6pk1 - Revision history

OCA at 07:31, 11 October 2023

OCA — Wed, 11 Oct 2023 07:31:04 GMT

←Older revision		Revision as of 07:31, 11 October 2023
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	<StructureSection load='6pk1' size='340' side='right'caption='[[6pk1]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6pk1' size='340' side='right'caption='[[6pk1]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pk1]] is a 2 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=6PK1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pk1]] is a 2 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=6PK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PK1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=3PY:3~~-~~HYDROXYPYRUVIC+ACID'>3PY</scene>~~, ~~<scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6pk3\|6pk3]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PY:3-HYDROXYPYRUVIC+ACID'>3PY</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">AGT1, At2g13360, F14O4.7 ([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=6pk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pk1 OCA], [https://pdbe.org/6pk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pk1 RCSB], [https://www.ebi.ac.uk/pdbsum/6pk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pk1 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=6pk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pk1 OCA], [~~http~~://pdbe.org/6pk1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pk1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pk1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pk1 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SGAT_ARATH SGAT_ARATH]] Photorespiratory enzyme that catalyzes transamination reactions with multiple substrates, including asparagine. Function exclusively as a catabolic enzyme in Asn metabolism.<ref>PMID:18235971</ref> <ref>PMID:23098902</ref>	+	[https://www.uniprot.org/uniprot/SGAT_ARATH SGAT_ARATH] Photorespiratory enzyme that catalyzes transamination reactions with multiple substrates, including asparagine. Function exclusively as a catabolic enzyme in Asn metabolism.<ref>PMID:18235971</ref> <ref>PMID:23098902</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6pk1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6pk1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminotransferase 3D structures\|Aminotransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Liepman~~, A H~~]]	+	[[Category: Liepman AH]]
-	[[Category: Saper~~, M A]]~~	+	[[Category: Saper MA]]
-	~~[[Category: Peroxisomal enzyme]]~~	+
-	~~[[Category: Photorespiration]]~~	+
-	~~[[Category: Plp]]~~	+
-	~~[[Category: Serine-glyoxylate aminotransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 17:51, 20 November 2019

OCA — Wed, 20 Nov 2019 17:51:25 GMT

←Older revision		Revision as of 17:51, 20 November 2019
Line 3:		Line 3:
	<StructureSection load='6pk1' size='340' side='right'caption='[[6pk1]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6pk1' size='340' side='right'caption='[[6pk1]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pk1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pk1]] is a 2 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=6PK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PK1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3PY:3-HYDROXYPYRUVIC+ACID'>3PY</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3PY:3-HYDROXYPYRUVIC+ACID'>3PY</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6pk3\|6pk3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6pk3\|6pk3]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AGT1, At2g13360, F14O4.7 ([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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6pk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pk1 OCA], [http://pdbe.org/6pk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pk1 RCSB], [http://www.ebi.ac.uk/pdbsum/6pk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pk1 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=6pk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pk1 OCA], [http://pdbe.org/6pk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pk1 RCSB], [http://www.ebi.ac.uk/pdbsum/6pk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pk1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SGAT_ARATH SGAT_ARATH]] Photorespiratory enzyme that catalyzes transamination reactions with multiple substrates, including asparagine. Function exclusively as a catabolic enzyme in Asn metabolism.<ref>PMID:18235971</ref> <ref>PMID:23098902</ref>		[[http://www.uniprot.org/uniprot/SGAT_ARATH SGAT_ARATH]] Photorespiratory enzyme that catalyzes transamination reactions with multiple substrates, including asparagine. Function exclusively as a catabolic enzyme in Asn metabolism.<ref>PMID:18235971</ref> <ref>PMID:23098902</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Photorespiration is an energetically costly metabolic pathway for the recycling of phosphoglycolate produced by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) to phosphoglycerate. Arabidopsis alanine:glyoxylate aminotransferase 1 (AGT1) is a peroxisomal aminotransferase with a central role in photorespiration. This enzyme catalyzes various aminotransferase reactions, including serine:glyoxylate, alanine:glyoxylate, and asparagine:glyoxylate transaminations. To better understand structural features that govern the specificity of this enzyme, its crystal structures in the native form (2.2-A resolution) and in the presence of l-serine (2.1-A resolution) were solved. The structures confirm that this enzyme is dimeric, in agreement with studies of the active enzyme in solution. In the crystal, another dimer related by noncrystallographic symmetry makes close interactions to form a tetramer mediated in part by an extra carboxyl-terminal helix conserved in plant homologs of AGT1. Pyridoxal 5'-phosphate (PLP) is bound at the active site but is not held in place by covalent interactions. Residues Tyr35' and Arg36', entering the active site from the other subunits in the dimer, mediate interactions between AGT and l-serine when used as a substrate. In comparison, AGT1 from humans and AGT1 from Anabaena lack these two residues and instead position a tyrosine ring into the binding site, which accounts for their preference for l-alanine instead of l-serine. The structure also rationalizes the phenotype of the sat mutant, Pro251 to Leu, which likely affects the dimer interface near the catalytic site. This structural model of AGT1 provides valuable new information about this protein that may enable improvements to the efficiency of photorespiration.
		+
		+	Crystal Structure Of Photorespiratory Alanine:Glyoxylate Aminotransferase 1 (AGT1) From Arabidopsis thaliana.,Liepman AH, Vijayalakshmi J, Peisach D, Hulsebus B, Olsen LJ, Saper MA Front Plant Sci. 2019 Oct 11;10:1229. doi: 10.3389/fpls.2019.01229. eCollection, 2019. PMID:31681359<ref>PMID:31681359</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6pk1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Liepman, A H]]		[[Category: Liepman, A H]]

