5css - Revision history

OCA at 16:12, 8 November 2023

2023-11-08T16:12:01Z

← Older revision		Revision as of 16:12, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5css]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum_DSM_1728 Thermoplasma acidophilum DSM 1728]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CSS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5css]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum_DSM_1728 Thermoplasma acidophilum DSM 1728]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CSS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</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]] 2.17Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</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=5css FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5css OCA], [https://pdbe.org/5css PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5css RCSB], [https://www.ebi.ac.uk/pdbsum/5css PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5css 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=5css FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5css OCA], [https://pdbe.org/5css PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5css RCSB], [https://www.ebi.ac.uk/pdbsum/5css PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5css ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:26, 14 June 2023

2023-06-14T12:26:32Z

← Older revision		Revision as of 12:26, 14 June 2023
Line 3:		Line 3:
	<StructureSection load='5css' size='340' side='right'caption='[[5css]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='5css' size='340' side='right'caption='[[5css]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5css]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Theac Theac~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CSS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CSS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5css]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum_DSM_1728 Thermoplasma acidophilum DSM 1728]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CSS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene~~></td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5csr\|5csr]]</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=5css FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5css OCA], [https://pdbe.org/5css PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5css RCSB], [https://www.ebi.ac.uk/pdbsum/5css PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5css ProSAT]</span></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpiA, Ta0313 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273075 THEAC])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </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=5css FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5css OCA], [~~http~~://pdbe.org/5css PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5css RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5css PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5css ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/TPIS_THEAC TPIS_THEAC]] Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P).		[https://www.uniprot.org/uniprot/TPIS_THEAC TPIS_THEAC] Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 20:

	==See Also==		==See Also==
	*[[Triose ~~Phosphate Isomerase~~\|Triose ~~Phosphate Isomerase~~]]		*[[Triose phosphate isomerase 3D structures\|Triose phosphate isomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Theac]]~~		[[Category: Thermoplasma acidophilum DSM 1728]]
	~~[[Category: Triose-phosphate isomerase~~]]		[[Category: Han BW]]
	[[Category: Han~~, B W~~]]		[[Category: Kim HS]]
	[[Category: Kim~~, H S~~]]		[[Category: Kim KR]]
	[[Category: Kim~~, K R~~]]		[[Category: Park JS]]
	[[Category: Park~~, J S~~]]		[[Category: Park SH]]
	[[Category: Park~~, S H~~]]		[[Category: Song MK]]
	[[Category: Song~~, M K]]~~
	~~[[Category: Glycerol 3-phosphate]]~~
	~~[[Category: Isomerase]]~~
	~~[[Category: Thermoplasma acidophilum]]~~
	~~[[Category: Tim]]~~
	~~[[Category: Tpi]]~~
	~~[[Category: Triosephosphate isomerase~~]]

OCA at 07:10, 19 February 2020

2020-02-19T07:10:28Z

← Older revision		Revision as of 07:10, 19 February 2020
Line 1:		Line 1:

	==Crystal structure of triosephosphate isomerase from Thermoplasma acidophilum with glycerol 3-phosphate==		==Crystal structure of triosephosphate isomerase from Thermoplasma acidophilum with glycerol 3-phosphate==
	<StructureSection load='5css' size='340' side='right' caption='[[5css]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='5css' size='340' side='right'caption='[[5css]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5css]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CSS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CSS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5css]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Theac Theac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CSS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CSS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5csr\|5csr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5csr\|5csr]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpiA, Ta0313 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273075 THEAC])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </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=5css FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5css OCA], [http://pdbe.org/5css PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5css RCSB], [http://www.ebi.ac.uk/pdbsum/5css PDBsum]</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=5css FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5css OCA], [http://pdbe.org/5css PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5css RCSB], [http://www.ebi.ac.uk/pdbsum/5css PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5css ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5css" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5css" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Triose Phosphate Isomerase\|Triose Phosphate Isomerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Theac]]
	[[Category: Triose-phosphate isomerase]]		[[Category: Triose-phosphate isomerase]]
	[[Category: Han, B W]]		[[Category: Han, B W]]

OCA at 15:20, 20 June 2016

2016-06-20T15:20:55Z

← Older revision		Revision as of 15:20, 20 June 2016
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 5css is ~~ON HOLD until Paper~~ Publication		==Crystal structure of triosephosphate isomerase from Thermoplasma acidophilum with glycerol 3-phosphate==
			<StructureSection load='5css' size='340' side='right' caption='[[5css]], [[Resolution\|resolution]] 2.17Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[5css]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CSS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CSS FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5csr\|5csr]]</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </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=5css FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5css OCA], [http://pdbe.org/5css PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5css RCSB], [http://www.ebi.ac.uk/pdbsum/5css PDBsum]</span></td></tr>
			</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/TPIS_THEAC TPIS_THEAC]] Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P).
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Thermoplasma acidophilum is a thermophilic archaeon that uses both non-phosphorylative Entner-Doudoroff (ED) pathway and Embden-Meyerhof-Parnas (EMP) pathway for glucose degradation. While triosephosphate isomerase (TPI), a well-known glycolytic enzyme, is not involved in the ED pathway in T. acidophilum, it has been considered to play an important role in the EMP pathway. Here, we report crystal structures of apo- and glycerol-3-phosphate-bound TPI from T. acidophilum (TaTPI). TaTPI adopts the canonical TIM-barrel fold with eight alpha-helices and parallel eight beta-strands. Although TaTPI shares ~30% sequence identity to other TPIs from thermophilic species that adopt tetrameric conformation for enzymatic activity in their harsh physiological environments, TaTPI exists as a dimer in solution. We confirmed the dimeric conformation of TaTPI by analytical ultracentrifugation and size-exclusion chromatography. Helix 5 as well as helix 4 of thermostable tetrameric TPIs have been known to play crucial roles in oligomerization, forming a hydrophobic interface. However, TaTPI contains unique charged-amino acid residues in the helix 5 and adopts dimer conformation. TaTPI exhibits the apparent Td value of 74.6 degrees C and maintains its overall structure with some changes in the secondary structure contents at extremely acidic conditions (pH 1-2). Based on our structural and biophysical analyses of TaTPI, more compact structure of the protomer with reduced length of loops and certain patches on the surface could account for the robust nature of Thermoplasma acidophilum TPI.

