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| | <StructureSection load='4ur7' size='340' side='right'caption='[[4ur7]], [[Resolution|resolution]] 1.50Å' scene=''> | | <StructureSection load='4ur7' size='340' side='right'caption='[[4ur7]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ur7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UR7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UR7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ur7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UR7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UR7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.499Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ur5|4ur5]], [[4ur8|4ur8]]</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=4ur7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur7 OCA], [https://pdbe.org/4ur7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ur7 RCSB], [https://www.ebi.ac.uk/pdbsum/4ur7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ur7 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=4ur7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur7 OCA], [http://pdbe.org/4ur7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ur7 RCSB], [http://www.ebi.ac.uk/pdbsum/4ur7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ur7 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/KDGD_AGRFC KDGD_AGRFC] |
| | <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: Agrobacterium tumefaciens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hakulinen, N]] | + | [[Category: Hakulinen N]] |
| - | [[Category: Parkkinen, T]] | + | [[Category: Parkkinen T]] |
| - | [[Category: Rouvinen, J]] | + | [[Category: Rouvinen J]] |
| - | [[Category: Taberman, H]] | + | [[Category: Taberman H]] |
| - | [[Category: Biocatalysis]]
| + | |
| - | [[Category: D-galacturonic acid]]
| + | |
| - | [[Category: Decarboxylate]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Oxidative pathway]]
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| Structural highlights
Function
KDGD_AGRFC
Publication Abstract from PubMed
Agrobacterium tumefaciens (At) strain C58 contains an oxidative enzyme pathway that can function on both D-glucuronic and D-galacturonic acid. The corresponding gene coding for At KDG dehydratase is located in the same gene cluster as those coding for uronate dehydrogenase (At Udh) and galactarolactone cycloisomerase (At Gci) which we have previously characterised. Here, we present the kinetic characterisation and crystal structure of At keto-deoxy-D-galactarate (KDG, 3-deoxy-2-keto-L-threo-hexulosarate) dehydratase, which catalyses the next step, the decarboxylating hydrolyase reaction of KDG to produce alpha-ketoglutaric semialdehyde (alpha-KGSA) and carbon dioxide. The crystal structures of At KDG dehydratase and its complexes with pyruvate and 2-oxoadipic acid, two substrate analogues, were determined to 1.7 A, 1.5 A, and 2.1 A resolutions, respectively. Furthermore, mass spectrometry was used to confirm reaction end-products. The results lead us to propose a structure-based mechanism for At KDG dehydratase, suggesting that while the enzyme belongs to the Class I aldolase protein family, it does not follow a typical retro-aldol condensation mechanism.
The Structure and Function of a Decarboxylating Agrobacterium tumefaciens Keto-deoxy-D-galactarate Dehydratase.,Taberman H, Andberg MB, Parkkinen T, Janis J, Penttila M, Hakulinen N, Koivula A, Rouvinen J Biochemistry. 2014 Dec 2. PMID:25454257[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Taberman H, Andberg MB, Parkkinen T, Janis J, Penttila M, Hakulinen N, Koivula A, Rouvinen J. The Structure and Function of a Decarboxylating Agrobacterium tumefaciens Keto-deoxy-D-galactarate Dehydratase. Biochemistry. 2014 Dec 2. PMID:25454257 doi:http://dx.doi.org/10.1021/bi501290k
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