5uni - Revision history

OCA at 14:28, 6 March 2024

OCA — Wed, 06 Mar 2024 14:28:15 GMT

←Older revision		Revision as of 14:28, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5uni' size='340' side='right'caption='[[5uni]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5uni' size='340' side='right'caption='[[5uni]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uni]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UNI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uni]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UNI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C1779 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), TT_C1778 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(Re/Si-specific) NAD(P)(+) transhydrogenase (Re/Si-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </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=5uni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uni OCA], [https://pdbe.org/5uni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uni RCSB], [https://www.ebi.ac.uk/pdbsum/5uni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uni 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=5uni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uni OCA], [~~http~~://pdbe.org/5uni PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5uni RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5uni PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5uni ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~Q72GS0_THET2 Q72GS0_THET2~~]~~] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity).[PIRNR:PIRNR000204]~~	+	[https://www.uniprot.org/uniprot/Q72GR9_THET2 Q72GR9_THET2]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The nicotinamide nucleotide transhydrogenase (TH) is an integral membrane enzyme that uses the proton-motive force to drive hydride transfer from NADH to NADP+ in bacteria and eukaryotes. Here we solved a 2.2-A crystal structure of the TH transmembrane domain (Thermus thermophilus) at pH 6.5. This structure exhibits conformational changes of helix positions from a previous structure solved at pH 8.5, and reveals internal water molecules interacting with residues implicated in proton translocation. Together with molecular dynamics simulations, we show that transient water flows across a narrow pore and a hydrophobic "dry" region in the middle of the membrane channel, with key residues His42alpha2 (chain A) being protonated and Thr214beta (chain B) displaying a conformational change, respectively, to gate the channel access to both cytoplasmic and periplasmic chambers. Mutation of Thr214beta to Ala deactivated the enzyme. These data provide new insights into the gating mechanism of proton translocation in TH.	+
-		+
-	Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase.,Padayatti PS, Leung JH, Mahinthichaichan P, Tajkhorshid E, Ishchenko A, Cherezov V, Soltis SM, Jackson JB, Stout CD, Gennis RB, Zhang Q Structure. 2017 Jul 5;25(7):1111-1119.e3. doi: 10.1016/j.str.2017.05.022. Epub, 2017 Jun 22. PMID:28648609<ref>PMID:28648609</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5uni" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[NAD(P) transhydrogenase 3D structures\|NAD(P) transhydrogenase 3D structures]]		*[[NAD(P) transhydrogenase 3D structures\|NAD(P) transhydrogenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Leung, J H~~]]	+	[[Category: Thermus thermophilus]]
-	[[Category: ~~Padayatti, P S~~]]	+	[[Category: Leung JH]]
-	[[Category: ~~High resolution]]~~	+	[[Category: Padayatti PS]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Proton channel]]~~	+
-	~~[[Category: Transmembrane~~]]	+

OCA at 09:19, 1 January 2020

OCA — Wed, 01 Jan 2020 09:19:32 GMT

←Older revision		Revision as of 09:19, 1 January 2020
Line 1:		Line 1:

	==Critical role of water molecules for proton translocation of the membrane-bound transhydrogenase==		==Critical role of water molecules for proton translocation of the membrane-bound transhydrogenase==
-	<StructureSection load='5uni' size='340' side='right' caption='[[5uni]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5uni' size='340' side='right'caption='[[5uni]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uni]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UNI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uni]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UNI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C1779 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), TT_C1778 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(Re/Si-specific) NAD(P)(+) transhydrogenase (Re/Si-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(Re/Si-specific) NAD(P)(+) transhydrogenase (Re/Si-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </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=5uni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uni OCA], [http://pdbe.org/5uni PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uni RCSB], [http://www.ebi.ac.uk/pdbsum/5uni PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uni 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=5uni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uni OCA], [http://pdbe.org/5uni PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uni RCSB], [http://www.ebi.ac.uk/pdbsum/5uni PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uni ProSAT]</span></td></tr>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5uni" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5uni" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[NAD(P) transhydrogenase 3D structures\|NAD(P) transhydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: Large Structures]]
	[[Category: Leung, J H]]		[[Category: Leung, J H]]
	[[Category: Padayatti, P S]]		[[Category: Padayatti, P S]]

OCA at 17:00, 20 October 2017

OCA — Fri, 20 Oct 2017 17:00:14 GMT

←Older revision		Revision as of 17:00, 20 October 2017
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5uni" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5uni" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[NAD(P) transhydrogenase\|NAD(P) transhydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:56, 13 September 2017

