8a5w - Revision history

OCA at 08:09, 7 February 2024

OCA — Wed, 07 Feb 2024 08:09:10 GMT

←Older revision		Revision as of 08:09, 7 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8a5w]] is a 8 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=8A5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5W FirstGlance]. <br>		<table><tr><td colspan='2'>[[8a5w]] is a 8 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=8A5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E1U:(2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic+acid'>E1U</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U93:(2~{S})-2-[[(~{R})-[[(5~{S})-5-azanyl-6-oxidanylidene-hexyl]amino]-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methyl]amino]-3-phosphonooxy-propanoic+acid'>U93</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]] 2.78Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E1U:(2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic+acid'>E1U</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U93:(2~{S})-2-[[(~{R})-[[(5~{S})-5-azanyl-6-oxidanylidene-hexyl]amino]-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methyl]amino]-3-phosphonooxy-propanoic+acid'>U93</scene></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=8a5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5w OCA], [https://pdbe.org/8a5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5w RCSB], [https://www.ebi.ac.uk/pdbsum/8a5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5w 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=8a5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5w OCA], [https://pdbe.org/8a5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5w RCSB], [https://www.ebi.ac.uk/pdbsum/8a5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5w ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Organisms from all kingdoms of life synthesize L-serine from 3-phosphoglycerate through the phosphorylated pathway, a three-step diversion of glycolysis. Phosphoserine aminotransferase (PSAT) catalyzes the intermediate step, the pyridoxal 5'-phosphate-dependent transamination of 3-phosphohydroxypyruvate and L-glutamate to O-phosphoserine and alpha-ketoglutarate. PSAT is particularly relevant in the central nervous system of mammals because L-serine is the metabolic precursor of D-serine, cysteine, phospholipids, and nucleotides. Several mutations in the human psat gene have been linked to serine deficiency disorders, characterized by severe neurological symptoms. Furthermore, PSAT is overexpressed in many tumors and this overexpression has been associated with poor clinical outcomes. Here, we report the detailed functional and structural characterization of the recombinant human PSAT. The reaction catalyzed by PSAT is reversible, with an equilibrium constant of about 10, and the enzyme is very efficient, with a k(cat) /K(m) of 5.9 x 10(6) M(-1) s(-1) , thus contributing in driving the pathway towards the products despite the extremely unfavorable first step catalyzed by 3-phosphoglycerate dehydrogenase. The three-dimensional X-ray crystal structure of PSAT was solved in the substrate-free as well as in the O-phosphoserine-bound forms. Both structures contain eight protein molecules in the asymmetric unit, arranged in four dimers, with a bound cofactor in each subunit. In the substrate-free form, the active site of PSAT contains a sulfate ion that, in the substrate-bound form, is replaced by the phosphate group of O-phosphoserine. Interestingly, fast crystal soaking used to produce the substrate-bound form allowed the trapping of different intermediates along the catalytic cycle. This article is protected by copyright. All rights reserved.

-	L-Serine Biosynthesis in The Human Central Nervous System: Structure and Function of Phosphoserine Aminotransferase.,Marchesani F, Zangelmi E, Murtas G, Costanzi E, Ullah R, Peracchi A, Bruno S, Pollegioni L, Mozzarelli A, Storici P, Campanini B Protein Sci. 2023 Feb 27:e4609. doi: 10.1002/pro.4609. PMID:36851825<ref>PMID:36851825</ref>	+	==See Also==
-		+	*[[Phosphoserine aminotransferase\|Phosphoserine aminotransferase]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 8a5w" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:46, 29 March 2023

