5n2n - Revision history

OCA at 17:58, 8 November 2023

OCA — Wed, 08 Nov 2023 17:58:50 GMT

←Older revision		Revision as of 17:58, 8 November 2023
Line 3:		Line 3:
	<StructureSection load='5n2n' size='340' side='right'caption='[[5n2n]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5n2n' size='340' side='right'caption='[[5n2n]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n2n]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N2N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5N2N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n2n]] 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=5N2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N2N FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.05Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[3mm4\|3mm4]], [[3mmn\|3mmn]], [[5lnm\|5lnm]], [[5lnn\|5lnn]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3]~~ </~~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=5n2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n2n OCA], [https://pdbe.org/5n2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n2n RCSB], [https://www.ebi.ac.uk/pdbsum/5n2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n2n 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=5n2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n2n OCA], [~~http~~://pdbe.org/5n2n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5n2n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5n2n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5n2n ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CKI1_ARATH CKI1_ARATH]] Essential protein. Functions as a histidine kinase and transmits the stress signal to a downstream MAPK cascade. This protein undergoes an ATP-dependent autophosphorylation at a conserved histidine residue in the kinase core, and a phosphoryl group is then transferred to a conserved aspartate residue in the receiver domain. Required for the development of megagametophyte in female gametophyte (embryo sac) independently of cytokinin. Contributes to vascular bundle formation and secondary growth in a cytokinin-independent manner, probably by promoting the maintenance of mitotic activity and/or identity of procambial cells. Seems to influence and promote the cytokinin signaling pathway.<ref>PMID:10610126</ref> <ref>PMID:12426401</ref> <ref>PMID:12774227</ref> <ref>PMID:18077346</ref> <ref>PMID:19622803</ref> <ref>PMID:20363773</ref> <ref>PMID:8875940</ref>	+	[https://www.uniprot.org/uniprot/CKI1_ARATH CKI1_ARATH] Essential protein. Functions as a histidine kinase and transmits the stress signal to a downstream MAPK cascade. This protein undergoes an ATP-dependent autophosphorylation at a conserved histidine residue in the kinase core, and a phosphoryl group is then transferred to a conserved aspartate residue in the receiver domain. Required for the development of megagametophyte in female gametophyte (embryo sac) independently of cytokinin. Contributes to vascular bundle formation and secondary growth in a cytokinin-independent manner, probably by promoting the maintenance of mitotic activity and/or identity of procambial cells. Seems to influence and promote the cytokinin signaling pathway.<ref>PMID:10610126</ref> <ref>PMID:12426401</ref> <ref>PMID:12774227</ref> <ref>PMID:18077346</ref> <ref>PMID:19622803</ref> <ref>PMID:20363773</ref> <ref>PMID:8875940</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Histidine kinase~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Demo, G]]	+	[[Category: Demo G]]
-	[[Category: Gelova, Z]]	+	[[Category: Gelova Z]]
-	[[Category: Hejatko, J]]	+	[[Category: Hejatko J]]
-	[[Category: Hritz, J]]	+	[[Category: Hritz J]]
-	[[Category: Iwai, H]]	+	[[Category: Iwai H]]
-	[[Category: Janda, L]]	+	[[Category: Janda L]]
-	[[Category: Jansen, S]]	+	[[Category: Jansen S]]
-	[[Category: Jasenakova, Z]]	+	[[Category: Jasenakova Z]]
-	[[Category: Kaderavek, P]]	+	[[Category: Kaderavek P]]
-	[[Category: Klumpler, T]]	+	[[Category: Klumpler T]]
-	[[Category: Marek, J]]	+	[[Category: Marek J]]
-	[[Category: Otrusinova, O]]	+	[[Category: Otrusinova O]]
-	[[Category: Padrta, P]]	+	[[Category: Padrta P]]
-	[[Category: Pekarova, B]]	+	[[Category: Pekarova B]]
-	[[Category: Szmitkowska, A]]	+	[[Category: Szmitkowska A]]
-	[[Category: Wimmerova, M]]	+	[[Category: Wimmerova M]]
-	[[Category: Zachrdla, M]]	+	[[Category: Zachrdla M]]
-	[[Category: Zidek, L]]	+	[[Category: Zidek L]]
-	~~[[Category: Histidine kinase cki1]]~~	+
-	~~[[Category: Receiver domain]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 11:56, 26 August 2020

OCA — Wed, 26 Aug 2020 11:56:33 GMT

←Older revision		Revision as of 11:56, 26 August 2020
Line 1:		Line 1:

