4kdf - Revision history

OCA at 15:58, 20 September 2023

OCA — Wed, 20 Sep 2023 15:58:05 GMT

←Older revision		Revision as of 15:58, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kdf]] is a 4 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=4KDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KDF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kdf]] is a 4 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=4KDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KDF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.356Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4kdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kdf OCA], [https://pdbe.org/4kdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kdf RCSB], [https://www.ebi.ac.uk/pdbsum/4kdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kdf 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=4kdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kdf OCA], [https://pdbe.org/4kdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kdf RCSB], [https://www.ebi.ac.uk/pdbsum/4kdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kdf ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:53, 30 November 2022

OCA — Wed, 30 Nov 2022 11:53:13 GMT

←Older revision		Revision as of 11:53, 30 November 2022
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	==Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD==		==Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD==
-	<StructureSection load='4kdf' size='340' side='right' caption='[[4kdf]], [[Resolution\|resolution]] 2.36Å' scene=''>	+	<StructureSection load='4kdf' size='340' side='right'caption='[[4kdf]], [[Resolution\|resolution]] 2.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kdf]] is a 4 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=4KDF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KDF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kdf]] is a 4 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=4KDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KDF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdh ([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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4kdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kdf OCA], [https://pdbe.org/4kdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kdf RCSB], [https://www.ebi.ac.uk/pdbsum/4kdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kdf ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] </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=4kdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kdf OCA], [~~http~~://pdbe.org/4kdf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kdf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kdf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kdf ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MDH_THETH MDH_THETH]] Catalyzes the reversible oxidation of malate to oxaloacetate.	+	[https://www.uniprot.org/uniprot/MDH_THETH MDH_THETH] Catalyzes the reversible oxidation of malate to oxaloacetate.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:

	==See Also==		==See Also==
-	*[[Malate ~~dehydrogenase~~\|Malate ~~dehydrogenase~~]]	+	*[[Malate Dehydrogenase 3D structures\|Malate Dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Flavobacterium thermophilum yoshida and oshima 1971~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Malate dehydrogenase~~]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Chang, Y Y]]	+	[[Category: Chang Y-Y]]
-	[[Category: Hong, C H]]	+	[[Category: Hong C-H]]
-	[[Category: Hsu, C H]]	+	[[Category: Hsu C-H]]
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 20:58, 5 August 2016

OCA — Fri, 05 Aug 2016 20:58:38 GMT

←Older revision		Revision as of 20:58, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD==		==Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD==
	<StructureSection load='4kdf' size='340' side='right' caption='[[4kdf]], [[Resolution\|resolution]] 2.36Å' scene=''>		<StructureSection load='4kdf' size='340' side='right' caption='[[4kdf]], [[Resolution\|resolution]] 2.36Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdh ([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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdh ([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/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] </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=4kdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kdf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kdf RCSB], [http://www.ebi.ac.uk/pdbsum/4kdf 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=4kdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kdf OCA], [http://pdbe.org/4kdf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kdf RCSB], [http://www.ebi.ac.uk/pdbsum/4kdf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kdf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4kdf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 05:50, 25 December 2014

