6czz - Revision history

OCA at 15:14, 4 October 2023

2023-10-04T15:14:46Z

←Older revision		Revision as of 15:14, 4 October 2023
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	<StructureSection load='6czz' size='340' side='right'caption='[[6czz]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6czz' size='340' side='right'caption='[[6czz]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6czz]] is a 4 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=6CZZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CZZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6czz]] is a 4 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=6CZZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CZZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=NA:SODIUM+ION'~~>~~NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL~~-~~5-PHOSPHATE'>PLP</scene>~~, ~~<scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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]] 1.7Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~PSAT1, At4g35630, F8D20.140 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=3702 ARATH])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Phosphoserine_transaminase Phosphoserine transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.52 2.6.1.52]~~ </~~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=6czz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czz OCA], [https://pdbe.org/6czz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6czz RCSB], [https://www.ebi.ac.uk/pdbsum/6czz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6czz 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=6czz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czz OCA], [~~http~~://pdbe.org/6czz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6czz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6czz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6czz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SERB1_ARATH SERB1_ARATH]] Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine.<ref>PMID:16289358</ref> <ref>PMID:9881164</ref>	+	[https://www.uniprot.org/uniprot/SERB1_ARATH SERB1_ARATH] Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine.<ref>PMID:16289358</ref> <ref>PMID:9881164</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: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Phosphoserine transaminase]]~~	+	[[Category: Dauter Z]]
-	[[Category: Dauter, Z]]	+	[[Category: Ruszkowski M]]
-	[[Category: Ruszkowski, M]]	+	[[Category: Sekula B]]
-	[[Category: Sekula, B]]	+
-	~~[[Category: Plp]]~~	+
-	~~[[Category: Psat]]~~	+
-	~~[[Category: Pyridoxal 5'-phosphate]]~~	+
-	~~[[Category: Serine biosynthesis]]~~	+
-	~~[[Category: Transaminase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:01, 4 December 2019

2019-12-04T10:01:35Z

←Older revision		Revision as of 10:01, 4 December 2019
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	==Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with PLP-phosphoserine geminal diamine intermediate==		==Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with PLP-phosphoserine geminal diamine intermediate==
-	<StructureSection load='6czz' size='340' side='right' caption='[[6czz]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='6czz' size='340' side='right'caption='[[6czz]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6czz]] is a 4 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=6CZZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6czz]] is a 4 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=6CZZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZZ FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6czz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6czz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphoserine aminotransferase\|Phosphoserine aminotransferase]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Arath]]		[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Phosphoserine transaminase]]		[[Category: Phosphoserine transaminase]]
	[[Category: Dauter, Z]]		[[Category: Dauter, Z]]

