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| ==Crystal structure of a proposed galactarolactone cycloisomerase from agrobacterium tumefaciens, TARGET EFI-500704, WITH BOUND CA, DISORDERED LOOPS== | | ==Crystal structure of a proposed galactarolactone cycloisomerase from agrobacterium tumefaciens, TARGET EFI-500704, WITH BOUND CA, DISORDERED LOOPS== |
| <StructureSection load='4ggb' size='340' side='right' caption='[[4ggb]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='4ggb' size='340' side='right'caption='[[4ggb]], [[Resolution|resolution]] 2.00Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4ggb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrt5 Agrt5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GGB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GGB FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4ggb]] is a 1 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=4GGB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GGB FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2Å</td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Atu3139 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRT5])</td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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=4ggb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ggb OCA], [http://pdbe.org/4ggb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ggb RCSB], [http://www.ebi.ac.uk/pdbsum/4ggb PDBsum]</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=4ggb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ggb OCA], [https://pdbe.org/4ggb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ggb RCSB], [https://www.ebi.ac.uk/pdbsum/4ggb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ggb ProSAT]</span></td></tr> |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/GCI_AGRT5 GCI_AGRT5]] Catalyzes the ring opening of D-galactaro-1,4-lactone to yield 5-keto-4-deoxy-D-glucarate (KDG) via a beta-elimination reaction. This is a step in the oxidative degradation pathway of D-galacturonate, which allows A.tumefaciens to utilize D-galacturonate as a sole carbon source. To a lesser extent, can also use D-glucaro-1,4-lactone as substrate to produce KDG, but cannot use D-galactaro-1,5-lactone, D-glucaro-6,3-lactone and linear D-glucarate.<ref>PMID:22493433</ref> <ref>PMID:24450804</ref> | | [https://www.uniprot.org/uniprot/GCI_AGRFC GCI_AGRFC] Catalyzes the ring opening of D-galactaro-1,4-lactone to yield 5-keto-4-deoxy-D-glucarate (KDG) via a beta-elimination reaction. This is a step in the oxidative degradation pathway of D-galacturonate, which allows A.tumefaciens to utilize D-galacturonate as a sole carbon source. To a lesser extent, can also use D-glucaro-1,4-lactone as substrate to produce KDG, but cannot use D-galactaro-1,5-lactone, D-glucaro-6,3-lactone and linear D-glucarate.<ref>PMID:22493433</ref> <ref>PMID:24450804</ref> |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| Pectin is found in the cell wall of plants and is often discarded as waste. A number of research groups are interested in redirecting this biomass waste stream for the production of fuel and bulk chemicals. The primary monomeric subunit of this polysaccharide is D-galacturonate, a six-carbon acid sugar that is degraded in a five-step pathway to central metabolic intermediates by some bacteria, including Agrobacterium tumefaciens. In the third step of the pathway, D-galactaro-1,4-lactone is converted to 2-keto-3-deoxy-L-threo-hexarate by a member of the mandelate racemase subgroup of the enolase superfamily with a novel activity for the superfamily. The 1.6 A resolution structure of this enzyme was determined, revealing an overall modified (beta/alpha)7beta TIM-barrel domain, a hallmark of the superfamily. D-Galactaro-1,4-lactone was manually docked into the active site located at the interface between the N-terminal lid domain and the C-terminal barrel domain. On the basis of the position of the lactone in the active site, Lys166 is predicted to be the active-site base responsible for abstraction of the alpha proton. His296 on the opposite side of the active site is predicted to be the general acid that donates a proton to the beta carbon as the lactone ring opens. The lactone ring appears to be oriented within the active site by stacking interactions with Trp298.
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| Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation.,Vetting MW, Bouvier JT, Gerlt JA, Almo SC Acta Crystallogr F Struct Biol Commun. 2016 Jan;72(Pt 1):36-41. doi:, 10.1107/S2053230X15023286. Epub 2016 Jan 1. PMID:26750482<ref>PMID:26750482</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 4ggb" style="background-color:#fffaf0;"></div>
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| == References == | | == References == |
| <references/> | | <references/> |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Agrt5]] | | [[Category: Agrobacterium fabrum str. C58]] |
| [[Category: Almo, S C]] | | [[Category: Large Structures]] |
| [[Category: Bouvier, J T]] | | [[Category: Almo SC]] |
| [[Category: EFI, Enzyme Function Initiative]] | | [[Category: Bouvier JT]] |
| [[Category: Gerlt, J A]] | | [[Category: Gerlt JA]] |
| [[Category: Imker, H J]] | | [[Category: Imker HJ]] |
| [[Category: Morisco, L L]] | | [[Category: Morisco LL]] |
| [[Category: Sojitra, S]] | | [[Category: Sojitra S]] |
| [[Category: Vetting, M W]] | | [[Category: Vetting MW]] |
| [[Category: Wasserman, S R]] | | [[Category: Wasserman SR]] |
| [[Category: Efi]]
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| [[Category: Enolase]]
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| [[Category: Enzyme function initiative]]
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| [[Category: Isomerase]]
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| [[Category: Proposed galactarolactone cycloisomerase]]
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| [[Category: Structural genomic]]
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