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| | <StructureSection load='6ouv' size='340' side='right'caption='[[6ouv]], [[Resolution|resolution]] 1.94Å' scene=''> | | <StructureSection load='6ouv' size='340' side='right'caption='[[6ouv]], [[Resolution|resolution]] 1.94Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6ouv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OUV FirstGlance]. <br> | + | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6ouw|6ouw]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dxs, DR_1475 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_synthase 1-deoxy-D-xylulose-5-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.2.1.7 2.2.1.7] </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=6ouv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ouv OCA], [http://pdbe.org/6ouv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ouv RCSB], [http://www.ebi.ac.uk/pdbsum/6ouv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ouv ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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] | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Micrococcus radiodurans raj et al. 1960]] | + | [[Category: Deinococcus radiodurans]] |
| - | [[Category: 1-deoxy-D-xylulose-5-phosphate synthase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Chen, P Y.T]] | + | [[Category: Chen PY-T]] |
| - | [[Category: Drennan, C L]] | + | [[Category: Drennan CL]] |
| - | [[Category: 1-deoxy-d-xylulose 5-phosphate synthase]]
| + | |
| - | [[Category: Change]]
| + | |
| - | [[Category: Dxp]]
| + | |
| - | [[Category: Thdp]]
| + | |
| - | [[Category: The mep pathway]]
| + | |
| - | [[Category: Thiamine diphosphate]]
| + | |
| - | [[Category: Thiamine pyrophosphate]]
| + | |
| - | [[Category: Tpp]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
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]
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Chen PY, DeColli AA, Freel Meyers CL, Drennan CL. X-ray crystallography-based structural elucidation of enzyme-bound intermediates along the 1deoxydxylulose 5-phosphate synthase reaction coordinate. J Biol Chem. 2019 Jun 25. pii: RA119.009321. doi: 10.1074/jbc.RA119.009321. PMID:31239351 doi:http://dx.doi.org/10.1074/jbc.RA119.009321
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