OCA at 22:11, 9 August 2018

2018-08-09T22:11:28Z

←Older revision		Revision as of 22:11, 9 August 2018
Line 3:		Line 3:
	<StructureSection load='6czz' size='340' side='right' caption='[[6czz]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6czz' size='340' side='right' caption='[[6czz]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6czz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6czz]] is a 4 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=6CZZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PSAT1, At4g35630, F8D20.140 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoserine_transaminase Phosphoserine transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.52 2.6.1.52] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoserine_transaminase Phosphoserine transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.52 2.6.1.52] </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=6czz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czz OCA], [http://pdbe.org/6czz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6czz RCSB], [http://www.ebi.ac.uk/pdbsum/6czz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6czz 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=6czz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czz OCA], [http://pdbe.org/6czz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6czz RCSB], [http://www.ebi.ac.uk/pdbsum/6czz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6czz ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SERB1_ARATH SERB1_ARATH]] Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine.<ref>PMID:16289358</ref> <ref>PMID:9881164</ref>		[[http://www.uniprot.org/uniprot/SERB1_ARATH SERB1_ARATH]] Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine.<ref>PMID:16289358</ref> <ref>PMID:9881164</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phosphoserine aminotransferase (PSAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of 3-phosphohydroxypyruvate (3-PHP) to 3-phosphoserine (PSer) in an L-glutamate (Glu)-linked reversible transamination reaction. This process proceeds through a bimolecular ping-pong mechanism and in plants takes place in plastids. It is a part of the phosphorylated pathway of serine biosynthesis, one of three routes recognized in plant organisms that yield serine. In this three-step biotransformation, 3-phosphoglycerate (3-PGA) delivered from plastidial glycolysis and Calvin cycle is oxidized by 3-PGA dehydrogenase. Then, 3-PHP is subjected to transamination with Glu to yield PSer and alpha-ketoglutarate (AKG). In the last step of the pathway, serine is produced by the action of phosphoserine phosphatase. Here we present the structural characterization of PSAT isoform 1 from Arabidopsis thaliana (AtPSAT1), a dimeric S-shaped protein that truncated of its 71-residue-long chloroplast-targeting signal peptide. Three crystal structures of AtPSAT1 captured at different stages of the reaction: (i) internal aldimine state with PLP covalently bound to the catalytic K265, (ii) holoenzyme in complex with pyridoxamine-5'-phosphate (PMP) after transfer of the amino group from glutamate and (iii) the geminal diamine intermediate state wherein the cofactor is covalently bound to both, K265 and PSer. These snapshots over the course of the reaction present detailed architecture of AtPSAT1 and allow for the comparison of this plant enzyme with other PSATs. Conformational changes of the protein during the catalytic event concern (i) the neighborhood of K265 when the amino group is transferred to the cofactor to form PMP and (ii) movement of the gate-keeping loop (residues 391-401) upon binding of 3-PHP and PSer. The latter conformational change of the loop may likely be one of key elements that regulate catalytic activity of PSATs.
		+
		+	Structural Analysis of Phosphoserine Aminotransferase (Isoform 1) From Arabidopsis thaliana- the Enzyme Involved in the Phosphorylated Pathway of Serine Biosynthesis.,Sekula B, Ruszkowski M, Dauter Z Front Plant Sci. 2018 Jul 6;9:876. doi: 10.3389/fpls.2018.00876. eCollection, 2018. PMID:30034403<ref>PMID:30034403</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6czz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Phosphoserine transaminase]]		[[Category: Phosphoserine transaminase]]
	[[Category: Dauter, Z]]		[[Category: Dauter, Z]]

OCA at 07:25, 23 May 2018

2018-05-23T07:25:13Z

←Older revision		Revision as of 07:25, 23 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6czz is ON HOLD until Paper Publication~~	+	==Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with PLP-phosphoserine geminal diamine intermediate==
-		+	<StructureSection load='6czz' size='340' side='right' caption='[[6czz]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors: Sekula, B., Ruszkowski, M., Dauter, Z.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6czz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZZ FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with PLP-phosphoserine geminal diamine intermediate	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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/Phosphoserine_transaminase Phosphoserine transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.52 2.6.1.52] </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=6czz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czz OCA], [http://pdbe.org/6czz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6czz RCSB], [http://www.ebi.ac.uk/pdbsum/6czz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6czz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SERB1_ARATH SERB1_ARATH]] Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine.<ref>PMID:16289358</ref> <ref>PMID:9881164</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Phosphoserine transaminase]]
		+	[[Category: Dauter, Z]]
		+	[[Category: Ruszkowski, M]]
	[[Category: Sekula, B]]		[[Category: Sekula, B]]
-	[[Category: ~~Ruszkowski, M~~]]	+	[[Category: Plp]]
-	[[Category: ~~Dauter, Z~~]]	+	[[Category: Psat]]
		+	[[Category: Pyridoxal 5'-phosphate]]
		+	[[Category: Serine biosynthesis]]
		+	[[Category: Transaminase]]
		+	[[Category: Transferase]]

OCA at 06:40, 2 May 2018

2018-05-02T06:40:08Z

←Older revision		Revision as of 06:40, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Sekula, B., Ruszkowski, M., Dauter, Z.		Authors: Sekula, B., Ruszkowski, M., Dauter, Z.

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

2018-04-18T04:16:51Z

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

←Older revision

Revision as of 04:16, 18 April 2018

OCA: New page: '''Unreleased structure''' The entry 6czz is ON HOLD Authors: Sekula, B., Ruszkowski, M., Dauter, Z. Description: Crystal structure of Arabidopsis thaliana phosphoserine aminotransfera...

2018-04-18T04:16:50Z

New page: '''Unreleased structure''' The entry 6czz is ON HOLD Authors: Sekula, B., Ruszkowski, M., Dauter, Z. Description: Crystal structure of Arabidopsis thaliana phosphoserine aminotransfera...

New page

'''Unreleased structure'''

The entry 6czz is ON HOLD

Authors: Sekula, B., Ruszkowski, M., Dauter, Z.

Description: Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with PLP-phosphoserine geminal diamine intermediate
[[Category: Unreleased Structures]]
[[Category: Sekula, B]]
[[Category: Ruszkowski, M]]
[[Category: Dauter, Z]]