5hwm: Difference between revisions
New page: '''Unreleased structure''' The entry 5hwm is ON HOLD Authors: Taberman, H., Parkkinen, T., Hakulinen, N., Rouvinen, J. Description: Crystal structure of keto-deoxy-D-galactarate dehydr... |
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The | ==Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid== | ||
<StructureSection load='5hwm' size='340' side='right'caption='[[5hwm]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5hwm]] 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=5HWM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HWM 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=5hwm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hwm OCA], [https://pdbe.org/5hwm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hwm RCSB], [https://www.ebi.ac.uk/pdbsum/5hwm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hwm 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> | |||
[[Category: | </div> | ||
[[Category: Hakulinen | <div class="pdbe-citations 5hwm" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: Taberman | __TOC__ | ||
</StructureSection> | |||
[[Category: Agrobacterium fabrum str. C58]] | |||
[[Category: Large Structures]] | |||
[[Category: Hakulinen N]] | |||
[[Category: Parkkinen T]] | |||
[[Category: Rouvinen J]] | |||
[[Category: Taberman H]] | |||
Latest revision as of 13:57, 16 August 2023
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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