1y7t
From Proteopedia
(Difference between revisions)
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<StructureSection load='1y7t' size='340' side='right'caption='[[1y7t]], [[Resolution|resolution]] 1.65Å' scene=''> | <StructureSection load='1y7t' size='340' side='right'caption='[[1y7t]], [[Resolution|resolution]] 1.65Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1y7t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[1y7t]] 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=1Y7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y7T FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65Å</td></tr> |
| - | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1y7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y7t OCA], [https://pdbe.org/1y7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y7t RCSB], [https://www.ebi.ac.uk/pdbsum/1y7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y7t 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=1y7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y7t OCA], [https://pdbe.org/1y7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y7t RCSB], [https://www.ebi.ac.uk/pdbsum/1y7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y7t ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [https://www.uniprot.org/uniprot/MDH_THETH MDH_THETH] Catalyzes the reversible oxidation of malate to oxaloacetate. | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1y7t ConSurf]. | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1y7t ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | For better understanding of the coenzyme specificity in NAD-dependent MDH (tMDH) from Thermus flavus AT-62, we determined the crystal structures of tMDH-NADP(H) complex at maximally 1.65 A resolution. The overall structure is almost the same as that of the tMDH-NADH complex. However, NADP(H) binds to tMDH in the reverse orientation, where adenine occupies the position near the catalytic center and nicotinamide is positioned at the adenine binding site of the tMDH-NADH complex. Consistent with this, kinetic analysis of the malate-oxidizing reaction revealed that NADP(+) inhibited tMDH at high concentrations. This has provided the first evidence for the alternative binding mode of the nicotinamide coenzyme, that has pseudo-symmetry in its structure, in a single enzyme. | ||
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| - | Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H).,Tomita T, Fushinobu S, Kuzuyama T, Nishiyama M Biochem Biophys Res Commun. 2005 Aug 26;334(2):613-8. PMID:16009341<ref>PMID:16009341</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1y7t" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]] | *[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Flavobacterium thermophilum yoshida and oshima 1971]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Thermus thermophilus]] |
| - | [[Category: Fushinobu | + | [[Category: Fushinobu S]] |
| - | [[Category: Kuzuyama | + | [[Category: Kuzuyama T]] |
| - | [[Category: Nishiyama | + | [[Category: Nishiyama M]] |
| - | [[Category: Tomita | + | [[Category: Tomita T]] |
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Current revision
Crystal structure of NAD(H)-depenent malate dehydrogenase complexed with NADPH
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