5i3i - Revision history

OCA at 08:22, 23 August 2023

OCA — Wed, 23 Aug 2023 08:22:01 GMT

←Older revision		Revision as of 08:22, 23 August 2023
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	<StructureSection load='5i3i' size='340' side='right'caption='[[5i3i]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5i3i' size='340' side='right'caption='[[5i3i]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i3i]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Trybb Trybb~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I3I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5I3I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i3i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I3I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I3I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PGA:~~2~~-PHOSPHOGLYCOLIC+ACID'>PGA</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5i3f\|5i3f]], [[5i3j\|5i3j]], [[5i3k\|5i3k]], [[5i3g\|5i3g]], [[5i3h\|5i3h]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5i3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3i OCA], [https://pdbe.org/5i3i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i3i RCSB], [https://www.ebi.ac.uk/pdbsum/5i3i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i3i ProSAT]</span></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=5i3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3i OCA], [~~http~~://pdbe.org/5i3i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i3i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i3i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i3i ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TPIS_TRYBB TPIS_TRYBB]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Triose-phosphate isomerase]]~~	+	[[Category: Trypanosoma brucei brucei]]
-	~~[[Category: Trybb~~]]	+	[[Category: Drake EJ]]
-	[[Category: Drake~~, E J~~]]	+	[[Category: Gulick AM]]
-	[[Category: Gulick~~, A M~~]]	+	[[Category: Kim K]]
-	[[Category: Kim, K]]	+	[[Category: Reinhardt CJ]]
-	[[Category: Reinhardt~~, C J~~]]	+	[[Category: Richard JP]]
-	[[Category: Richard~~, J P~~]]	+	[[Category: Zhai X]]
-	[[Category: Zhai, X]]	+
-	~~[[Category: Catalysis]]~~	+
-	~~[[Category: Hydrophobic clamping]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Pga]]~~	+
-	~~[[Category: Triosephosphate isomerase~~]]	+

OCA at 08:44, 27 May 2020

OCA — Wed, 27 May 2020 08:44:03 GMT

←Older revision		Revision as of 08:44, 27 May 2020
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	==Structure-Function Studies on Role of Hydrophobic Clamping of a Basic Glutamate in Catalysis by Triosephosphate Isomerase==		==Structure-Function Studies on Role of Hydrophobic Clamping of a Basic Glutamate in Catalysis by Triosephosphate Isomerase==
-	<StructureSection load='5i3i' size='340' side='right' caption='[[5i3i]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5i3i' size='340' side='right'caption='[[5i3i]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i3i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I3I OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I3I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i3i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I3I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5I3I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i3f\|5i3f]], [[5i3j\|5i3j]], [[5i3k\|5i3k]], [[5i3g\|5i3g]], [[5i3h\|5i3h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i3f\|5i3f]], [[5i3j\|5i3j]], [[5i3k\|5i3k]], [[5i3g\|5i3g]], [[5i3h\|5i3h]]</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=5i3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3i OCA], [http://pdbe.org/5i3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i3i RCSB], [http://www.ebi.ac.uk/pdbsum/5i3i PDBsum]</span></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=5i3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3i OCA], [http://pdbe.org/5i3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i3i RCSB], [http://www.ebi.ac.uk/pdbsum/5i3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i3i ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5i3i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5i3i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Triose phosphate isomerase 3D structures\|Triose phosphate isomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Triose-phosphate isomerase]]		[[Category: Triose-phosphate isomerase]]
		+	[[Category: Trybb]]
	[[Category: Drake, E J]]		[[Category: Drake, E J]]
	[[Category: Gulick, A M]]		[[Category: Gulick, A M]]

OCA at 15:54, 1 June 2016

OCA — Wed, 01 Jun 2016 15:54:50 GMT

←Older revision		Revision as of 15:54, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i3i is ~~ON HOLD until Paper~~ Publication	+	==Structure-Function Studies on Role of Hydrophobic Clamping of a Basic Glutamate in Catalysis by Triosephosphate Isomerase==
		+	<StructureSection load='5i3i' size='340' side='right' caption='[[5i3i]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5i3i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I3I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I3I FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i3f\|5i3f]], [[5i3j\|5i3j]], [[5i3k\|5i3k]], [[5i3g\|5i3g]], [[5i3h\|5i3h]]</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=5i3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3i OCA], [http://pdbe.org/5i3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i3i RCSB], [http://www.ebi.ac.uk/pdbsum/5i3i PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Kinetic parameters are reported for the reactions of whole substrates (kcat/Km, M(-1) s(-1)) (R)-glyceraldehyde 3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP) and for the substrate pieces [(kcat/Km)E.HPi/Kd, M(-2) s(-1)] glycolaldehyde (GA) and phosphite dianion (HPi) catalyzed by the I172A/L232A mutant of triosephosphate isomerase from Trypanosoma brucei brucei (TbbTIM). A comparison with the corresponding parameters for wild-type, I172A, and L232A TbbTIM-catalyzed reactions shows that the effect of I172A and L232A mutations on DeltaG() for the wild-type TbbTIM-catalyzed reactions of the substrate pieces is nearly the same as the effect of the same mutations on TbbTIM previously mutated at the second side chain. This provides strong evidence that mutation of the first hydrophobic side chain does not affect the functioning of the second side chain in catalysis of the reactions of the substrate pieces. By contrast, the effects of I172A and L232A mutations on DeltaG() for wild-type TbbTIM-catalyzed reactions of the whole substrate are different from the effect of the same mutations on TbbTIM previously mutated at the second side chain. This is due to the change in the rate-determining step that determines the barrier to the isomerization reaction. X-ray crystal structures are reported for I172A, L232A, and I172A/L232A TIMs and for the complexes of these mutants to the intermediate analogue phosphoglycolate (PGA). The structures of the PGA complexes with wild-type and mutant enzymes are nearly superimposable, except that the space opened by replacement of the hydrophobic side chain is occupied by a water molecule that lies approximately 3.5 A from the basic side chain of Glu167. The new water at I172A mutant TbbTIM provides a simple rationalization for the increase in the activation barrier DeltaG() observed for mutant enzyme-catalyzed reactions of the whole substrate and substrate pieces. By contrast, the new water at the L232A mutant does not predict the decrease in DeltaG() observed for the mutant enzyme-catalyzed reactions of the substrate piece GA.

