4ggb: Difference between revisions

← Older edit Newer edit →

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==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]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ggb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. 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 [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>
 </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>
-<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=358 Agrobacterium tumefaciens])</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='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://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'>[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>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/A9CEQ8_AGRT5 A9CEQ8_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>
+[[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>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4ggb" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Agrobacterium tumefaciens]]
+[[Category: Agrt5]]
 [[Category: Almo, S C]]
 [[Category: Bouvier, J T]]