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| | <StructureSection load='4b5s' size='340' side='right'caption='[[4b5s]], [[Resolution|resolution]] 1.68Å' scene=''> | | <StructureSection load='4b5s' size='340' side='right'caption='[[4b5s]], [[Resolution|resolution]] 1.68Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4b5s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecolc Ecolc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B5S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B5S FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4b5s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_ATCC_8739 Escherichia coli ATCC 8739]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B5S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B5S FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3GR:GLYCERALDEHYDE'>3GR</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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]] 1.68Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4b5t|4b5t]], [[4b5u|4b5u]], [[4b5v|4b5v]], [[4b5w|4b5w]], [[4b5x|4b5x]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3GR:GLYCERALDEHYDE'>3GR</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-dehydro-3-deoxyglucarate_aldolase 2-dehydro-3-deoxyglucarate aldolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.20 4.1.2.20] </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=4b5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b5s OCA], [https://pdbe.org/4b5s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b5s RCSB], [https://www.ebi.ac.uk/pdbsum/4b5s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b5s 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=4b5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b5s OCA], [https://pdbe.org/4b5s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b5s RCSB], [https://www.ebi.ac.uk/pdbsum/4b5s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b5s ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/HPCH_ECOLC HPCH_ECOLC]] Catalyzes the reversible retro-aldol cleavage of 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) to pyruvate and succinic semialdehyde.[HAMAP-Rule:MF_01292]
| + | [https://www.uniprot.org/uniprot/HPCH_ECOLC HPCH_ECOLC] Catalyzes the reversible retro-aldol cleavage of 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) to pyruvate and succinic semialdehyde.[HAMAP-Rule:MF_01292] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 2-dehydro-3-deoxyglucarate aldolase]] | + | [[Category: Escherichia coli ATCC 8739]] |
| - | [[Category: Ecolc]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Coincon, M]] | + | [[Category: Coincon M]] |
| - | [[Category: Seah, S Y.K]] | + | [[Category: Seah SYK]] |
| - | [[Category: Sygusch, J]] | + | [[Category: Sygusch J]] |
| - | [[Category: Wang, W]] | + | [[Category: Wang W]] |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
4b5s is a 2 chain structure with sequence from Escherichia coli ATCC 8739. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.68Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
HPCH_ECOLC Catalyzes the reversible retro-aldol cleavage of 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) to pyruvate and succinic semialdehyde.[HAMAP-Rule:MF_01292]
Publication Abstract from PubMed
Crystal structures of divalent metal dependent pyruvate aldolase, HpaI, in complex with substrate and cleavage products were determined to 1.8 - 2.0 A resolution. The enzyme-substrate complex with 4-hydroxy-2-ketoheptane-1,7-dioate indicates water molecule, W2, bound to the divalent metal ion initiates C3-C4 bond cleavage. Binding mode of the aldehyde donor delineated a solvent filled capacious binding locus lined with predominantly hydrophobic residues. Absence of direct interactions with the aldehyde aliphatic carbons accounts for the broad specificity and lack of stereospecific control by the enzyme. Enzymatic complex structures formed with keto acceptors, pyruvate and 2-ketobutyrate, revealed bidentate interaction with the divalent metal ion by C1-carboxyl and C2-carbonyl oxygens and water molecule W4 that is within close contact of the C3 carbon. Arg70 assumes a multivalent role through its guanidinium moiety interacting with all active site enzymatic species: C2 oxygen in substrate, pyruvate and ketobutyrate, substrate C4 hydroxyl, aldehyde C1 oxygen, and W4. The multiple interactions made by Arg70 stabilize the negatively charged C4 oxygen following proton abstraction, the aldehyde alignment in aldol condensation, the pyruvate enolate upon aldol cleavage, as well as supporting proton exchange at C3. This role is corroborated by loss of aldol cleavage ability and pyruvate C3-proton exchange activity, and by a 730-fold increase in dissociation constant towards the pyruvate enolate analogue, oxalate, in the Arg70Ala mutant. Based on the crystal structures, a mechanism is proposed involving the two enzyme-bound water molecules, W2 and W4, in acid/base catalysis that facilitates reversible aldol cleavage. The same reaction mechanism promotes decarboyxlation of oxaloacetate.
Crystal structure of reaction intermediates in pyruvate Class II aldolase: Substrate Cleavage, Enolate Stabilization and Substrate Specificity.,Coincon M, Wang W, Sygusch J, Seah SY J Biol Chem. 2012 Aug 20. PMID:22908224[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Coincon M, Wang W, Sygusch J, Seah SY. Crystal structure of reaction intermediates in pyruvate Class II aldolase: Substrate Cleavage, Enolate Stabilization and Substrate Specificity. J Biol Chem. 2012 Aug 20. PMID:22908224 doi:http://dx.doi.org/10.1074/jbc.M112.400705
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