7upv - Revision history

OCA at 17:19, 18 October 2023

OCA — Wed, 18 Oct 2023 17:19:02 GMT

←Older revision		Revision as of 17:19, 18 October 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7upv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zea_mays Zea mays]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UPV FirstGlance]. <br>		<table><tr><td colspan='2'>[[7upv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zea_mays Zea mays]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UPV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.84Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=7upv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7upv OCA], [https://pdbe.org/7upv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7upv RCSB], [https://www.ebi.ac.uk/pdbsum/7upv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7upv 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=7upv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7upv OCA], [https://pdbe.org/7upv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7upv RCSB], [https://www.ebi.ac.uk/pdbsum/7upv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7upv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A1D6QTZ9_MAIZE A0A1D6QTZ9_MAIZE]]	+	[https://www.uniprot.org/uniprot/A0A1D6QTZ9_MAIZE A0A1D6QTZ9_MAIZE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 19:51, 7 September 2022

OCA — Wed, 07 Sep 2022 19:51:17 GMT

←Older revision		Revision as of 19:51, 7 September 2022
Line 1:		Line 1:

	==Structure of maize BZR1-type beta-amylase provides new insights into its noncatalytic adaptation==		==Structure of maize BZR1-type beta-amylase provides new insights into its noncatalytic adaptation==
-	<StructureSection load='7upv' size='340' side='right'caption='[[7upv]]' scene=''>	+	<StructureSection load='7upv' size='340' side='right'caption='[[7upv]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UPV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7upv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zea_mays Zea mays]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UPV 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=7upv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7upv OCA], [https://pdbe.org/7upv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7upv RCSB], [https://www.ebi.ac.uk/pdbsum/7upv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7upv ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=7upv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7upv OCA], [https://pdbe.org/7upv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7upv RCSB], [https://www.ebi.ac.uk/pdbsum/7upv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7upv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A1D6QTZ9_MAIZE A0A1D6QTZ9_MAIZE]]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plant beta-amylase (BAM) proteins play an essential role in growth, development, stress response, and hormone regulation. Despite their typical (beta/alpha)8 barrel structure as active catalysts in starch breakdown, catalytically inactive BAMs are implicated in diverse yet elusive functions in plants. The noncatalytic BAM7/8 contain N-terminal BZR1 domains and were shown to be involved in the regulation of brassinosteroid signaling and possibly serve as sensors of yet an uncharacterized metabolic signal. While the structures of several catalytically active BAMs have been reported, structural characterization of the catalytically inactive BZR1-type BAMs remain unknown. Here, we determine the crystal structure of beta-amylase domain of Zea mays BAM8/BES1/BZR1-5 and provide comprehensive insights into its noncatalytic adaptation. Using structural-guided comparison combined with biochemical analysis and molecular dynamics simulations, we revealed conformational changes in multiple distinct highly conserved regions resulting in rearrangement of the binding pocket. Altogether, this study adds a new layer of understanding to starch breakdown mechanism and elucidates the acquired adjustments of noncatalytic BZR1-type BAMs as putative regulatory domains and/or metabolic sensors in plants.
		+
		+	Structure of maize BZR1-type beta-amylase BAM8 provides new insights into its noncatalytic adaptation.,Sun F, Palayam M, Shabek N J Struct Biol. 2022 Aug 10;214(3):107885. doi: 10.1016/j.jsb.2022.107885. PMID:35961473<ref>PMID:35961473</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7upv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Zea mays]]
	[[Category: Palayam M]]		[[Category: Palayam M]]
	[[Category: Shabek N]]		[[Category: Shabek N]]
	[[Category: Sun F]]		[[Category: Sun F]]

OCA at 11:11, 31 August 2022

OCA — Wed, 31 Aug 2022 11:11:33 GMT

←Older revision		Revision as of 11:11, 31 August 2022
Line 1:		Line 1:

	==Structure of maize BZR1-type beta-amylase provides new insights into its noncatalytic adaptation==		==Structure of maize BZR1-type beta-amylase provides new insights into its noncatalytic adaptation==
-	<StructureSection load='7upv' size='340' side='right'caption='[[7upv]]~~, [[Resolution\|resolution]] 1.84Å~~' scene=''>	+	<StructureSection load='7upv' size='340' side='right'caption='[[7upv]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7upv]] is a 1 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UPV FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UPV FirstGlance]. <br>
-	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=7upv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7upv OCA], [https://pdbe.org/7upv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7upv RCSB], [https://www.ebi.ac.uk/pdbsum/7upv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7upv ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </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=7upv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7upv OCA], [https://pdbe.org/7upv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7upv RCSB], [https://www.ebi.ac.uk/pdbsum/7upv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7upv ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Plant beta-amylase (BAM) proteins play an essential role in growth, development, stress response, and hormone regulation. Despite their typical (beta/alpha)8 barrel structure as active catalysts in starch breakdown, catalytically inactive BAMs are implicated in diverse yet elusive functions in plants. The noncatalytic BAM7/8 contain N-terminal BZR1 domains and were shown to be involved in the regulation of brassinosteroid signaling and possibly serve as sensors of yet an uncharacterized metabolic signal. While the structures of several catalytically active BAMs have been reported, structural characterization of the catalytically inactive BZR1-type BAMs remain unknown. Here, we determine the crystal structure of beta-amylase domain of Zea mays BAM8/BES1/BZR1-5 and provide comprehensive insights into its noncatalytic adaptation. Using structural-guided comparison combined with biochemical analysis and molecular dynamics simulations, we revealed conformational changes in multiple distinct highly conserved regions resulting in rearrangement of the binding pocket. Altogether, this study adds a new layer of understanding to starch breakdown mechanism and elucidates the acquired adjustments of noncatalytic BZR1-type BAMs as putative regulatory domains and/or metabolic sensors in plants.
-
-	Structure of maize BZR1-type beta-amylase BAM8 provides new insights into its noncatalytic adaptation.,Sun F, Palayam M, Shabek N J Struct Biol. 2022 Aug 10;214(3):107885. doi: 10.1016/j.jsb.2022.107885. PMID:35961473<ref>PMID:35961473</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7upv" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-amylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Palayam, M]]	+	[[Category: Palayam M]]
-	[[Category: Shabek, N]]	+	[[Category: Shabek N]]
-	[[Category: Sun, F]]	+	[[Category: Sun F]]
-	~~[[Category: Bzr1-bam8]]~~	+
-	~~[[Category: Gh-14]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Maize beta-amylase~~]]	+

