5vjz - Revision history

OCA at 07:07, 16 March 2022

OCA — Wed, 16 Mar 2022 07:07:19 GMT

←Older revision		Revision as of 07:07, 16 March 2022
Line 1:		Line 1:

	==Joint X-ray/neutron structure of aspartate aminotransferase with alpha-methyl-aspartate at pH 7.5==		==Joint X-ray/neutron structure of aspartate aminotransferase with alpha-methyl-aspartate at pH 7.5==
-	<StructureSection load='5vjz' size='340' side='right' caption='[[5vjz]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5vjz' size='340' side='right'caption='[[5vjz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vjz]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vjz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VJZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=PLA:2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC+ACID'>PLA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=PLA:2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC+ACID'>PLA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GOT1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GOT1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</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=5vjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjz OCA], [~~http~~://pdbe.org/5vjz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vjz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vjz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjz 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=5vjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjz OCA], [https://pdbe.org/5vjz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vjz RCSB], [https://www.ebi.ac.uk/pdbsum/5vjz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AATC_PIG AATC_PIG]] Plays a key role in amino acid metabolism.	+	[[https://www.uniprot.org/uniprot/AATC_PIG AATC_PIG]] Plays a key role in amino acid metabolism.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Aspartate ~~Aminotransferase~~\|Aspartate ~~Aminotransferase~~]]	+	*[[Aspartate aminotransferase 3D structures\|Aspartate aminotransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pig]]		[[Category: Pig]]
	[[Category: Dajnowicz, S]]		[[Category: Dajnowicz, S]]

OCA at 09:22, 30 January 2019

OCA — Wed, 30 Jan 2019 09:22:01 GMT

←Older revision		Revision as of 09:22, 30 January 2019
Line 3:		Line 3:
	<StructureSection load='5vjz' size='340' side='right' caption='[[5vjz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5vjz' size='340' side='right' caption='[[5vjz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vjz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vjz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=PLA:2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC+ACID'>PLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=PLA:2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC+ACID'>PLA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GOT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</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=5vjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjz OCA], [http://pdbe.org/5vjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vjz RCSB], [http://www.ebi.ac.uk/pdbsum/5vjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjz 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=5vjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjz OCA], [http://pdbe.org/5vjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vjz RCSB], [http://www.ebi.ac.uk/pdbsum/5vjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjz ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5vjz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vjz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aspartate Aminotransferase\|Aspartate Aminotransferase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pig]]
	[[Category: Dajnowicz, S]]		[[Category: Dajnowicz, S]]
	[[Category: Kovalevsky, A Y]]		[[Category: Kovalevsky, A Y]]

OCA at 06:00, 1 November 2017

OCA — Wed, 01 Nov 2017 06:00:42 GMT

←Older revision		Revision as of 06:00, 1 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vjz is ~~ON HOLD until Paper~~ Publication	+	==Joint X-ray/neutron structure of aspartate aminotransferase with alpha-methyl-aspartate at pH 7.5==
		+	<StructureSection load='5vjz' size='340' side='right' caption='[[5vjz]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vjz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=PLA:2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC+ACID'>PLA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></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=5vjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjz OCA], [http://pdbe.org/5vjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vjz RCSB], [http://www.ebi.ac.uk/pdbsum/5vjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AATC_PIG AATC_PIG]] Plays a key role in amino acid metabolism.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Enzymes dependent on pyridoxal 5'-phosphate (PLP, the active form of vitamin B6) perform a myriad of diverse chemical transformations. They promote various reactions by modulating the electronic states of PLP through weak interactions in the active site. Neutron crystallography has the unique ability of visualizing the nuclear positions of hydrogen atoms in macromolecules. Here we present a room-temperature neutron structure of a homodimeric PLP-dependent enzyme, aspartate aminotransferase, which was reacted in situ with alpha-methylaspartate. In one monomer, the PLP remained as an internal aldimine with a deprotonated Schiff base. In the second monomer, the external aldimine formed with the substrate analog. We observe a deuterium equidistant between the Schiff base and the C-terminal carboxylate of the substrate, a position indicative of a low-barrier hydrogen bond. Quantum chemical calculations and a low-pH room-temperature X-ray structure provide insight into the physical phenomena that control the electronic modulation in aspartate aminotransferase.Pyridoxal 5'-phosphate (PLP) is a ubiquitous co factor for diverse enzymes, among them aspartate aminotransferase. Here the authors use neutron crystallography, which allows the visualization of the positions of hydrogen atoms, and computation to characterize the catalytic mechanism of the enzyme.

