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| | ==Sulfolobus sulfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDPG== | | ==Sulfolobus sulfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDPG== |
| - | <StructureSection load='6g3z' size='340' side='right' caption='[[6g3z]], [[Resolution|resolution]] 2.35Å' scene=''> | + | <StructureSection load='6g3z' size='340' side='right'caption='[[6g3z]], [[Resolution|resolution]] 2.35Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6g3z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'saccharolobus_solfataricus' 'saccharolobus solfataricus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G3Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G3Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6g3z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G3Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6G3Z FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ELE:2-keto+3+deoxy+6+phospho+gluconate'>ELE</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</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]] 2.35Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4uxd|4uxd]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ELE:(4~{S},5~{R})-4,5-bis(oxidanyl)-2-oxidanylidene-6-phosphonooxy-hexanoic+acid'>ELE</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate_aldolase 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.55 4.1.2.55] </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=6g3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g3z OCA], [https://pdbe.org/6g3z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6g3z RCSB], [https://www.ebi.ac.uk/pdbsum/6g3z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6g3z ProSAT]</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=6g3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g3z OCA], [http://pdbe.org/6g3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g3z RCSB], [http://www.ebi.ac.uk/pdbsum/6g3z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g3z ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KDGA_SULSF KDGA_SULSF]] Involved in the degradation of glucose and galactose 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:10527934</ref> <ref>PMID:12824170</ref> <ref>PMID:16330030</ref> | + | [https://www.uniprot.org/uniprot/KDGA_SACSO KDGA_SACSO] Involved in the degradation of glucose and galactose 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:10527934</ref> <ref>PMID:12824170</ref> <ref>PMID:16330030</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6g3z" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6g3z" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Aldolase 3D structures|Aldolase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Saccharolobus solfataricus]] | | [[Category: Saccharolobus solfataricus]] |
| - | [[Category: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase]]
| + | [[Category: Crennell SJ]] |
| - | [[Category: Crennell, S J]] | + | |
| - | [[Category: 2-dehydro-3-deoxy-6-phospho-d-gluconate]]
| + | |
| - | [[Category: 2-keto-3-deoxygluconate aldolase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Sulfolobus sulfataricus]]
| + | |
| Structural highlights
Function
KDGA_SACSO Involved in the degradation of glucose and galactose 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.[1] [2] [3]
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[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Buchanan CL, Connaris H, Danson MJ, Reeve CD, Hough DW. An extremely thermostable aldolase from Sulfolobus solfataricus with specificity for non-phosphorylated substrates. Biochem J. 1999 Nov 1;343 Pt 3:563-70. PMID:10527934
- ↑ Lamble HJ, Heyer NI, Bull SD, Hough DW, Danson MJ. Metabolic pathway promiscuity in the archaeon Sulfolobus solfataricus revealed by studies on glucose dehydrogenase and 2-keto-3-deoxygluconate aldolase. J Biol Chem. 2003 Sep 5;278(36):34066-72. Epub 2003 Jun 24. PMID:12824170 doi:http://dx.doi.org/10.1074/jbc.M305818200
- ↑ Lamble HJ, Theodossis A, Milburn CC, Taylor GL, Bull SD, Hough DW, Danson MJ. Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett. 2005 Dec 19;579(30):6865-9. Epub 2005 Dec 1. PMID:16330030 doi:http://dx.doi.org/10.1016/j.febslet.2005.11.028
- ↑ Zaitsev V, Johnsen U, Reher M, Ortjohann M, Taylor GL, Danson MJ, Schonheit P, Crennell SJ. 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. Biochemistry. 2018 Jun 13. doi: 10.1021/acs.biochem.8b00535. PMID:29812914 doi:http://dx.doi.org/10.1021/acs.biochem.8b00535
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