OCA — Wed, 13 Sep 2017 10:56:20 GMT

←Older revision		Revision as of 10:56, 13 September 2017
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/Q72GS0_THET2 Q72GS0_THET2]] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity).[PIRNR:PIRNR000204]		[[http://www.uniprot.org/uniprot/Q72GS0_THET2 Q72GS0_THET2]] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity).[PIRNR:PIRNR000204]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The nicotinamide nucleotide transhydrogenase (TH) is an integral membrane enzyme that uses the proton-motive force to drive hydride transfer from NADH to NADP+ in bacteria and eukaryotes. Here we solved a 2.2-A crystal structure of the TH transmembrane domain (Thermus thermophilus) at pH 6.5. This structure exhibits conformational changes of helix positions from a previous structure solved at pH 8.5, and reveals internal water molecules interacting with residues implicated in proton translocation. Together with molecular dynamics simulations, we show that transient water flows across a narrow pore and a hydrophobic "dry" region in the middle of the membrane channel, with key residues His42alpha2 (chain A) being protonated and Thr214beta (chain B) displaying a conformational change, respectively, to gate the channel access to both cytoplasmic and periplasmic chambers. Mutation of Thr214beta to Ala deactivated the enzyme. These data provide new insights into the gating mechanism of proton translocation in TH.
		+
		+	Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase.,Padayatti PS, Leung JH, Mahinthichaichan P, Tajkhorshid E, Ishchenko A, Cherezov V, Soltis SM, Jackson JB, Stout CD, Gennis RB, Zhang Q Structure. 2017 Jul 5;25(7):1111-1119.e3. doi: 10.1016/j.str.2017.05.022. Epub, 2017 Jun 22. PMID:28648609<ref>PMID:28648609</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5uni" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[NAD(P) transhydrogenase\|NAD(P) transhydrogenase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:01, 10 May 2017

OCA — Wed, 10 May 2017 13:01:31 GMT

←Older revision		Revision as of 13:01, 10 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5uni ~~is ON HOLD until Paper Publication~~	+	==Critical role of water molecules for proton translocation of the membrane-bound transhydrogenase==
-		+	<StructureSection load='5uni' size='340' side='right' caption='[[5uni]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~: ~~Padayatti~~, P.S., ~~Leung~~, J.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5uni]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UNI FirstGlance]. <br>
-	~~Description~~: ~~Critical role of water molecules for~~ proton ~~translocation of~~ the membrane~~-bound transhydrogenase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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/NAD(P)(+)_transhydrogenase_(Re/Si-specific) NAD(P)(+) transhydrogenase (Re/Si-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </span></td></tr>
-	[[Category: Leung, J.H]]	+	<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=5uni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uni OCA], [http://pdbe.org/5uni PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uni RCSB], [http://www.ebi.ac.uk/pdbsum/5uni PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uni ProSAT]</span></td></tr>
-	[[Category: Padayatti, P.S]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q72GS0_THET2 Q72GS0_THET2]] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity).[PIRNR:PIRNR000204]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Leung, J H]]
		+	[[Category: Padayatti, P S]]
		+	[[Category: High resolution]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Proton channel]]
		+	[[Category: Transmembrane]]

OCA at 19:13, 15 March 2017

OCA — Wed, 15 Mar 2017 19:13:00 GMT

←Older revision		Revision as of 19:13, 15 March 2017
Line 7:		Line 7:
	Description: Critical role of water molecules for proton translocation of the membrane-bound transhydrogenase		Description: Critical role of water molecules for proton translocation of the membrane-bound transhydrogenase
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Padayatti, P.S]]
	[[Category: Leung, J.H]]		[[Category: Leung, J.H]]
		+	[[Category: Padayatti, P.S]]

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

OCA — Thu, 09 Mar 2017 14:38:57 GMT

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

←Older revision

Revision as of 14:38, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5uni is ON HOLD until Paper Publication Authors: Padayatti, P.S., Leung, J.H. Description: Critical role of water molecules for proton translocatio...

OCA — Thu, 09 Mar 2017 14:38:56 GMT

New page: '''Unreleased structure''' The entry 5uni is ON HOLD until Paper Publication Authors: Padayatti, P.S., Leung, J.H. Description: Critical role of water molecules for proton translocatio...

New page

'''Unreleased structure'''

The entry 5uni is ON HOLD until Paper Publication

Authors: Padayatti, P.S., Leung, J.H.

Description: Critical role of water molecules for proton translocation of the membrane-bound transhydrogenase
[[Category: Unreleased Structures]]
[[Category: Padayatti, P.S]]
[[Category: Leung, J.H]]