6git - Revision history

OCA at 09:02, 9 October 2024

2024-10-09T09:02:19Z

← Older revision		Revision as of 09:02, 9 October 2024
Line 3:		Line 3:
	<StructureSection load='6git' size='340' side='right'caption='[[6git]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='6git' size='340' side='right'caption='[[6git]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6git]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Canadian_hard_winter_wheat Canadian hard winter wheat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GIT FirstGlance]. <br>		<table><tr><td colspan='2'>[[6git]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Triticum_aestivum Triticum aestivum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GIT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.418Å</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAPhy ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4565 Canadian hard winter wheat])</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Acid_phosphatase Acid phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.2 3.1.3.2] </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=6git FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6git OCA], [https://pdbe.org/6git PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6git RCSB], [https://www.ebi.ac.uk/pdbsum/6git PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6git 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=6git FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6git OCA], [https://pdbe.org/6git PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6git RCSB], [https://www.ebi.ac.uk/pdbsum/6git PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6git ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/F6MIW5_WHEAT F6MIW5_WHEAT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Grain phytate, a mixed metal ion salt of inositol hexakisphosphate, accounts for 60%-80% of stored phosphorus in plants and is a potent antinutrient of non-ruminant animals including humans. Through neofunctionalization of purple acid phytases (PAPhy), some cereals such as wheat and rye have acquired particularly high mature grain phytase activity. As PAPhy activity supplies phosphate, liberates metal ions necessary for seedling emergence, and obviates antinutrient effects of phytate, its manipulation and control are targeted crop traits. Here we show the X-ray crystal structure of the b2 isoform of wheat PAPhy induced during germination. This high-resolution crystal structure suggests a model for phytate recognition that, validated by molecular dynamics simulations, implicates elements of two sequence inserts (termed PAPhy motifs) relative to a canonical metallophosphoesterase (MPE) domain in forming phytate-specific substrate specificity pockets. These motifs are well conserved in PAPhys from monocot cereals, enzymes which are characterized by high specificity for phytate. Tested by mutagenesis, residues His229 in PAPhy motif 4 and Lys410 in the MPE domain, both conserved in PAPhys, are found to strongly influence phytase activity. These results explain the observed phytase activity of cereal PAPhys and open the way to the rational engineering of phytase activity in planta.		Grain phytate, a mixed metal ion salt of inositol hexakisphosphate, accounts for 60%-80% of stored phosphorus in plants and is a potent antinutrient of non-ruminant animals including humans. Through neofunctionalization of purple acid phytases (PAPhy), some cereals such as wheat and rye have acquired particularly high mature grain phytase activity. As PAPhy activity supplies phosphate, liberates metal ions necessary for seedling emergence, and obviates antinutrient effects of phytate, its manipulation and control are targeted crop traits. Here we show the X-ray crystal structure of the b2 isoform of wheat PAPhy induced during germination. This high-resolution crystal structure suggests a model for phytate recognition that, validated by molecular dynamics simulations, implicates elements of two sequence inserts (termed PAPhy motifs) relative to a canonical metallophosphoesterase (MPE) domain in forming phytate-specific substrate specificity pockets. These motifs are well conserved in PAPhys from monocot cereals, enzymes which are characterized by high specificity for phytate. Tested by mutagenesis, residues His229 in PAPhy motif 4 and Lys410 in the MPE domain, both conserved in PAPhys, are found to strongly influence phytase activity. These results explain the observed phytase activity of cereal PAPhys and open the way to the rational engineering of phytase activity in planta.

	Structure of a cereal purple acid phytase provides new insights to phytate degradation in plants.,Faba-Rodriguez R, Gu Y, Salmon M, Dionisio G, Brinch-Pedersen H, Brearley CA, Hemmings AM Plant Commun. 2022 Feb 19;3(2):100305. doi: 10.1016/j.xplc.2022.100305., eCollection 2022 Mar 14. PMID:35529950<ref>PMID:35529950</ref>		Structure of a cereal purple acid phytase provides new insights to phytate degradation in plants.,Faba-Rodriguez R, Gu Y, Salmon M, Dionisio G, Brinch-Pedersen H, Brearley CA, Hemmings AM Plant Commun. 2022 Feb 19;3(2):100305. doi: 10.1016/j.xplc.2022.100305. , eCollection 2022 Mar 14. PMID:35529950<ref>PMID:35529950</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>
Line 21:		Line 22:
	==See Also==		==See Also==
	*[[Acid phosphatase 3D structures\|Acid phosphatase 3D structures]]		*[[Acid phosphatase 3D structures\|Acid phosphatase 3D structures]]
			*[[Phytase 3D structures\|Phytase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Acid phosphatase]]~~
	~~[[Category: Canadian hard winter wheat]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Brearley, C A~~]]		[[Category: Triticum aestivum]]
	[[Category: ~~Faba-Rodriguez, R~~]]		[[Category: Brearley CA]]
	[[Category: ~~Hemmings, A M~~]]		[[Category: Faba-Rodriguez R]]
	[[Category: ~~Ec 3 1.3 26]]~~		[[Category: Hemmings AM]]
	~~[[Category: Hydrolase]]~~
	~~[[Category: Purple acid phytase~~]]

