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| | <StructureSection load='2o1x' size='340' side='right'caption='[[2o1x]], [[Resolution|resolution]] 2.90Å' scene=''> | | <StructureSection load='2o1x' size='340' side='right'caption='[[2o1x]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2o1x]] is a 4 chain structure with sequence from [https://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=2O1X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O1X FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2o1x]] is a 4 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=2O1X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O1X FirstGlance]. <br> |
| - | </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=TDP:THIAMIN+DIPHOSPHATE'>TDP</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]] 2.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2o1s|2o1s]]</div></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=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dxs ([https://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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_synthase 1-deoxy-D-xylulose-5-phosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.2.1.7 2.2.1.7] </span></td></tr>
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| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2o1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o1x OCA], [https://pdbe.org/2o1x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o1x RCSB], [https://www.ebi.ac.uk/pdbsum/2o1x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o1x 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=2o1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o1x OCA], [https://pdbe.org/2o1x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o1x RCSB], [https://www.ebi.ac.uk/pdbsum/2o1x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o1x ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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]
| + | [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] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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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]]
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| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Busch, M]] | + | [[Category: Busch M]] |
| - | [[Category: Lange, G]] | + | [[Category: Lange G]] |
| - | [[Category: Tong, L]] | + | [[Category: Tong L]] |
| - | [[Category: Usunow, G]] | + | [[Category: Usunow G]] |
| - | [[Category: Xiang, S]] | + | [[Category: Xiang S]] |
| - | [[Category: 1-deoxy-d-xylulose-5-phosphate]]
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| - | [[Category: Dx]]
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| - | [[Category: Isoprenoid]]
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| - | [[Category: Thiamin]]
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| - | [[Category: Transferase]]
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| 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]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Isopentenyl pyrophosphate (IPP) is a common precursor for the synthesis of all isoprenoids, which have important functions in living organisms. IPP is produced by the mevalonate pathway in archaea, fungi, and animals. In contrast, IPP is synthesized by a mevalonate-independent pathway in most bacteria, algae, and plant plastids. 1-Deoxy-D-xylulose 5-phosphate synthase (DXS) catalyzes the first and the rate-limiting step of the mevalonate-independent pathway and is an attractive target for the development of novel antibiotics, antimalarials, and herbicides. We report here the first structural information on DXS, from Escherichia coli and Deinococcus radiodurans, in complex with the coenzyme thiamine pyrophosphate (TPP). The structure contains three domains (I, II, and III), each of which bears homology to the equivalent domains in transketolase and the E1 subunit of pyruvate dehydrogenase. However, DXS has a novel arrangement of these domains as compared with the other enzymes, such that the active site of DXS is located at the interface of domains I and II in the same monomer, whereas that of transketolase is located at the interface of the dimer. The coenzyme TPP is mostly buried in the complex, but the C-2 atom of its thiazolium ring is exposed to a pocket that is the substrate-binding site. The structures identify residues that may have important roles in catalysis, which have been confirmed by our mutagenesis studies.
Crystal structure of 1-deoxy-D-xylulose 5-phosphate synthase, a crucial enzyme for isoprenoids biosynthesis.,Xiang S, Usunow G, Lange G, Busch M, Tong L J Biol Chem. 2007 Jan 26;282(4):2676-82. Epub 2006 Nov 29. PMID:17135236[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Xiang S, Usunow G, Lange G, Busch M, Tong L. Crystal structure of 1-deoxy-D-xylulose 5-phosphate synthase, a crucial enzyme for isoprenoids biosynthesis. J Biol Chem. 2007 Jan 26;282(4):2676-82. Epub 2006 Nov 29. PMID:17135236 doi:10.1074/jbc.M610235200
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