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| | <StructureSection load='5hwn' size='340' side='right'caption='[[5hwn]], [[Resolution|resolution]] 1.50Å' scene=''> | | <StructureSection load='5hwn' size='340' side='right'caption='[[5hwn]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5hwn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrfc Agrfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HWN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HWN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5hwn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HWN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HWN FirstGlance]. <br> |
| - | </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=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]] 1.499Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ur7|4ur7]]</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=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Atu3140, AGR_L_3338 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRFC])</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=5hwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hwn OCA], [https://pdbe.org/5hwn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hwn RCSB], [https://www.ebi.ac.uk/pdbsum/5hwn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hwn 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/5-dehydro-4-deoxyglucarate_dehydratase 5-dehydro-4-deoxyglucarate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.41 4.2.1.41] </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=5hwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hwn OCA], [http://pdbe.org/5hwn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hwn RCSB], [http://www.ebi.ac.uk/pdbsum/5hwn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hwn 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: 5-dehydro-4-deoxyglucarate dehydratase]] | + | [[Category: Agrobacterium fabrum str. C58]] |
| - | [[Category: Agrfc]]
| + | |
| | [[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: Decarboxylating]]
| + | |
| - | [[Category: Dehydratase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Tim-barrel]]
| + | |
| 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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