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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]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='3ww3' size='340' side='right'caption='[[3ww3]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ww3]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ww1|3ww1]], [[3ww2|3ww2]], [[3ww4|3ww4]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ww1|3ww1]], [[3ww2|3ww2]], [[3ww4|3ww4]]</div></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=3ww3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww3 OCA], [http://pdbe.org/3ww3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ww3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ww3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww3 ProSAT]</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=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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Cellulomonas parahominis]] | | [[Category: Cellulomonas parahominis]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Kamitori, S]] | | [[Category: Kamitori, S]] |
| | [[Category: Takata, G]] | | [[Category: Takata, G]] |
| Structural highlights
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Terami Y, Yoshida H, Uechi K, Morimoto K, Takata G, Kamitori S. Essentiality of tetramer formation of Cellulomonas parahominis L-ribose isomerase involved in novel L-ribose metabolic pathway. Appl Microbiol Biotechnol. 2015 Feb 8. PMID:25661811 doi:http://dx.doi.org/10.1007/s00253-015-6417-4
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