	==Crystal structure of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana complexed with Mg2+ and BeF3-==		==Crystal structure of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana complexed with Mg2+ and BeF3-==
-	<StructureSection load='5n2n' size='340' side='right' caption='[[5n2n]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5n2n' size='340' side='right'caption='[[5n2n]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n2n]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N2N OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5N2N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n2n]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N2N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5N2N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3mm4\|3mm4]], [[3mmn\|3mmn]], [[5lnm\|5lnm]], [[5lnn\|5lnn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3mm4\|3mm4]], [[3mmn\|3mmn]], [[5lnm\|5lnm]], [[5lnn\|5lnn]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </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=5n2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n2n OCA], [http://pdbe.org/5n2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n2n RCSB], [http://www.ebi.ac.uk/pdbsum/5n2n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n2n 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=5n2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n2n OCA], [http://pdbe.org/5n2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n2n RCSB], [http://www.ebi.ac.uk/pdbsum/5n2n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n2n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
		+	[[Category: Large Structures]]
	[[Category: Demo, G]]		[[Category: Demo, G]]
	[[Category: Gelova, Z]]		[[Category: Gelova, Z]]

OCA at 10:35, 13 September 2017

OCA — Wed, 13 Sep 2017 10:35:24 GMT

←Older revision		Revision as of 10:35, 13 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5n2n is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana complexed with Mg2+ and BeF3-==
		+	<StructureSection load='5n2n' size='340' side='right' caption='[[5n2n]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5n2n]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N2N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N2N FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3mm4\|3mm4]], [[3mmn\|3mmn]], [[5lnm\|5lnm]], [[5lnn\|5lnn]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </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=5n2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n2n OCA], [http://pdbe.org/5n2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n2n RCSB], [http://www.ebi.ac.uk/pdbsum/5n2n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n2n ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CKI1_ARATH CKI1_ARATH]] Essential protein. Functions as a histidine kinase and transmits the stress signal to a downstream MAPK cascade. This protein undergoes an ATP-dependent autophosphorylation at a conserved histidine residue in the kinase core, and a phosphoryl group is then transferred to a conserved aspartate residue in the receiver domain. Required for the development of megagametophyte in female gametophyte (embryo sac) independently of cytokinin. Contributes to vascular bundle formation and secondary growth in a cytokinin-independent manner, probably by promoting the maintenance of mitotic activity and/or identity of procambial cells. Seems to influence and promote the cytokinin signaling pathway.<ref>PMID:10610126</ref> <ref>PMID:12426401</ref> <ref>PMID:12774227</ref> <ref>PMID:18077346</ref> <ref>PMID:19622803</ref> <ref>PMID:20363773</ref> <ref>PMID:8875940</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP-mediated phosphotransfer in a eukaryotic system, the phosphorylation of the receiver domain of the histidine kinase CYTOKININ INDEPENDENT 1 (CKI1RD) from Arabidopsis thaliana We observed that the crystal structures of free, Mg2+-bound, and beryllofluoridated CKI1RD (a stable analog of the labile phosphorylated form) were identical and similar to the active state of receiver domains of bacterial response regulators. However, the three CKI1RD variants exhibited different conformational dynamics in solution. NMR studies revealed that Mg2+ binding and beryllofluoridation alter the conformational equilibrium of the beta3-alpha3 loop close to the phosphorylation site. Mutations that perturbed the conformational behavior of the beta3-alpha3 loop while keeping the active site aspartate intact resulted in suppression of CKI1 function. Mechanistically, homology modeling indicated that the beta3-alpha3 loop directly interacts with the ATP-binding site of the CKI1 histidine kinase domain. The functional relevance of the conformational dynamics observed in the beta3-alpha3 loop of CKI1RD was supported by a comparison with another A. thaliana histidine kinase, ETR1. In contrast to the highly dynamic beta3-alpha3 loop of CKI1RD, the corresponding loop of the ETR1 receiver domain (ETR1RD) exhibited little conformational exchange and adopted a different orientation in crystals. Biochemical data indicated that ETR1RD is involved in phosphorylation-independent signaling, implying a direct link between conformational behavior and the ability of eukaryotic receiver domains to participate in MSP.

