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| | ==KDPGal complexed to KDPGal== | | ==KDPGal complexed to KDPGal== |
| - | <StructureSection load='2v82' size='340' side='right' caption='[[2v82]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='2v82' size='340' side='right'caption='[[2v82]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2v82]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V82 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V82 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2v82]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V82 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V82 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KDP:2-KETO-DEOXY-GALACTOSE'>KDP</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]] 2.1Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KDP:2-KETO-DEOXY-GALACTOSE'>KDP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2j6q|2j6q]], [[2j6n|2j6n]], [[2v81|2v81]]</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=2v82 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v82 OCA], [https://pdbe.org/2v82 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v82 RCSB], [https://www.ebi.ac.uk/pdbsum/2v82 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v82 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/2-dehydro-3-deoxy-6-phosphogalactonate_aldolase 2-dehydro-3-deoxy-6-phosphogalactonate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.21 4.1.2.21] </span></td></tr>
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| - | <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=2v82 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v82 OCA], [http://pdbe.org/2v82 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v82 RCSB], [http://www.ebi.ac.uk/pdbsum/2v82 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2v82 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DGOA_ECOLI DGOA_ECOLI]] Involved in the degradation of galactose via the DeLey-Doudoroff pathway. Catalyzes the reversible, stereospecific retro-aldol cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) to pyruvate and D-glyceraldehyde-3-phosphate. In the synthetic direction, it catalyzes the addition of pyruvate to electrophilic aldehydes with re-facial selectivity. It can use a limited number of aldehyde substrates, including D-glyceraldehyde-3-phosphate (natural substrate), D-glyceraldehyde, glycolaldehyde, 2-pyridinecarboxaldehyde, D-ribose, D-erythrose and D-threose. It efficiently catalyzes aldol addition only using pyruvate as the nucleophilic component and accepts both stereochemical configurations at C2 of the electrophile.<ref>PMID:324806</ref> <ref>PMID:17981470</ref> | + | [https://www.uniprot.org/uniprot/DGOA_ECOLI DGOA_ECOLI] Involved in the degradation of galactose via the DeLey-Doudoroff pathway. Catalyzes the reversible, stereospecific retro-aldol cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) to pyruvate and D-glyceraldehyde-3-phosphate. In the synthetic direction, it catalyzes the addition of pyruvate to electrophilic aldehydes with re-facial selectivity. It can use a limited number of aldehyde substrates, including D-glyceraldehyde-3-phosphate (natural substrate), D-glyceraldehyde, glycolaldehyde, 2-pyridinecarboxaldehyde, D-ribose, D-erythrose and D-threose. It efficiently catalyzes aldol addition only using pyruvate as the nucleophilic component and accepts both stereochemical configurations at C2 of the electrophile.<ref>PMID:324806</ref> <ref>PMID:17981470</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Aldolase|Aldolase]] | + | *[[Aldolase 3D structures|Aldolase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase]] | + | [[Category: Large Structures]] |
| - | [[Category: Naismith, J H]] | + | [[Category: Naismith JH]] |
| - | [[Category: Aldolase]]
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| - | [[Category: Kdpgal]]
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| - | [[Category: Lyase]]
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| Structural highlights
Function
DGOA_ECOLI Involved in the degradation of galactose via the DeLey-Doudoroff pathway. Catalyzes the reversible, stereospecific retro-aldol cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) to pyruvate and D-glyceraldehyde-3-phosphate. In the synthetic direction, it catalyzes the addition of pyruvate to electrophilic aldehydes with re-facial selectivity. It can use a limited number of aldehyde substrates, including D-glyceraldehyde-3-phosphate (natural substrate), D-glyceraldehyde, glycolaldehyde, 2-pyridinecarboxaldehyde, D-ribose, D-erythrose and D-threose. It efficiently catalyzes aldol addition only using pyruvate as the nucleophilic component and accepts both stereochemical configurations at C2 of the electrophile.[1] [2]
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
2-Keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolases catalyze an identical reaction differing in substrate specificity in only the configuration of a single stereocenter. However, the proteins show little sequence homology at the amino acid level. Here we investigate the determinants of substrate selectivity of these enzymes. The Escherichia coli KDPGal aldolase gene, cloned into a T7 expression vector and overexpressed in E. coli, catalyzes retro-aldol cleavage of the natural substrate, KDPGal, with values of k(cat)/K(M) and k(cat) of 1.9x10(4)M(-1)s(-1) and 4s(-1), respectively. In the synthetic direction, KDPGal aldolase efficiently catalyzes an aldol addition using a limited number of aldehyde substrates, including d-glyceraldehyde-3-phosphate (natural substrate), d-glyceraldehyde, glycolaldehyde, and 2-pyridinecarboxaldehyde. A preparative scale reaction between 2-pyridinecarboxaldehyde and pyruvate catalyzed by KDPGal aldolase produced the aldol adduct of the R stereochemistry in >99.7% ee, a result complementary to that observed using the related KDPG aldolase. The native crystal structure has been solved to a resolution of 2.4A and displays the same (alpha/beta)(8) topology, as KDPG aldolase. We have also determined a 2.1A structure of a Schiff base complex between the enzyme and its substrate. This model predicts that a single amino acid change, T161 in KDPG aldolase to V154 in KDPGal aldolase, plays an important role in determining the stereochemical course of enzyme catalysis and this prediction was borne out by site-directed mutagenesis studies. However, additional changes in the enzyme sequence are required to prepare an enzyme with both high catalytic efficiency and altered stereochemistry.
Characterization and crystal structure of Escherichia coli KDPGal aldolase.,Walters MJ, Srikannathasan V, McEwan AR, Naismith JH, Fierke CA, Toone EJ Bioorg Med Chem. 2008 Jan 15;16(2):710-20. Epub 2007 Oct 18. PMID:17981470[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Deacon J, Cooper RA. D-Galactonate utilisation by enteric bacteria. The catabolic pathway in Escherichia coli. FEBS Lett. 1977 May 15;77(2):201-5. PMID:324806
- ↑ Walters MJ, Srikannathasan V, McEwan AR, Naismith JH, Fierke CA, Toone EJ. Characterization and crystal structure of Escherichia coli KDPGal aldolase. Bioorg Med Chem. 2008 Jan 15;16(2):710-20. Epub 2007 Oct 18. PMID:17981470 doi:10.1016/j.bmc.2007.10.043
- ↑ Walters MJ, Srikannathasan V, McEwan AR, Naismith JH, Fierke CA, Toone EJ. Characterization and crystal structure of Escherichia coli KDPGal aldolase. Bioorg Med Chem. 2008 Jan 15;16(2):710-20. Epub 2007 Oct 18. PMID:17981470 doi:10.1016/j.bmc.2007.10.043
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