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| | <StructureSection load='5ulv' size='340' side='right'caption='[[5ulv]], [[Resolution|resolution]] 1.66Å' scene=''> | | <StructureSection load='5ulv' size='340' side='right'caption='[[5ulv]], [[Resolution|resolution]] 1.66Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ulv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_extorquens"_bassalik_1913 "bacillus extorquens" bassalik 1913]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ror 4ror]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ULV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ULV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ulv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylorubrum_extorquens Methylorubrum extorquens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ror 4ror]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ULV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ULV FirstGlance]. <br> |
| - | </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></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]] 1.66Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mdh ([https://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></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [https://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=5ulv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ulv OCA], [https://pdbe.org/5ulv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ulv RCSB], [https://www.ebi.ac.uk/pdbsum/5ulv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ulv 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=5ulv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ulv OCA], [https://pdbe.org/5ulv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ulv RCSB], [https://www.ebi.ac.uk/pdbsum/5ulv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ulv ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/MDH_METC4 MDH_METC4]] 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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus extorquens bassalik 1913]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Malate dehydrogenase]] | + | [[Category: Methylorubrum extorquens]] |
| - | [[Category: Gonzalez, J M]] | + | [[Category: Gonzalez JM]] |
| - | [[Category: Dehydrogenase]]
| + | |
| - | [[Category: Malate]]
| + | |
| - | [[Category: Nad]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
MDH_METEA Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487]
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Gonzalez JM, Marti-Arbona R, Chen JCH, Broom-Peltz B, Unkefer CJ. Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase. Acta Crystallogr F Struct Biol Commun. 2018 Oct 1;74(Pt 10):610-616. doi:, 10.1107/S2053230X18011809. Epub 2018 Sep 19. PMID:30279311 doi:http://dx.doi.org/10.1107/S2053230X18011809
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