OCA — Thu, 25 Dec 2014 05:50:33 GMT

←Older revision		Revision as of 05:50, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4kdf\| PDB=4kdf \| SCENE= }}~~	+	==Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD==
-	===Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD===	+	<StructureSection load='4kdf' size='340' side='right' caption='[[4kdf]], [[Resolution\|resolution]] 2.36Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24386145}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4kdf]] is a 4 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=4KDF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KDF FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdh ([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/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] </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=4kdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kdf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kdf RCSB], [http://www.ebi.ac.uk/pdbsum/4kdf PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/MDH_THETH MDH_THETH]] Catalyzes the reversible oxidation of malate to oxaloacetate.		[[http://www.uniprot.org/uniprot/MDH_THETH MDH_THETH]] Catalyzes the reversible oxidation of malate to oxaloacetate.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Malate dehydrogenase (MDH) catalyzes the conversion of oxaloacetate and malate by using the NAD/NADH coenzyme system. The system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in therapeutic applications and hormones. We elucidated the biochemical and structural features of MDH from Thermus thermophilus (TtMDH) for use in various biotechnological applications. The biochemical characterization of recombinant TtMDH revealed greatly increased activity above 60 degrees C and specific activity of about 2,600 U/mg with optimal temperature of 90 degrees C. Analysis of crystal structures of apo and NAD-bound forms of TtMDH revealed a slight movement of the binding loop and few structural elements around the co-substrate binding packet in the presence of NAD. The overall structures did not change much and retained all related positions, which agrees with the CD analyses. Further molecular dynamics (MD) simulation at higher temperatures were used to reconstruct structures from the crystal structure of TtMDH. Interestingly, at the simulated structure of 353 K, a large change occurred around the active site such that with increasing temperature, a mobile loop was closed to co-substrate binding region. From biochemical characterization, structural comparison and MD simulations, the thermal-induced conformational change of the co-substrate binding loop of TtMDH may contribute to the essential movement of the enzyme for admitting NAD and may benefit the enzyme's activity.
		+
		+	Crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding.,Hung CH, Hwang TS, Chang YY, Luo HR, Wu SP, Hsu CH PLoS One. 2013 Dec 26;8(12):e83091. doi: 10.1371/journal.pone.0083091., eCollection 2013. PMID:24386145<ref>PMID:24386145</ref>

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4kdf]] is~~ a ~~4 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4KDF OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:024386145</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Malate dehydrogenase\|Malate dehydrogenase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Malate dehydrogenase]]		[[Category: Malate dehydrogenase]]
-	[[Category: Chang, Y Y.]]	+	[[Category: Chang, Y Y]]
-	[[Category: Hong, C H.]]	+	[[Category: Hong, C H]]
-	[[Category: Hsu, C H.]]	+	[[Category: Hsu, C H]]
	[[Category: Dehydrogenase]]		[[Category: Dehydrogenase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 11:04, 5 February 2014

OCA — Wed, 05 Feb 2014 11:04:06 GMT

←Older revision		Revision as of 11:04, 5 February 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4kdf\| PDB=4kdf \| SCENE= }}
		+	===Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD===
		+	{{ABSTRACT_PUBMED_24386145}}

-	~~The entry 4kdf is ON HOLD~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/MDH_THETH MDH_THETH]] Catalyzes the reversible oxidation of malate to oxaloacetate.

-	~~Authors~~: ~~Hsu, C~~.~~-H., Hong, C.-H~~.~~, Chang, Y~~.-Y.	+	==About this Structure==
		+	[[4kdf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KDF OCA].

-	~~Description~~: ~~Crystal Structure of Thermus thermophilus~~ Malate Dehydrogenase ~~in Complex with NAD~~	+	==Reference==
		+	<ref group="xtra">PMID:024386145</ref><references group="xtra"/><references/>
		+	[[Category: Malate dehydrogenase]]
		+	[[Category: Chang, Y Y.]]
		+	[[Category: Hong, C H.]]
		+	[[Category: Hsu, C H.]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "4kdf" [edit=sysop:move=sysop]

OCA — Thu, 02 May 2013 07:17:18 GMT

Protected "4kdf" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:17, 2 May 2013

OCA: New page: '''Unreleased structure''' The entry 4kdf is ON HOLD Authors: Hsu, C.-H., Hong, C.-H., Chang, Y.-Y. Description: Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Compl...

OCA — Thu, 02 May 2013 07:17:16 GMT

New page: '''Unreleased structure''' The entry 4kdf is ON HOLD Authors: Hsu, C.-H., Hong, C.-H., Chang, Y.-Y. Description: Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Compl...

New page

'''Unreleased structure'''

The entry 4kdf is ON HOLD

Authors: Hsu, C.-H., Hong, C.-H., Chang, Y.-Y.

Description: Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD