSK has the capability to phosphorylate D-ribulose. In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. Using mutation and activity analysis, we further verified the key residues important for its catalytic activity. Moreover, our structural comparison with other family members suggests that there are major conformational changes in SePSK upon substrate binding, facilitating the catalytic process. Together, these results provide important information for a more detailed understanding of the cofactor and substrate binding mode as well as the catalytic mechanism of SePSK, and possible similarities with its plant homologue AtXK-1.
-
-	Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana.,Xie Y, Li M, Chang W PLoS One. 2016 May 25;11(5):e0156067. doi: 10.1371/journal.pone.0156067., eCollection 2016. PMID:27223615<ref>PMID:27223615</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5htr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:53, 16 August 2023

2023-08-16T10:53:46Z

←Older revision		Revision as of 10:53, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='5htr' size='340' side='right'caption='[[5htr]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5htr' size='340' side='right'caption='[[5htr]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5htr]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HTR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HTR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5htr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HTR FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5htn\|5htn]], [[5htj\|5htj]], [[5htp\|5htp]], [[5htv\|5htv]], [[5htx\|5htx]], [[5hty\|5hty]], [[5hu2\|5hu2]], [[5hux\|5hux]], [[5hv7\|5hv7]]</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]] 2Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">XK-1, At2g21370 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=3702 ARATH])~~</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=5htr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5htr OCA], [https://pdbe.org/5htr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5htr RCSB], [https://www.ebi.ac.uk/pdbsum/5htr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5htr ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5htr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5htr OCA], [~~http~~://pdbe.org/5htr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5htr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5htr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5htr ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/XK1_ARATH XK1_ARATH] Exhibits ATP hydrolysis without substrate. Can phosphorylate D-ribulose with low efficiency.<ref>PMID:27223615</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arath]]
-	[[Category: Large Structures]]
-	[[Category: Chang, W]]
-	[[Category: Li, M]]
-	[[Category: Xie, Y]]
-	[[Category: Apo form]]
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
-	[[Category: ~~Putative sugar kinase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Chang W]]
		+	[[Category: Li M]]
		+	[[Category: Xie Y]]

OCA at 08:31, 27 May 2020

2020-05-27T08:31:58Z

←Older revision		Revision as of 08:31, 27 May 2020
Line 1:		Line 1:

	==Putative sugar kinases from Arabidopsis thaliana in apo form==		==Putative sugar kinases from Arabidopsis thaliana in apo form==
-	<StructureSection load='5htr' size='340' side='right' caption='[[5htr]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5htr' size='340' side='right'caption='[[5htr]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5htr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HTR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HTR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5htr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HTR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HTR FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5htn\|5htn]], [[5htj\|5htj]], [[5htp\|5htp]], [[5htv\|5htv]], [[5htx\|5htx]], [[5hty\|5hty]], [[5hu2\|5hu2]], [[5hux\|5hux]], [[5hv7\|5hv7]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5htn\|5htn]], [[5htj\|5htj]], [[5htp\|5htp]], [[5htv\|5htv]], [[5htx\|5htx]], [[5hty\|5hty]], [[5hu2\|5hu2]], [[5hux\|5hux]], [[5hv7\|5hv7]]</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=5htr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5htr OCA], [http://pdbe.org/5htr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5htr RCSB], [http://www.ebi.ac.uk/pdbsum/5htr PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XK-1, At2g21370 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5htr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5htr OCA], [http://pdbe.org/5htr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5htr RCSB], [http://www.ebi.ac.uk/pdbsum/5htr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5htr ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Chang, W]]		[[Category: Chang, W]]
	[[Category: Li, M]]		[[Category: Li, M]]