	~~Authors:~~ Park, S.H., Kim, ~~H.S.~~, ~~Song~~, M.K.~~, Kim, K~~.R.~~, Park, J~~.S., ~~Han, B.W~~.		Structure and Stability of the Dimeric Triosephosphate Isomerase from the Thermophilic Archaeon Thermoplasma acidophilum.,Park SH, Kim HS, Park MS, Moon S, Song MK, Park HS, Hahn H, Kim SJ, Bae E, Kim HJ, Han BW PLoS One. 2015 Dec 28;10(12):e0145331. doi: 10.1371/journal.pone.0145331., eCollection 2015. PMID:26709515<ref>PMID:26709515</ref>

	~~Description~~: ~~Crystal structure of triosephosphate isomerase from Thermoplasma acidophilum with glycerol 3~~-phosphate		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased Structures~~]]		</div>
	[[Category: ~~Song~~, M.K]]		<div class="pdbe-citations 5css" style="background-color:#fffaf0;"></div>
	[[Category: Park, S.H]]		== References ==
	[[Category: Park, J.S]]		<references/>
	[[Category: ~~Kim~~, K.R]]		__TOC__
	[[Category: ~~Han, B.W~~]]		</StructureSection>
	[[Category: ~~Kim, H.S~~]]		[[Category: Triose-phosphate isomerase]]
			[[Category: Han, B W]]
			[[Category: Kim, H S]]
			[[Category: Kim, K R]]
			[[Category: Park, J S]]
			[[Category: Park, S H]]
			[[Category: Song, M K]]
			[[Category: Glycerol 3-phosphate]]
			[[Category: Isomerase]]
			[[Category: Thermoplasma acidophilum]]
			[[Category: Tim]]
			[[Category: Tpi]]
			[[Category: Triosephosphate isomerase]]

OCA at 10:42, 16 December 2015

2015-12-16T10:42:16Z

← Older revision		Revision as of 10:42, 16 December 2015
Line 7:		Line 7:
	Description: Crystal structure of triosephosphate isomerase from Thermoplasma acidophilum with glycerol 3-phosphate		Description: Crystal structure of triosephosphate isomerase from Thermoplasma acidophilum with glycerol 3-phosphate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	~~[[Category: Kim, K.R]]~~
	[[Category: Song, M.K]]		[[Category: Song, M.K]]
	[[Category: Park, S.H]]		[[Category: Park, S.H]]
	[[Category: Park, J.S]]		[[Category: Park, J.S]]
			[[Category: Kim, K.R]]
	[[Category: Han, B.W]]		[[Category: Han, B.W]]
	[[Category: Kim, H.S]]		[[Category: Kim, H.S]]

OCA at 13:26, 12 August 2015

2015-08-12T13:26:13Z

← Older revision		Revision as of 13:26, 12 August 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 5css is ON HOLD		The entry 5css is ON HOLD until Paper Publication

	Authors: Park, S.H., Kim, H.S., Song, M.K., Kim, K.R., Park, J.S., Han, B.W.		Authors: Park, S.H., Kim, H.S., Song, M.K., Kim, K.R., Park, J.S., Han, B.W.

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

2015-07-29T13:50:22Z

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

← Older revision	Revision as of 13:50, 29 July 2015
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5css is ON HOLD Authors: Park, S.H., Kim, H.S., Song, M.K., Kim, K.R., Park, J.S., Han, B.W. Description: Crystal structure of triosephosphate isom...

2015-07-29T13:50:21Z

New page: '''Unreleased structure''' The entry 5css is ON HOLD Authors: Park, S.H., Kim, H.S., Song, M.K., Kim, K.R., Park, J.S., Han, B.W. Description: Crystal structure of triosephosphate isom...

New page

'''Unreleased structure'''

The entry 5css is ON HOLD

Authors: Park, S.H., Kim, H.S., Song, M.K., Kim, K.R., Park, J.S., Han, B.W.

Description: Crystal structure of triosephosphate isomerase from Thermoplasma acidophilum with glycerol 3-phosphate
[[Category: Unreleased Structures]]
[[Category: Kim, K.R]]
[[Category: Song, M.K]]
[[Category: Park, S.H]]
[[Category: Park, J.S]]
[[Category: Han, B.W]]
[[Category: Kim, H.S]]