5ofy - Revision history

OCA at 16:48, 13 December 2023

2023-12-13T16:48:44Z

←Older revision		Revision as of 16:48, 13 December 2023
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	<StructureSection load='5ofy' size='340' side='right'caption='[[5ofy]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5ofy' size='340' side='right'caption='[[5ofy]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ofy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OFY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ofy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OFY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DIO:1,4~~-~~DIETHYLENE+DIOXIDE'>DIO</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]] 2.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5luc\|5luc]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></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=5ofy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofy OCA], [~~http~~://pdbe.org/5ofy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ofy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ofy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofy 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=5ofy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofy OCA], [https://pdbe.org/5ofy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ofy RCSB], [https://www.ebi.ac.uk/pdbsum/5ofy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofy ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/~~SPYA_HUMAN SPYA_HUMAN~~]~~] Defects in AGXT are the cause of~~ hyperoxaluria ~~primary~~ type 1 ~~(HP1)~~ [~~MIM:[http~~://~~omim~~.org/~~entry~~/~~259900 259900~~]~~]; also known as primary hyperoxaluria type I (PH1) and oxalosis I. HP1 is a rare autosomal recessive inborn error~~ of glyoxylate ~~metabolism characterized by increased excretion of oxalate and glycolate,~~ and the ~~progressive accumulation of insoluble calcium oxalate in the kidney and urinary tract.<ref>PMID~~:~~1703535</ref> <ref>PMID~~:~~2039493</ref> <ref>PMID~~:~~1349575</ref> <ref>PMID~~:~~1301173</ref> <ref>PMID~~:~~8101040</ref> <ref>PMID~~:~~9192270</ref>~~ <ref>PMID:~~9604803</ref> <ref>PMID:10394939</ref> <ref>PMID:10453743</ref> <ref>PMID:10541294</ref> <ref>PMID:10862087~~</ref> <ref>PMID:10960483~~</ref> <ref>PMID:12559847~~</ref> <ref>PMID:12777626</ref> <ref>PMID:~~15253729</ref> <ref>PMID:15849466~~</ref> <ref>PMID:~~15961946~~</ref> <ref>PMID:~~15963748~~</ref>	+	[https://www.uniprot.org/uniprot/AGT1_HUMAN AGT1_HUMAN] Primary hyperoxaluria type 1. The disease is caused by variants affecting the gene represented in this entry.
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AGT1_HUMAN AGT1_HUMAN] Peroxisomal aminotransferase that catalyzes the transamination of glyoxylate to glycine and contributes to the glyoxylate detoxification (PubMed:10960483, PubMed:12777626, PubMed:24055001, PubMed:23229545, PubMed:26149463). Also catalyzes the transamination between L-serine and pyruvate and contributes to gluconeogenesis from the L-serine metabolism (PubMed:10347152).<ref>PMID:10347152</ref> <ref>PMID:10960483</ref> <ref>PMID:12777626</ref> <ref>PMID:23229545</ref> <ref>PMID:24055001</ref> <ref>PMID:26149463</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Cellini, B]]~~	+	[[Category: Borri Voltattorni C]]
-	~~[[Category: Cutruzzola, F]]~~	+	[[Category: Cellini B]]
-	~~[[Category: Giardina, G]]~~	+	[[Category: Cutruzzola F]]
-	~~[[Category: Montioli, R]]~~	+	[[Category: Giardina G]]
-	~~[[Category:~~ Voltattorni, C ~~Borri~~]]	+	[[Category: Montioli R]]
-	[[Category: ~~Aminotransferase~~]]	+
-	[[Category: ~~Detoxification~~]]	+
-	[[Category: ~~Liver~~]]	+
-	[[Category: ~~Transferase~~]]	+

OCA at 12:22, 26 August 2020

2020-08-26T12:22:52Z

←Older revision		Revision as of 12:22, 26 August 2020
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	==Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at pH 9.0. 2.8 Ang; internal aldimine with PLP in the active site==		==Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at pH 9.0. 2.8 Ang; internal aldimine with PLP in the active site==
-	<StructureSection load='5ofy' size='340' side='right' caption='[[5ofy]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5ofy' size='340' side='right'caption='[[5ofy]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ofy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OFY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ofy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OFY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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">[[5luc\|5luc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5luc\|5luc]]</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=5ofy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofy OCA], [http://pdbe.org/5ofy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ofy RCSB], [http://www.ebi.ac.uk/pdbsum/5ofy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofy 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=5ofy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofy OCA], [http://pdbe.org/5ofy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ofy RCSB], [http://www.ebi.ac.uk/pdbsum/5ofy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofy ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ofy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ofy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminotransferase 3D structures\|Aminotransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Cellini, B]]		[[Category: Cellini, B]]
	[[Category: Cutruzzola, F]]		[[Category: Cutruzzola, F]]