OCA at 07:58, 20 June 2016

2016-06-20T07:58:41Z

←Older revision		Revision as of 07:58, 20 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5htr is ~~ON HOLD~~	+	==Putative sugar kinases from Arabidopsis thaliana in apo form==
		+	<StructureSection load='5htr' size='340' side='right' caption='[[5htr]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5htr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HTR FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5htn\|5htn]], [[5htj\|5htj]], [[5htp\|5htp]], [[5htv\|5htv]], [[5htx\|5htx]], [[5hty\|5hty]], [[5hu2\|5hu2]], [[5hux\|5hux]], [[5hv7\|5hv7]]</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=5htr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5htr OCA], [http://pdbe.org/5htr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5htr RCSB], [http://www.ebi.ac.uk/pdbsum/5htr PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The genome of the Synechococcus elongatus strain PCC 7942 encodes a putative sugar kinase (SePSK), which shares 44.9% sequence identity with the xylulose kinase-1 (AtXK-1) from Arabidopsis thaliana. Sequence alignment suggests that both kinases belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. However, their exact physiological function and real substrates remain unknown. Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. The two kinases exhibit nearly identical overall architecture, with both kinases possessing ATP hydrolysis activity in the absence of substrates. In addition, our enzymatic assays suggested that SePSK has the capability to phosphorylate D-ribulose. In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. Using mutation and activity analysis, we further verified the key residues important for its catalytic activity. Moreover, our structural comparison with other family members suggests that there are major conformational changes in SePSK upon substrate binding, facilitating the catalytic process. Together, these results provide important information for a more detailed understanding of the cofactor and substrate binding mode as well as the catalytic mechanism of SePSK, and possible similarities with its plant homologue AtXK-1.

-	~~Authors: Xie~~, Y., Li, M., Chang, W.	+	Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana.,Xie Y, Li M, Chang W PLoS One. 2016 May 25;11(5):e0156067. doi: 10.1371/journal.pone.0156067., eCollection 2016. PMID:27223615<ref>PMID:27223615</ref>

-	~~Description: Putative sugar kinases from Arabidopsis thaliana in apo form~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5htr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Chang, W]]		[[Category: Chang, W]]
-	[[Category: Xie, Y]]
	[[Category: Li, M]]		[[Category: Li, M]]
		+	[[Category: Xie, Y]]
		+	[[Category: Apo form]]
		+	[[Category: Arabidopsis thaliana]]
		+	[[Category: Putative sugar kinase]]
		+	[[Category: Transferase]]

OCA at 15:42, 10 February 2016

2016-02-10T15:42:38Z

←Older revision		Revision as of 15:42, 10 February 2016
Line 3:		Line 3:
	The entry 5htr is ON HOLD		The entry 5htr is ON HOLD

-	Authors: ~~Yuan~~, X, ~~Mei~~, L, ~~Wenrui~~, Ch	+	Authors: Xie, Y., Li, M., Chang, W.

-	Description: ~~putative~~ sugar kinases from Arabidopsis thaliana in apo form	+	Description: Putative sugar kinases from Arabidopsis thaliana in apo form
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Yuan~~, X, ~~Mei~~, ~~L, Wenrui, Ch~~]]	+	[[Category: Chang, W]]
		+	[[Category: Xie, Y]]
		+	[[Category: Li, M]]

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

2016-02-03T14:20:19Z

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

←Older revision

Revision as of 14:20, 3 February 2016

OCA: New page: '''Unreleased structure''' The entry 5htr is ON HOLD Authors: Yuan, X, Mei, L, Wenrui, Ch Description: putative sugar kinases from Arabidopsis thaliana in apo form [[Category: Unreleas...

2016-02-03T14:20:18Z

New page: '''Unreleased structure''' The entry 5htr is ON HOLD Authors: Yuan, X, Mei, L, Wenrui, Ch Description: putative sugar kinases from Arabidopsis thaliana in apo form [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 5htr is ON HOLD

Authors: Yuan, X, Mei, L, Wenrui, Ch

Description: putative sugar kinases from Arabidopsis thaliana in apo form
[[Category: Unreleased Structures]]
[[Category: Yuan, X, Mei, L, Wenrui, Ch]]