-	~~Authors:~~ Otrusinova, O., Demo, G., Padrta, P., Jasenakova, Z., Pekarova, B., Gelova, Z., Szmitkowska, A., Kaderavek, P., Jansen, S., Zachrdla, M., Klumpler, T., Marek, J., Hritz, J., Janda, L., Iwai, H., Wimmerova, M., Hejatko, J., Zidek, L.	+	Conformational dynamics as a key factor of signaling mediated by the receiver domain of sensor histidine kinase from Arabidopsis thaliana.,Otrusinova O, Demo G, Padrta P, Jasenakova Z, Pekarova B, Gelova Z, Szmitkowska A, Kaderavek P, Jansen S, Zachrdla M, Klumpler T, Marek J, Hritz J, Janda L, Iwai H, Wimmerova M, Hejatko J, Zidek L J Biol Chem. 2017 Aug 31. pii: jbc.M117.790212. doi: 10.1074/jbc.M117.790212. PMID:28860196<ref>PMID:28860196</ref>

-	~~Description: Crystal structure~~ of the ~~receiver domain~~ of ~~the histidine kinase CKI1 from Arabidopsis thaliana complexed with Mg2+ and BeF3-~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Hritz, J]]~~	+	<div class="pdbe-citations 5n2n" style="background-color:#fffaf0;"></div>
-	~~[[Category: Jasenakova, Z]]~~	+	== References ==
-	~~[[Category: Zachrdla, M]]~~	+	<references/>
-	~~[[Category: Wimmerova, M]]~~	+	__TOC__
-	~~[[Category: Padrta, P]]~~	+	</StructureSection>
-	[[Category: ~~Iwai, H~~]]	+	[[Category: Histidine kinase]]
	[[Category: Demo, G]]		[[Category: Demo, G]]
-	[[Category: Zidek, L]]
-	[[Category: Szmitkowska, A]]
-	[[Category: Jansen, S]]
-	[[Category: Pekarova, B]]
	[[Category: Gelova, Z]]		[[Category: Gelova, Z]]
		+	[[Category: Hejatko, J]]
		+	[[Category: Hritz, J]]
		+	[[Category: Iwai, H]]
	[[Category: Janda, L]]		[[Category: Janda, L]]
		+	[[Category: Jansen, S]]
		+	[[Category: Jasenakova, Z]]
		+	[[Category: Kaderavek, P]]
	[[Category: Klumpler, T]]		[[Category: Klumpler, T]]
	[[Category: Marek, J]]		[[Category: Marek, J]]
-	[[Category: Kaderavek, P]]
-	[[Category: Hejatko, J]]
	[[Category: Otrusinova, O]]		[[Category: Otrusinova, O]]
		+	[[Category: Padrta, P]]
		+	[[Category: Pekarova, B]]
		+	[[Category: Szmitkowska, A]]
		+	[[Category: Wimmerova, M]]
		+	[[Category: Zachrdla, M]]
		+	[[Category: Zidek, L]]
		+	[[Category: Histidine kinase cki1]]
		+	[[Category: Receiver domain]]
		+	[[Category: Transferase]]

OCA: Protected "5n2n" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 11:58:07 GMT

Protected "5n2n" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:58, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5n2n is ON HOLD until Paper Publication Authors: Otrusinova, O., Demo, G., Padrta, P., Jasenakova, Z., Pekarova, B., Gelova, Z., Szmitkowska, A., Ka...

OCA — Thu, 09 Mar 2017 11:58:05 GMT

New page: '''Unreleased structure''' The entry 5n2n is ON HOLD until Paper Publication Authors: Otrusinova, O., Demo, G., Padrta, P., Jasenakova, Z., Pekarova, B., Gelova, Z., Szmitkowska, A., Ka...

New page

'''Unreleased structure'''

The entry 5n2n is ON HOLD until Paper Publication

Authors: Otrusinova, O., Demo, G., Padrta, P., Jasenakova, Z., Pekarova, B., Gelova, Z., Szmitkowska, A., Kaderavek, P., Jansen, S., Zachrdla, M., Klumpler, T., Marek, J., Hritz, J., Janda, L., Iwai, H., Wimmerova, M., Hejatko, J., Zidek, L.

Description: Crystal structure of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana complexed with Mg2+ and BeF3-
[[Category: Unreleased Structures]]
[[Category: Hritz, J]]
[[Category: Jasenakova, Z]]
[[Category: Zachrdla, M]]
[[Category: Wimmerova, M]]
[[Category: Padrta, P]]
[[Category: Iwai, H]]
[[Category: Demo, G]]
[[Category: Zidek, L]]
[[Category: Szmitkowska, A]]
[[Category: Jansen, S]]
[[Category: Pekarova, B]]
[[Category: Gelova, Z]]
[[Category: Janda, L]]
[[Category: Klumpler, T]]
[[Category: Marek, J]]
[[Category: Kaderavek, P]]
[[Category: Hejatko, J]]
[[Category: Otrusinova, O]]