-	~~Authors: Dajnowicz~~, S., ~~Kovalevsky~~, A~~.Y.~~, Mueser~~, T~~.C.	+	Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme.,Dajnowicz S, Johnston RC, Parks JM, Blakeley MP, Keen DA, Weiss KL, Gerlits O, Kovalevsky A, Mueser TC Nat Commun. 2017 Oct 16;8(1):955. doi: 10.1038/s41467-017-01060-y. PMID:29038582<ref>PMID:29038582</ref>

-	~~Description: Joint X-ray~~/~~neutron structure~~ of ~~aspartate aminotransferase with alpha-methyl-aspartate at pH 7~~.5	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Kovalevsky, A.Y]]~~	+	<div class="pdbe-citations 5vjz" style="background-color:#fffaf0;"></div>
-	~~[[Category: Mueser, T.C]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Dajnowicz, S]]		[[Category: Dajnowicz, S]]
		+	[[Category: Kovalevsky, A Y]]
		+	[[Category: Mueser, T C]]
		+	[[Category: Aspartate aminotransferase]]
		+	[[Category: Neutron structure]]
		+	[[Category: Transferase]]

OCA at 14:05, 27 September 2017

OCA — Wed, 27 Sep 2017 14:05:11 GMT

←Older revision		Revision as of 14:05, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5vjz is ON HOLD	+	The entry 5vjz is ON HOLD until Paper Publication

	Authors: Dajnowicz, S., Kovalevsky, A.Y., Mueser, T.C.		Authors: Dajnowicz, S., Kovalevsky, A.Y., Mueser, T.C.
Line 7:		Line 7:
	Description: Joint X-ray/neutron structure of aspartate aminotransferase with alpha-methyl-aspartate at pH 7.5		Description: Joint X-ray/neutron structure of aspartate aminotransferase with alpha-methyl-aspartate at pH 7.5
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Dajnowicz, S]]
	[[Category: Kovalevsky, A.Y]]		[[Category: Kovalevsky, A.Y]]
	[[Category: Mueser, T.C]]		[[Category: Mueser, T.C]]
		+	[[Category: Dajnowicz, S]]

OCA at 11:23, 4 May 2017

OCA — Thu, 04 May 2017 11:23:20 GMT

←Older revision		Revision as of 11:23, 4 May 2017
Line 3:		Line 3:
	The entry 5vjz is ON HOLD		The entry 5vjz is ON HOLD

-	Authors: Dajnowicz, S. , Kovalevsky, A.Y., Mueser, T.C.	+	Authors: Dajnowicz, S., Kovalevsky, A.Y., Mueser, T.C.

-	Description: ""Joint X-ray/neutron structure of aspartate aminotransferase with alpha-methyl-aspartate at pH 7.5""	+	Description: Joint X-ray/neutron structure of aspartate aminotransferase with alpha-methyl-aspartate at pH 7.5
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Dajnowicz, S~~. ,~~ Kovalevsky, A.Y]]	+	[[Category: Dajnowicz, S]]
		+	[[Category: Kovalevsky, A.Y]]
	[[Category: Mueser, T.C]]		[[Category: Mueser, T.C]]

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

OCA — Thu, 27 Apr 2017 12:22:47 GMT

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

←Older revision

Revision as of 12:22, 27 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vjz is ON HOLD Authors: Dajnowicz, S. , Kovalevsky, A.Y., Mueser, T.C. Description: ""Joint X-ray/neutron structure of aspartate aminotransferase ...

OCA — Thu, 27 Apr 2017 12:22:45 GMT

New page: '''Unreleased structure''' The entry 5vjz is ON HOLD Authors: Dajnowicz, S. , Kovalevsky, A.Y., Mueser, T.C. Description: ""Joint X-ray/neutron structure of aspartate aminotransferase ...

New page

'''Unreleased structure'''

The entry 5vjz is ON HOLD

Authors: Dajnowicz, S. , Kovalevsky, A.Y., Mueser, T.C.

Description: ""Joint X-ray/neutron structure of aspartate aminotransferase with alpha-methyl-aspartate at pH 7.5""
[[Category: Unreleased Structures]]
[[Category: Dajnowicz, S. , Kovalevsky, A.Y]]
[[Category: Mueser, T.C]]