6ouv
From Proteopedia
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(New page: '''Unreleased structure''' The entry 6ouv is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures) |
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| - | '''Unreleased structure''' | ||
| - | + | ==1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus radiodurans with methylacetylphosphonate (MAP) bound== | |
| + | <StructureSection load='6ouv' size='340' side='right'caption='[[6ouv]], [[Resolution|resolution]] 1.94Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6ouv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OUV FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.937Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TDK:3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM'>TDK</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=6ouv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ouv OCA], [https://pdbe.org/6ouv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ouv RCSB], [https://www.ebi.ac.uk/pdbsum/6ouv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ouv ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/DXS_DEIRA DXS_DEIRA] Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP) (By similarity).[HAMAP-Rule:MF_00315] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 1-Deoxy-D-xylulose 5-phosphate synthase (DXPS) uses thiamine diphosphate (ThDP) to convert pyruvate and D-glyceraldehyde 3phosphate (D-GAP) into 1-deoxy-D-xylulose 5-phosphate (DXP), an essential bacterial metabolite. DXP is not utilized by humans; hence, DXPS has been an attractive antibacterial target. Here, we investigate DXPS from Deinococcus radiodurans (DrDXPS), showing that it has similar kinetic parameters Km (d-GAP )and Km (pyruvate )(54 +/- 3 microM and 11 +/- 1 microM, respectively) and comparable catalytic activity (k cat = 45 +/- 2 min(-1)) to previously studied bacterial DXPS enzymes, and employing it to obtain missing structural data on this enzyme family. In particular, we have determined crystallographic snapshots of DrDXPS in two states along the reaction coordinate - a structure of DrDXPS bound to C2alpha-phosphonolactylThDP (PLThDP), mimicking the native pre-decarboxylation intermediate C2alpha-lactylThDP (LThDP), and a native post-decarboxylation state with a bound enamine intermediate. The 1.94-A resolution structure of PLThDP-bound DrDXPS delineates how two active site histidine residues stabilize the LThDP intermediate. Meanwhile, the 2.40-A resolution structure of an enamine intermediate-bound DrDXPS reveals how a previously unknown 17-A conformational change removes one of the two histidine residues from the active site, likely triggering LThDP decarboxylation to form the enamine intermediate. These results provide insight into how the bi-substrate enzyme DXPS limits side reactions by arresting the reaction on the less reactive LThDP intermediate when its co-substrate is absent. They also offer a molecular basis for previous low-resolution experimental observations that correlate decarboxylation of LThDP with protein conformational changes. | ||
| - | + | X-ray crystallography-based structural elucidation of enzyme-bound intermediates along the 1deoxydxylulose 5-phosphate synthase reaction coordinate.,Chen PY, DeColli AA, Freel Meyers CL, Drennan CL J Biol Chem. 2019 Jun 25. pii: RA119.009321. doi: 10.1074/jbc.RA119.009321. PMID:31239351<ref>PMID:31239351</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 6ouv" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Deinococcus radiodurans]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Chen PY-T]] | ||
| + | [[Category: Drennan CL]] | ||
Current revision
1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus radiodurans with methylacetylphosphonate (MAP) bound
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