OCA at 06:58, 23 October 2019

OCA — Wed, 23 Oct 2019 06:58:50 GMT

←Older revision		Revision as of 06:58, 23 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6pk1 is ~~ON HOLD until Paper Publication~~	+	==Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis thaliana in presence of serine==
-		+	<StructureSection load='6pk1' size='340' side='right'caption='[[6pk1]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors~~: ~~Liepman~~, A.H., ~~Saper~~, M.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6pk1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PK1 FirstGlance]. <br>
-	~~Description~~: ~~Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis thaliana~~ in ~~presence of serine~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3PY:3-HYDROXYPYRUVIC+ACID'>3PY</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6pk3\|6pk3]]</td></tr>
-	[[Category: ~~Saper~~, M.A]]	+	<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=6pk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pk1 OCA], [http://pdbe.org/6pk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pk1 RCSB], [http://www.ebi.ac.uk/pdbsum/6pk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pk1 ProSAT]</span></td></tr>
-	[[Category: ~~Liepman~~, A.H]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SGAT_ARATH SGAT_ARATH]] Photorespiratory enzyme that catalyzes transamination reactions with multiple substrates, including asparagine. Function exclusively as a catabolic enzyme in Asn metabolism.<ref>PMID:18235971</ref> <ref>PMID:23098902</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Liepman, A H]]
		+	[[Category: Saper, M A]]
		+	[[Category: Peroxisomal enzyme]]
		+	[[Category: Photorespiration]]
		+	[[Category: Plp]]
		+	[[Category: Serine-glyoxylate aminotransferase]]
		+	[[Category: Transferase]]

OCA at 04:15, 7 August 2019

OCA — Wed, 07 Aug 2019 04:15:02 GMT

←Older revision		Revision as of 04:15, 7 August 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6pk1 is ON HOLD	+	The entry 6pk1 is ON HOLD until Paper Publication

	Authors: Liepman, A.H., Saper, M.A.		Authors: Liepman, A.H., Saper, M.A.

OCA: Protected "6pk1" [edit=sysop:move=sysop]

OCA — Wed, 10 Jul 2019 04:09:59 GMT

Protected "6pk1" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:09, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pk1 is ON HOLD Authors: Liepman, A.H., Saper, M.A. Description: Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis thaliana in presence...

OCA — Wed, 10 Jul 2019 04:09:57 GMT

New page: '''Unreleased structure''' The entry 6pk1 is ON HOLD Authors: Liepman, A.H., Saper, M.A. Description: Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis thaliana in presence...

New page

'''Unreleased structure'''

The entry 6pk1 is ON HOLD

Authors: Liepman, A.H., Saper, M.A.

Description: Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis thaliana in presence of serine
[[Category: Unreleased Structures]]
[[Category: Saper, M.A]]
[[Category: Liepman, A.H]]