4ur8: Difference between revisions
New page: '''Unreleased structure''' The entry 4ur8 is ON HOLD until sometime in the future Authors: Taberman, H., Parkkinen, T., Hakulinen, N., Rouvinen, J. Description: Crystal structure of ke... |
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The | ==Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid== | ||
<StructureSection load='4ur8' size='340' side='right'caption='[[4ur8]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4ur8]] 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=4UR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UR8 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.097Å</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=OOG:2-OXOADIPIC+ACID'>OOG</scene></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=4ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ur8 OCA], [https://pdbe.org/4ur8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ur8 RCSB], [https://www.ebi.ac.uk/pdbsum/4ur8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ur8 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/KDGD_AGRFC KDGD_AGRFC] | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:25454257</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4ur8" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Agrobacterium tumefaciens]] | |||
[[Category: Large Structures]] | |||
[[Category: Hakulinen N]] | |||
[[Category: Parkkinen T]] | |||
[[Category: Rouvinen J]] | |||
[[Category: Taberman H]] | |||
Latest revision as of 13:33, 10 January 2024
Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acidCrystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid
Structural highlights
FunctionPublication Abstract from PubMedAgrobacterium 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
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