5ujk: Difference between revisions

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 ==Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD==
-<StructureSection load='5ujk' size='340' side='right' caption='[[5ujk]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
+<StructureSection load='5ujk' size='340' side='right'caption='[[5ujk]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ujk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_extorquens"_bassalik_1913 "bacillus extorquens" bassalik 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UJK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ujk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylorubrum_extorquens Methylorubrum extorquens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UJK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 1.53&#8491;</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=408 "Bacillus extorquens" Bassalik 1913])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5ujk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujk OCA], [https://pdbe.org/5ujk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ujk RCSB], [https://www.ebi.ac.uk/pdbsum/5ujk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujk 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=5ujk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujk OCA], [http://pdbe.org/5ujk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ujk RCSB], [http://www.ebi.ac.uk/pdbsum/5ujk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MDH_METEP MDH_METEP]] Catalyzes the reversible oxidation of malate to oxaloacetate.
+[https://www.uniprot.org/uniprot/MDH_METEA MDH_METEA] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD(+), and a ternary complex of MDH and oxaloacetate with ADP-ribose occupying the pyridine nucleotide-binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate-binding site is accessible in the enzyme resting state or NAD(+)-bound forms, the substrate-bound form exhibits a closed conformation. This conformational change involves the transition of an alpha-helix to a 310-helix, which causes the adjacent loop to close the active site following coenzyme and substrate binding. In the ternary complex, His284 forms a hydrogen bond to the C2 carbonyl of oxaloacetate, placing it in a position to donate a proton in the formation of (2S)-malate.
+Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase.,Gonzalez JM, Marti-Arbona R, Chen JCH, Broom-Peltz B, Unkefer CJ Acta Crystallogr F Struct Biol Commun. 2018 Oct 1;74(Pt 10):610-616. doi:, 10.1107/S2053230X18011809. Epub 2018 Sep 19. PMID:30279311<ref>PMID:30279311</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5ujk" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Malate dehydrogenase|Malate dehydrogenase]]
+*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus extorquens bassalik 1913]]
+[[Category: Large Structures]]
-[[Category: Malate dehydrogenase]]
+[[Category: Methylorubrum extorquens]]
-[[Category: Gonzalez, J M]]
+[[Category: Gonzalez JM]]
-[[Category: Dehydrogenase]]
-[[Category: Malate]]
-[[Category: Nad]]
-[[Category: Oxidoreductase]]