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| | <StructureSection load='2iz1' size='340' side='right'caption='[[2iz1]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='2iz1' size='340' side='right'caption='[[2iz1]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2iz1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_lactis"_lister_1873 "bacterium lactis" lister 1873]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IZ1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2IZ1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2iz1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IZ1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATR:2-MONOPHOSPHOADENOSINE-5-DIPHOSPHATE'>ATR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=RES:4-PHOSPHO-D-ERYTHRONOHYDROXAMIC+ACID'>RES</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2iyo|2iyo]], [[2iyp|2iyp]], [[2iz0|2iz0]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATR:2-MONOPHOSPHOADENOSINE-5-DIPHOSPHATE'>ATR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=RES:4-PHOSPHO-D-ERYTHRONOHYDROXAMIC+ACID'>RES</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(NADP(+)-dependent,_decarboxylating) Phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </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=2iz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iz1 OCA], [https://pdbe.org/2iz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iz1 RCSB], [https://www.ebi.ac.uk/pdbsum/2iz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iz1 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2iz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iz1 OCA], [http://pdbe.org/2iz1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2iz1 RCSB], [http://www.ebi.ac.uk/pdbsum/2iz1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2iz1 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/6PGD_LACLM 6PGD_LACLM]] Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH (By similarity). | + | [https://www.uniprot.org/uniprot/6PGD_LACLM 6PGD_LACLM] Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH (By similarity). |
| | == 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: Bacterium lactis lister 1873]] | + | [[Category: Lactococcus lactis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hunter, W N]] | + | [[Category: Hunter WN]] |
| - | [[Category: Iulek, J]] | + | [[Category: Iulek J]] |
| - | [[Category: Sundaramoorthy, R]] | + | [[Category: Sundaramoorthy R]] |
| - | [[Category: Gluconate utilization]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Pentose shunt]]
| + | |
| Structural highlights
2iz1 is a 3 chain structure with sequence from Lactococcus lactis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.3Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
6PGD_LACLM Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH (By similarity).
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
Crystal structures of recombinant Lactococcus lactis 6-phosphogluconate dehydrogenase (LlPDH) in complex with substrate, cofactor, product and inhibitors have been determined. LlPDH shares significant sequence identity with the enzymes from sheep liver and the protozoan parasite Trypanosoma brucei for which structures have been reported. Comparisons indicate that the key residues in the active site are highly conserved, as are the interactions with the cofactor and the product ribulose 5-phosphate. However, there are differences in the conformation of the substrate 6-phosphogluconate which may reflect distinct states relevant to catalysis. Analysis of the complex formed with the potent inhibitor 4-phospho-d-erythronohydroxamic acid, suggests that this molecule does indeed mimic the high-energy intermediate state that it was designed to. The analysis also identified, as a contaminant by-product of the inhibitor synthesis, 4-phospho-d-erythronamide, which binds in similar fashion. LlPDH can now serve as a model system for structure-based inhibitor design targeting the enzyme from Trypanosoma species.
Crystal structures of a bacterial 6-phosphogluconate dehydrogenase reveal aspects of specificity, mechanism and mode of inhibition by analogues of high-energy reaction intermediates.,Sundaramoorthy R, Iulek J, Barrett MP, Bidet O, Ruda GF, Gilbert IH, Hunter WN FEBS J. 2007 Jan;274(1):275-86. PMID:17222187[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Sundaramoorthy R, Iulek J, Barrett MP, Bidet O, Ruda GF, Gilbert IH, Hunter WN. Crystal structures of a bacterial 6-phosphogluconate dehydrogenase reveal aspects of specificity, mechanism and mode of inhibition by analogues of high-energy reaction intermediates. FEBS J. 2007 Jan;274(1):275-86. PMID:17222187 doi:10.1111/j.1742-4658.2006.05585.x
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