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

2017-09-27T09:18:15Z

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

←Older revision

Revision as of 09:18, 27 September 2017

OCA: New page: ==Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at pH 9.0. 2.8 Ang; internal aldimine with PLP in the active site==
2017-09-27T09:18:12Z

New page: ==Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at pH 9.0. 2.8 Ang; internal aldimine with PLP in the active site== <StructureS...

New page

==Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at pH 9.0. 2.8 Ang; internal aldimine with PLP in the active site==
<StructureSection load='5ofy' size='340' side='right' caption='[[5ofy]], [[Resolution|resolution]] 2.80Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ofy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OFY FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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">[[5luc|5luc]]</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=5ofy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofy OCA], [http://pdbe.org/5ofy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ofy RCSB], [http://www.ebi.ac.uk/pdbsum/5ofy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofy ProSAT]</span></td></tr>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/SPYA_HUMAN SPYA_HUMAN]] Defects in AGXT are the cause of hyperoxaluria primary type 1 (HP1) [MIM:[http://omim.org/entry/259900 259900]]; also known as primary hyperoxaluria type I (PH1) and oxalosis I. HP1 is a rare autosomal recessive inborn error of glyoxylate metabolism characterized by increased excretion of oxalate and glycolate, and the progressive accumulation of insoluble calcium oxalate in the kidney and urinary tract.<ref>PMID:1703535</ref> <ref>PMID:2039493</ref> <ref>PMID:1349575</ref> <ref>PMID:1301173</ref> <ref>PMID:8101040</ref> <ref>PMID:9192270</ref> <ref>PMID:9604803</ref> <ref>PMID:10394939</ref> <ref>PMID:10453743</ref> <ref>PMID:10541294</ref> <ref>PMID:10862087</ref> <ref>PMID:10960483</ref> <ref>PMID:12559847</ref> <ref>PMID:12777626</ref> <ref>PMID:15253729</ref> <ref>PMID:15849466</ref> <ref>PMID:15961946</ref> <ref>PMID:15963748</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The alanine:glyoxylate aminotransferase (AGT), a hepatocyte-specific pyridoxal-5'-phosphate (PLP) dependent enzyme, transaminates L-alanine and glyoxylate to glycine and pyruvate, thus detoxifying glyoxylate and preventing pathological oxalate precipitation in tissues. In the widely accepted catalytic mechanism of the aminotransferase family, the lysine binding to PLP acts as a catalyst in the stepwise 1,3-proton transfer, interconverting the external aldimine to ketimine. This step requires protonation by a conserved aspartate of the pyridine nitrogen of PLP to enhance its ability to stabilize the carbanionic intermediate. The aspartate residue is also responsible for a significant geometrical distortion of the internal aldimine, crucial for catalysis. We present the structure of human AGT in which complete X-ray photoreduction of the Schiff base has occurred. This result, together with two crystal structures of the conserved aspartate pathogenic variant (D183N) and the molecular modeling of the transaldimination step, led us to propose that an interplay of opposite forces, which we named spring mechanism, finely tunes PLP geometry during catalysis and is essential to move the external aldimine in the correct position in order for the 1,3-proton transfer to occur.

Radiation damage at the active site of human alanine:glyoxylate aminotransferase reveals that the cofactor position is finely tuned during catalysis.,Giardina G, Paiardini A, Montioli R, Cellini B, Voltattorni CB, Cutruzzola F Sci Rep. 2017 Sep 15;7(1):11704. doi: 10.1038/s41598-017-11948-w. PMID:28916765<ref>PMID:28916765</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5ofy" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Cellini, B]]
[[Category: Cutruzzola, F]]
[[Category: Giardina, G]]
[[Category: Montioli, R]]
[[Category: Voltattorni, C Borri]]
[[Category: Aminotransferase]]
[[Category: Detoxification]]
[[Category: Liver]]
[[Category: Transferase]]