6yne - Revision history

OCA at 13:31, 24 January 2024

OCA — Wed, 24 Jan 2024 13:31:09 GMT

←Older revision		Revision as of 13:31, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6yne' size='340' side='right'caption='[[6yne]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6yne' size='340' side='right'caption='[[6yne]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yne]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YNE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YNE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yne]] is a 4 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=6YNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YNE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=XPE:3~~,~~6,9,12,15,18,21,24,27-NONAOXANONACOSANE-~~1~~,29-DIOL'>XPE</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]] 1.853Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6ynd\|6ynd]]~~, ~~[[6ynf\|6ynf]]~~, ~~[[6ynh\|6ynh]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XPE:3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL'>XPE</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=6yne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yne OCA], [~~http~~://pdbe.org/6yne PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yne RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yne PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yne 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=6yne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yne OCA], [https://pdbe.org/6yne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yne RCSB], [https://www.ebi.ac.uk/pdbsum/6yne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yne ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/G3P_HUMAN G3P_HUMAN]] Has both glyceraldehyde-3-phosphate dehydrogenase and nitrosylase activities, thereby playing a role in glycolysis and nuclear functions, respectively. Participates in nuclear events including transcription, RNA transport, DNA replication and apoptosis. Nuclear functions are probably due to the nitrosylase activity that mediates cysteine S-nitrosylation of nuclear target proteins such as SIRT1, HDAC2 and PRKDC. Modulates the organization and assembly of the cytoskeleton. Facilitates the CHP1-dependent microtubule and membrane associations through its ability to stimulate the binding of CHP1 to microtubules (By similarity). Glyceraldehyde-3-phosphate dehydrogenase is a key enzyme in glycolysis that catalyzes the first step of the pathway by converting D-glyceraldehyde 3-phosphate (G3P) into 3-phospho-D-glyceroyl phosphate. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma treatment assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation.<ref>PMID:3170585</ref> <ref>PMID:11724794</ref> <ref>PMID:23071094</ref>	+	[https://www.uniprot.org/uniprot/G3P_HUMAN G3P_HUMAN] Has both glyceraldehyde-3-phosphate dehydrogenase and nitrosylase activities, thereby playing a role in glycolysis and nuclear functions, respectively. Participates in nuclear events including transcription, RNA transport, DNA replication and apoptosis. Nuclear functions are probably due to the nitrosylase activity that mediates cysteine S-nitrosylation of nuclear target proteins such as SIRT1, HDAC2 and PRKDC. Modulates the organization and assembly of the cytoskeleton. Facilitates the CHP1-dependent microtubule and membrane associations through its ability to stimulate the binding of CHP1 to microtubules (By similarity). Glyceraldehyde-3-phosphate dehydrogenase is a key enzyme in glycolysis that catalyzes the first step of the pathway by converting D-glyceraldehyde 3-phosphate (G3P) into 3-phospho-D-glyceroyl phosphate. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma treatment assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation.<ref>PMID:3170585</ref> <ref>PMID:11724794</ref> <ref>PMID:23071094</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6yne" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6yne" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures\|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lia, A]]	+	[[Category: Lia A]]
-	[[Category: Roversi, P]]	+	[[Category: Roversi P]]
-	~~[[Category: Biosynthetic protein]]~~	+
-	~~[[Category: Hek293f]]~~	+
-	~~[[Category: Kifunensine~~]]	+

OCA at 06:17, 14 October 2020

OCA — Wed, 14 Oct 2020 06:17:39 GMT

←Older revision		Revision as of 06:17, 14 October 2020
Line 1:		Line 1:

