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==Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD== | ==Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD== | ||
<StructureSection load='5ujk' size='340' side='right' caption='[[5ujk]], [[Resolution|resolution]] 1.53Å' scene=''> | <StructureSection load='5ujk' size='340' side='right'caption='[[5ujk]], [[Resolution|resolution]] 1.53Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ujk]] is a 1 chain structure. 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 [ | <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><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.53Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [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®/PubMed®, 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 3D structures|Malate Dehydrogenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Methylorubrum extorquens]] | ||
[[Category: | [[Category: Gonzalez JM]] | ||
Latest revision as of 16:28, 4 October 2023
Malate dehydrogenase from Methylobacterium extorquens, complexed with NADMalate dehydrogenase from Methylobacterium extorquens, complexed with NAD
Structural highlights
FunctionMDH_METEA Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487] Publication Abstract from PubMedThree 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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