4uxd
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==2-keto 3-deoxygluconate aldolase from Picrophilus torridus== | |
| + | <StructureSection load='4uxd' size='340' side='right'caption='[[4uxd]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[4uxd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Picrophilus_torridus Picrophilus torridus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UXD 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]] 2.5Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=4uxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxd OCA], [https://pdbe.org/4uxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uxd RCSB], [https://www.ebi.ac.uk/pdbsum/4uxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uxd ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/KDGA_PICTO KDGA_PICTO] Involved in the degradation of glucose via the Entner-Doudoroff pathway. Catalyzes the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxygluconate (KDG) forming pyruvate and glyceraldehyde 3-phosphate or glyceraldehyde, respectively. It is also able to catalyze the reversible cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) and 2-keto-3-deoxygalactonate (KDGal). It is equally active with both D- and L-glyceraldehyde.<ref>PMID:20023024</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The thermoacidophilic archaea Picrophilus torridus and Sulfolobus solfataricus catabolize glucose via a nonphosphorylative Entner-Doudoroff pathway and a branched Entner-Doudoroff pathway, respectively. Key enzymes for these Entner-Doudoroff pathways are the aldolases, 2-keto-3-deoxygluconate aldolase (KDG-aldolase) and 2-keto-3-deoxy-6-phosphogluconate aldolase [KD(P)G-aldolase]. KDG-aldolase from P. torridus (Pt-KDG-aldolase) is highly specific for the nonphosphorylated substrate, 2-keto-3-deoxygluconate (KDG), whereas KD(P)G-aldolase from S. solfataricus [Ss-KD(P)G-aldolase] is an enzyme that catalyzes the cleavage of both KDG and 2-keto-3-deoxy-6-phosphogluconate (KDPG), with a preference for KDPG. The structural basis for the high specificity of Pt-KDG-aldolase for KDG as compared to the more promiscuous Ss-KD(P)G-aldolase has not been analyzed before. In this work, we report the elucidation of the structure of Ss-KD(P)G-aldolase in complex with KDPG at 2.35 A and that of KDG-aldolase from P. torridus at 2.50 A resolution. By superimposition of the active sites of the two enzymes, and subsequent site-directed mutagenesis studies, a network of four amino acids, namely, Arg106, Tyr132, Arg237, and Ser241, was identified in Ss-KD(P)G-aldolase that interact with the negatively charged phosphate group of KDPG, thereby increasing the affinity of the enzyme for KDPG. This KDPG-binding network is absent in Pt-KDG-aldolase, which explains the low catalytic efficiency of KDPG cleavage. | ||
| - | + | Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3-deoxy-6-phosphogluconate Aldolase in Complex with 2-Keto-3-deoxy-6-phosphogluconate.,Zaitsev V, Johnsen U, Reher M, Ortjohann M, Taylor GL, Danson MJ, Schonheit P, Crennell SJ Biochemistry. 2018 Jun 13. doi: 10.1021/acs.biochem.8b00535. PMID:29812914<ref>PMID:29812914</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 4uxd" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: Danson | + | <references/> |
| - | [[Category: | + | __TOC__ |
| - | [[Category: | + | </StructureSection> |
| - | [[Category: Schoenheit | + | [[Category: Large Structures]] |
| - | [[Category: | + | [[Category: Picrophilus torridus]] |
| - | [[Category: | + | [[Category: Crennell SJ]] |
| + | [[Category: Danson MJ]] | ||
| + | [[Category: Johnsen U]] | ||
| + | [[Category: Priftis A]] | ||
| + | [[Category: Reher M]] | ||
| + | [[Category: Schoenheit P]] | ||
| + | [[Category: Taylor GL]] | ||
| + | [[Category: Zaitsev V]] | ||
Current revision
2-keto 3-deoxygluconate aldolase from Picrophilus torridus
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