-	~~Authors: Drake, E.J., Gulick, A.M~~., Richard, ~~J.P.~~, ~~Zhai~~, X., Kim~~, K.~~, Reinhardt, C.J.	+	Structure-Function Studies of Hydrophobic Residues That Clamp a Basic Glutamate Side Chain during Catalysis by Triosephosphate Isomerase.,Richard JP, Amyes TL, Malabanan MM, Zhai X, Kim KJ, Reinhardt CJ, Wierenga RK, Drake EJ, Gulick AM Biochemistry. 2016 May 31;55(21):3036-47. doi: 10.1021/acs.biochem.6b00311. Epub , 2016 May 17. PMID:27149328<ref>PMID:27149328</ref>

-	~~Description: Structure-Function Studies on Role~~ of ~~Hydrophobic Clamping~~ of ~~a Basic Glutamate in Catalysis by Triosephosphate Isomerase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Zhai, X~~]]	+	<div class="pdbe-citations 5i3i" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Richard~~, J.P]]	+	== References ==
-	[[Category: ~~Drake~~, ~~E.J~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Triose-phosphate isomerase]]
		+	[[Category: Drake, E J]]
		+	[[Category: Gulick, A M]]
	[[Category: Kim, K]]		[[Category: Kim, K]]
-	[[Category: ~~Gulick~~, ~~A.M~~]]	+	[[Category: Reinhardt, C J]]
-	[[Category: ~~Reinhardt~~, C.J]]	+	[[Category: Richard, J P]]
		+	[[Category: Zhai, X]]
		+	[[Category: Catalysis]]
		+	[[Category: Hydrophobic clamping]]
		+	[[Category: Isomerase]]
		+	[[Category: Pga]]
		+	[[Category: Triosephosphate isomerase]]

OCA at 16:43, 26 February 2016

OCA — Fri, 26 Feb 2016 16:43:07 GMT

←Older revision		Revision as of 16:43, 26 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i3i is ON HOLD	+	The entry 5i3i is ON HOLD until Paper Publication

-	Authors: ~~Eric~~ J. ~~Drake~~, ~~Andrew~~ M. ~~Gulick~~, ~~John~~ P. ~~Richard~~, ~~Xiang~~ Zhai, ~~Kalvin~~ Kim, ~~Christopher J~~. Reinhardt	+	Authors: Drake, E.J., Gulick, A.M., Richard, J.P., Zhai, X., Kim, K., Reinhardt, C.J.

	Description: Structure-Function Studies on Role of Hydrophobic Clamping of a Basic Glutamate in Catalysis by Triosephosphate Isomerase		Description: Structure-Function Studies on Role of Hydrophobic Clamping of a Basic Glutamate in Catalysis by Triosephosphate Isomerase
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Eric~~ J. Drake, ~~Andrew M~~. Gulick, ~~John P~~. ~~Richard~~, ~~Xiang Zhai, Kalvin Kim, Christopher J~~. ~~Reinhardt~~]]	+	[[Category: Zhai, X]]
		+	[[Category: Richard, J.P]]
		+	[[Category: Drake, E.J]]
		+	[[Category: Kim, K]]
		+	[[Category: Gulick, A.M]]
		+	[[Category: Reinhardt, C.J]]

OCA: Protected "5i3i" [edit=sysop:move=sysop]

OCA — Sun, 21 Feb 2016 01:32:55 GMT

Protected "5i3i" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:32, 21 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i3i is ON HOLD Authors: Eric J. Drake, Andrew M. Gulick, John P. Richard, Xiang Zhai, Kalvin Kim, Christopher J. Reinhardt Description: Structure-...

OCA — Sun, 21 Feb 2016 01:32:53 GMT

New page: '''Unreleased structure''' The entry 5i3i is ON HOLD Authors: Eric J. Drake, Andrew M. Gulick, John P. Richard, Xiang Zhai, Kalvin Kim, Christopher J. Reinhardt Description: Structure-...

New page

'''Unreleased structure'''

The entry 5i3i is ON HOLD

Authors: Eric J. Drake, Andrew M. Gulick, John P. Richard, Xiang Zhai, Kalvin Kim, Christopher J. Reinhardt

Description: Structure-Function Studies on Role of Hydrophobic Clamping of a Basic Glutamate in Catalysis by Triosephosphate Isomerase
[[Category: Unreleased Structures]]
[[Category: Eric J. Drake, Andrew M. Gulick, John P. Richard, Xiang Zhai, Kalvin Kim, Christopher J. Reinhardt]]