	==GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.==		==GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.==
-	<StructureSection load='6yne' size='340' side='right'caption='[[6yne]]' scene=''>	+	<StructureSection load='6yne' size='340' side='right'caption='[[6yne]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YNE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YNE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yne]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YNE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YNE FirstGlance]. <br>
-	</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=6yne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yne OCA], [http://pdbe.org/6yne PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yne RCSB], [http://www.ebi.ac.uk/pdbsum/6yne PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yne ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XPE:3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL'>XPE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ynd\|6ynd]], [[6ynf\|6ynf]], [[6ynh\|6ynh]]</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=6yne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yne OCA], [http://pdbe.org/6yne PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yne RCSB], [http://www.ebi.ac.uk/pdbsum/6yne PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yne ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/G3P_HUMAN G3P_HUMAN]] Has both glyceraldehyde-3-phosphate dehydrogenase and nitrosylase activities, thereby playing a role in glycolysis and nuclear functions, respectively. Participates in nuclear events including transcription, RNA transport, DNA replication and apoptosis. Nuclear functions are probably due to the nitrosylase activity that mediates cysteine S-nitrosylation of nuclear target proteins such as SIRT1, HDAC2 and PRKDC. Modulates the organization and assembly of the cytoskeleton. Facilitates the CHP1-dependent microtubule and membrane associations through its ability to stimulate the binding of CHP1 to microtubules (By similarity). Glyceraldehyde-3-phosphate dehydrogenase is a key enzyme in glycolysis that catalyzes the first step of the pathway by converting D-glyceraldehyde 3-phosphate (G3P) into 3-phospho-D-glyceroyl phosphate. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma treatment assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation.<ref>PMID:3170585</ref> <ref>PMID:11724794</ref> <ref>PMID:23071094</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Background: n-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyses the NAD (+)-dependent oxidative phosphorylation of n-glyceraldehyde-3-phosphate to 1,3-diphospho-n-glycerate and its reverse reaction in glycolysis and gluconeogenesis. Methods: Four distinct crystal structures of human n-Glyceraldehyde-3-phosphate dehydrogenase ( HsGAPDH) have been determined from protein purified from the supernatant of HEK293F human epithelial kidney cells. Results: X-ray crystallography and mass-spectrometry indicate that the catalytic cysteine of the protein ( HsGAPDH Cys152) is partially oxidised to cysteine S-sulfonic acid. The average occupancy for the Cys152-S-sulfonic acid modification over the 20 crystallographically independent copies of HsGAPDH across three of the crystal forms obtained is 0.31+/-0.17. Conclusions: The modification induces no significant structural changes on the tetrameric enzyme, and only makes aspecific contacts to surface residues in the active site, in keeping with the hypothesis that the oxidising conditions of the secreted mammalian cell expression system result in HsGAPDH catalytic cysteine S-sulfonic acid modification and irreversible inactivation of the enzyme.
		+
		+	Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid.,Lia A, Dowle A, Taylor C, Santino A, Roversi P Wellcome Open Res. 2020 Aug 25;5:114. doi: 10.12688/wellcomeopenres.15893.2., eCollection 2020. PMID:32802964<ref>PMID:32802964</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yne" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lia A]]	+	[[Category: Lia, A]]
-	[[Category: Roversi P]]	+	[[Category: Roversi, P]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Hek293f]]
		+	[[Category: Kifunensine]]

OCA at 06:08, 6 May 2020

OCA — Wed, 06 May 2020 06:08:48 GMT

←Older revision		Revision as of 06:08, 6 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6yne is ON HOLD until Paper Publication~~	+	==GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.==
-		+	<StructureSection load='6yne' size='340' side='right'caption='[[6yne]]' scene=''>
-	~~Authors: Roversi, P., Lia, A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YNE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YNE FirstGlance]. <br>
-	~~Description:~~ GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.	+	</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=6yne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yne OCA], [http://pdbe.org/6yne PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yne RCSB], [http://www.ebi.ac.uk/pdbsum/6yne PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yne ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Lia, A]]	+	__TOC__
-	[[Category: Roversi, P]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lia A]]
		+	[[Category: Roversi P]]

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

OCA — Wed, 22 Apr 2020 04:24:00 GMT

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

←Older revision

Revision as of 04:24, 22 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yne is ON HOLD until Paper Publication Authors: Roversi, P., Lia, A. Description: GAPDH purified from the supernatant of HEK293F cells: crystal fo...

OCA — Wed, 22 Apr 2020 04:23:59 GMT

New page: '''Unreleased structure''' The entry 6yne is ON HOLD until Paper Publication Authors: Roversi, P., Lia, A. Description: GAPDH purified from the supernatant of HEK293F cells: crystal fo...

New page

'''Unreleased structure'''

The entry 6yne is ON HOLD until Paper Publication

Authors: Roversi, P., Lia, A.

Description: GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.
[[Category: Unreleased Structures]]
[[Category: Lia, A]]
[[Category: Roversi, P]]