OCA — Wed, 29 Mar 2023 06:46:45 GMT

←Older revision		Revision as of 06:46, 29 March 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8a5w is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the human phosphoserine aminotransferase (PSAT) in complex with O-phosphoserine==
		+	<StructureSection load='8a5w' size='340' side='right'caption='[[8a5w]], [[Resolution\|resolution]] 2.78Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8a5w]] is a 8 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=8A5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5W FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E1U:(2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic+acid'>E1U</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U93:(2~{S})-2-[[(~{R})-[[(5~{S})-5-azanyl-6-oxidanylidene-hexyl]amino]-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methyl]amino]-3-phosphonooxy-propanoic+acid'>U93</scene></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=8a5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5w OCA], [https://pdbe.org/8a5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5w RCSB], [https://www.ebi.ac.uk/pdbsum/8a5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5w ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Organisms from all kingdoms of life synthesize L-serine from 3-phosphoglycerate through the phosphorylated pathway, a three-step diversion of glycolysis. Phosphoserine aminotransferase (PSAT) catalyzes the intermediate step, the pyridoxal 5'-phosphate-dependent transamination of 3-phosphohydroxypyruvate and L-glutamate to O-phosphoserine and alpha-ketoglutarate. PSAT is particularly relevant in the central nervous system of mammals because L-serine is the metabolic precursor of D-serine, cysteine, phospholipids, and nucleotides. Several mutations in the human psat gene have been linked to serine deficiency disorders, characterized by severe neurological symptoms. Furthermore, PSAT is overexpressed in many tumors and this overexpression has been associated with poor clinical outcomes. Here, we report the detailed functional and structural characterization of the recombinant human PSAT. The reaction catalyzed by PSAT is reversible, with an equilibrium constant of about 10, and the enzyme is very efficient, with a k(cat) /K(m) of 5.9 x 10(6) M(-1) s(-1) , thus contributing in driving the pathway towards the products despite the extremely unfavorable first step catalyzed by 3-phosphoglycerate dehydrogenase. The three-dimensional X-ray crystal structure of PSAT was solved in the substrate-free as well as in the O-phosphoserine-bound forms. Both structures contain eight protein molecules in the asymmetric unit, arranged in four dimers, with a bound cofactor in each subunit. In the substrate-free form, the active site of PSAT contains a sulfate ion that, in the substrate-bound form, is replaced by the phosphate group of O-phosphoserine. Interestingly, fast crystal soaking used to produce the substrate-bound form allowed the trapping of different intermediates along the catalytic cycle. This article is protected by copyright. All rights reserved.

-	~~Authors~~:	+	L-Serine Biosynthesis in The Human Central Nervous System: Structure and Function of Phosphoserine Aminotransferase.,Marchesani F, Zangelmi E, Murtas G, Costanzi E, Ullah R, Peracchi A, Bruno S, Pollegioni L, Mozzarelli A, Storici P, Campanini B Protein Sci. 2023 Feb 27:e4609. doi: 10.1002/pro.4609. PMID:36851825<ref>PMID:36851825</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8a5w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Campanini B]]
		+	[[Category: Costanzi E]]
		+	[[Category: Demitri N]]
		+	[[Category: Marchesan F]]
		+	[[Category: Peracchi A]]
		+	[[Category: Storici P]]
		+	[[Category: Ullah R]]
		+	[[Category: Zangelmi E]]

OCA at 07:26, 15 March 2023

OCA — Wed, 15 Mar 2023 07:26:13 GMT

←Older revision		Revision as of 07:26, 15 March 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8a5w is ON HOLD	+	The entry 8a5w is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 04:47, 25 January 2023

OCA — Wed, 25 Jan 2023 04:47:16 GMT

←Older revision		Revision as of 04:47, 25 January 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8a5w is ON HOLD ~~until Paper Publication~~	+	The entry 8a5w is ON HOLD

	Authors:		Authors:

OCA at 04:12, 20 July 2022

OCA — Wed, 20 Jul 2022 04:12:14 GMT

←Older revision		Revision as of 04:12, 20 July 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8a5w is ON HOLD	+	The entry 8a5w is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8a5w" [edit=sysop:move=sysop]

OCA — Wed, 22 Jun 2022 07:22:07 GMT

Protected "8a5w" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:22, 22 June 2022

OCA: New page: '''Unreleased structure''' The entry 8a5w is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 Jun 2022 07:22:06 GMT

New page: '''Unreleased structure''' The entry 8a5w is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8a5w is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]