OCA at 05:15, 25 August 2022

OCA — Thu, 25 Aug 2022 05:15:20 GMT

←Older revision		Revision as of 05:15, 25 August 2022
Line 1:		Line 1:

	==Structure of maize BZR1-type beta-amylase provides new insights into its noncatalytic adaptation==		==Structure of maize BZR1-type beta-amylase provides new insights into its noncatalytic adaptation==
-	<StructureSection load='7upv' size='340' side='right'caption='[[7upv]]' scene=''>	+	<StructureSection load='7upv' size='340' side='right'caption='[[7upv]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UPV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7upv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UPV 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=7upv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7upv OCA], [https://pdbe.org/7upv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7upv RCSB], [https://www.ebi.ac.uk/pdbsum/7upv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7upv ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </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=7upv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7upv OCA], [https://pdbe.org/7upv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7upv RCSB], [https://www.ebi.ac.uk/pdbsum/7upv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7upv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plant beta-amylase (BAM) proteins play an essential role in growth, development, stress response, and hormone regulation. Despite their typical (beta/alpha)8 barrel structure as active catalysts in starch breakdown, catalytically inactive BAMs are implicated in diverse yet elusive functions in plants. The noncatalytic BAM7/8 contain N-terminal BZR1 domains and were shown to be involved in the regulation of brassinosteroid signaling and possibly serve as sensors of yet an uncharacterized metabolic signal. While the structures of several catalytically active BAMs have been reported, structural characterization of the catalytically inactive BZR1-type BAMs remain unknown. Here, we determine the crystal structure of beta-amylase domain of Zea mays BAM8/BES1/BZR1-5 and provide comprehensive insights into its noncatalytic adaptation. Using structural-guided comparison combined with biochemical analysis and molecular dynamics simulations, we revealed conformational changes in multiple distinct highly conserved regions resulting in rearrangement of the binding pocket. Altogether, this study adds a new layer of understanding to starch breakdown mechanism and elucidates the acquired adjustments of noncatalytic BZR1-type BAMs as putative regulatory domains and/or metabolic sensors in plants.
		+
		+	Structure of maize BZR1-type beta-amylase BAM8 provides new insights into its noncatalytic adaptation.,Sun F, Palayam M, Shabek N J Struct Biol. 2022 Aug 10;214(3):107885. doi: 10.1016/j.jsb.2022.107885. PMID:35961473<ref>PMID:35961473</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7upv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Beta-amylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Palayam M]]	+	[[Category: Palayam, M]]
-	[[Category: Shabek N]]	+	[[Category: Shabek, N]]
-	[[Category: Sun F]]	+	[[Category: Sun, F]]
		+	[[Category: Bzr1-bam8]]
		+	[[Category: Gh-14]]
		+	[[Category: Hydrolase]]
		+	[[Category: Maize beta-amylase]]

OCA at 06:21, 18 August 2022

OCA — Thu, 18 Aug 2022 06:21:04 GMT

←Older revision		Revision as of 06:21, 18 August 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7upv is ~~ON HOLD until Paper Publication~~	+	==Structure of maize BZR1-type beta-amylase provides new insights into its noncatalytic adaptation==
-		+	<StructureSection load='7upv' size='340' side='right'caption='[[7upv]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UPV FirstGlance]. <br>
-	~~Description~~:	+	</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=7upv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7upv OCA], [https://pdbe.org/7upv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7upv RCSB], [https://www.ebi.ac.uk/pdbsum/7upv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7upv ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Palayam M]]
		+	[[Category: Shabek N]]
		+	[[Category: Sun F]]

OCA at 11:30, 4 May 2022

OCA — Wed, 04 May 2022 11:30:49 GMT

←Older revision		Revision as of 11:30, 4 May 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7upv is ON HOLD	+	The entry 7upv is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7upv" [edit=sysop:move=sysop]

OCA — Wed, 27 Apr 2022 10:26:19 GMT

Protected "7upv" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:26, 27 April 2022

OCA: New page: '''Unreleased structure''' The entry 7upv is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Apr 2022 10:26:18 GMT

New page: '''Unreleased structure''' The entry 7upv is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7upv is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]