OCA at 05:32, 8 June 2022

2022-06-08T05:32:37Z

← Older revision		Revision as of 05:32, 8 June 2022
Line 3:		Line 3:
	<StructureSection load='6git' size='340' side='right'caption='[[6git]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='6git' size='340' side='right'caption='[[6git]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6git]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GIT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6GIT FirstGlance]. <br>		<table><tr><td colspan='2'>[[6git]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Canadian_hard_winter_wheat Canadian hard winter wheat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GIT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Acid_phosphatase Acid phosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.2 3.1.3.2] </span></td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAPhy ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4565 Canadian hard winter wheat])</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=6git FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6git OCA], [~~http~~://pdbe.org/6git PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6git RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6git PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6git 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/Acid_phosphatase Acid phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.2 3.1.3.2] </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=6git FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6git OCA], [https://pdbe.org/6git PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6git RCSB], [https://www.ebi.ac.uk/pdbsum/6git PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6git ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Grain phytate, a mixed metal ion salt of inositol hexakisphosphate, accounts for 60%-80% of stored phosphorus in plants and is a potent antinutrient of non-ruminant animals including humans. Through neofunctionalization of purple acid phytases (PAPhy), some cereals such as wheat and rye have acquired particularly high mature grain phytase activity. As PAPhy activity supplies phosphate, liberates metal ions necessary for seedling emergence, and obviates antinutrient effects of phytate, its manipulation and control are targeted crop traits. Here we show the X-ray crystal structure of the b2 isoform of wheat PAPhy induced during germination. This high-resolution crystal structure suggests a model for phytate recognition that, validated by molecular dynamics simulations, implicates elements of two sequence inserts (termed PAPhy motifs) relative to a canonical metallophosphoesterase (MPE) domain in forming phytate-specific substrate specificity pockets. These motifs are well conserved in PAPhys from monocot cereals, enzymes which are characterized by high specificity for phytate. Tested by mutagenesis, residues His229 in PAPhy motif 4 and Lys410 in the MPE domain, both conserved in PAPhys, are found to strongly influence phytase activity. These results explain the observed phytase activity of cereal PAPhys and open the way to the rational engineering of phytase activity in planta.

			Structure of a cereal purple acid phytase provides new insights to phytate degradation in plants.,Faba-Rodriguez R, Gu Y, Salmon M, Dionisio G, Brinch-Pedersen H, Brearley CA, Hemmings AM Plant Commun. 2022 Feb 19;3(2):100305. doi: 10.1016/j.xplc.2022.100305., eCollection 2022 Mar 14. PMID:35529950<ref>PMID:35529950</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6git" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Acid phosphatase 3D structures\|Acid phosphatase 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Acid phosphatase]]		[[Category: Acid phosphatase]]
			[[Category: Canadian hard winter wheat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Brearley, C A]]		[[Category: Brearley, C A]]

OCA at 06:41, 27 November 2019

2019-11-27T06:41:02Z

← Older revision		Revision as of 06:41, 27 November 2019
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6git is ~~ON HOLD~~		==PURPLE ACID PHYTASE FROM WHEAT ISOFORM B2 - PRODUCT COMPLEX==
			<StructureSection load='6git' size='340' side='right'caption='[[6git]], [[Resolution\|resolution]] 1.42Å' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>[[6git]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GIT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GIT FirstGlance]. <br>
	~~Description~~:		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acid_phosphatase Acid phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.2 3.1.3.2] </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=6git FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6git OCA], [http://pdbe.org/6git PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6git RCSB], [http://www.ebi.ac.uk/pdbsum/6git PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6git ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Acid phosphatase]]
			[[Category: Large Structures]]
			[[Category: Brearley, C A]]
			[[Category: Faba-Rodriguez, R]]
			[[Category: Hemmings, A M]]
			[[Category: Ec 3 1.3 26]]
			[[Category: Hydrolase]]
			[[Category: Purple acid phytase]]

OCA: Protected "6git" [edit=sysop:move=sysop]

2018-05-23T06:10:02Z

Protected "6git" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:10, 23 May 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6git is ON HOLD Authors: Description: Category: Unreleased Structures

2018-05-23T06:10:00Z

New page: '''Unreleased structure''' The entry 6git is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6git is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]