3ww3
From Proteopedia
(Difference between revisions)
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==X-ray structures of Cellulomonas parahominis L-ribose isomerase with no ligand== | ==X-ray structures of Cellulomonas parahominis L-ribose isomerase with no ligand== | ||
| - | <StructureSection load='3ww3' size='340' side='right'caption='[[3ww3]]' scene=''> | + | <StructureSection load='3ww3' size='340' side='right'caption='[[3ww3]], [[Resolution|resolution]] 1.90Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ww3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellulomonas_parahominis Cellulomonas parahominis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW3 FirstGlance]. <br> |
| - | </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=3ww3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww3 OCA], [https://pdbe.org/3ww3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ww3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ww3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww3 ProSAT]</span></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]] 1.9Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=3ww3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww3 OCA], [https://pdbe.org/3ww3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ww3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ww3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/L0N3Y0_9CELL L0N3Y0_9CELL] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | L-Ribose isomerase from Cellulomonas parahominis MB426 (CpL-RI) can catalyze the isomerization between L-ribose and L-ribulose, which are non-abundant in nature and called rare sugars. CpL-RI has a broad substrate specificity and can catalyze the isomerization between D-lyxose and D-xylulose, D-talose and D-tagatose, L-allose and L-psicose, L-gulose and L-sorbose, and D-mannose and D-fructose. To elucidate the molecular basis underlying the substrate recognition mechanism of CpL-RI, the crystal structures of CpL-RI alone and in complexes with L-ribose, L-allose, and L-psicose were determined. The structure of CpL-RI was very similar to that of L-ribose isomerase from Acinetobacter sp. strain DL-28, previously determined by us. CpL-RI had a cupin-type beta-barrel structure, and the catalytic site was detected between two large beta-sheets with a bound metal ion. The bound substrates coordinated to the metal ion, and Glu113 and Glu204 were shown to act as acid/base catalysts in the catalytic reaction via a cis-enediol intermediate. Glu211 and Arg243 were found to be responsible for the recognition of substrates with various configurations at 4- and 5-positions of sugar. CpL-RI formed a homo-tetramer in crystals, and the catalytic site independently consisted of residues within a subunit, suggesting that the catalytic site acted independently. Crystal structure and site-direct mutagenesis analyses showed that the tetramer structure is essential for the enzyme activity and that each subunit of CpL-RI could be structurally stabilized by intermolecular contacts with other subunits. The results of growth complementation assays suggest that CpL-RI is involved in a novel metabolic pathway using L-ribose as a carbon source. | ||
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| + | Essentiality of tetramer formation of Cellulomonas parahominis L-ribose isomerase involved in novel L-ribose metabolic pathway.,Terami Y, Yoshida H, Uechi K, Morimoto K, Takata G, Kamitori S Appl Microbiol Biotechnol. 2015 Feb 8. PMID:25661811<ref>PMID:25661811</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 3ww3" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Cellulomonas parahominis]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Kamitori S]] | [[Category: Kamitori S]] | ||
Current revision
X-ray structures of Cellulomonas parahominis L-ribose isomerase with no ligand
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