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| | <StructureSection load='4q0u' size='340' side='right'caption='[[4q0u]], [[Resolution|resolution]] 1.98Å' scene=''> | | <StructureSection load='4q0u' size='340' side='right'caption='[[4q0u]], [[Resolution|resolution]] 1.98Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4q0u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp._dl-28 Acinetobacter sp. dl-28]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q0U FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4q0u]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q0U FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0MK:L-RIBOPYRANOSE'>0MK</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=ROR:L-RIBOSE'>ROR</scene>, <scene name='pdbligand=Z6J:ALPHA-L-RIBOFURANOSE'>Z6J</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0MK:L-RIBOPYRANOSE'>0MK</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=ROR:L-RIBOSE'>ROR</scene>, <scene name='pdbligand=Z6J:ALPHA-L-RIBOFURANOSE'>Z6J</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4q0p|4q0p]], [[4q0q|4q0q]], [[4q0s|4q0s]], [[4q0v|4q0v]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4q0p|4q0p]], [[4q0q|4q0q]], [[4q0s|4q0s]], [[4q0v|4q0v]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">L-RI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160971 Acinetobacter sp. DL-28])</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=4q0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0u OCA], [https://pdbe.org/4q0u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q0u RCSB], [https://www.ebi.ac.uk/pdbsum/4q0u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0u ProSAT]</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=4q0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0u OCA], [http://pdbe.org/4q0u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q0u RCSB], [http://www.ebi.ac.uk/pdbsum/4q0u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0u ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Acinetobacter sp. dl-28]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| | [[Category: Izumori, K]] | | [[Category: Izumori, K]] |
| Structural highlights
Publication Abstract from PubMed
l-Ribose, a pentose, is not known to exist in nature. Although organisms typically do not have a metabolic pathway that uses l-ribose as a carbon source, prokaryotes use various sugars as carbon sources for survival. Acinetobacter sp. DL-28 has been shown to express the novel enzyme, l-ribose isomerase (AcL-RbI), which catalyzes reversible isomerization between l-ribose and l-ribulose. AcL-RbI showed the highest activity to l-ribose, followed by d-lyxose with 47% activity, and had no significant amino acid sequence similarity to structure-known proteins, except for weak homology with the d-lyxose isomerases from Escherichia coli O157 : H7 (18%) and Bacillus subtilis strain (19%). Thus, AcL-RbI is expected to have the unique three-dimensional structure to recognize l-ribose as its ideal substrate. The X-ray structures of AcL-RbI in complexes with substrates were determined. AcL-RbI had a cupin-type beta-barrel structure, and the catalytic site was found between two large beta-sheets with a bound metal ion. The catalytic site structures clearly showed that AcL-RbI adopted a cis-enediol intermediate mechanism for the isomerization reaction using two glutamate residues (Glu113 and Glu204) as acid/base catalysts. In its crystal form, AcL-RbI formed a unique homotetramer with many substrate sub-binding sites, which likely facilitated capture of the substrate. DATABASE: The atomic coordinates and structure factors of AcL-RbI/l-ribose, AcL-RbI/l-ribulose, AcL-RbI/ribitol, E204Q/l-ribose and E204Q/l-ribulose have been deposited in the Protein Data Bank under accession codes, 4Q0P, 4Q0Q, 4Q0S, 4Q0U and 4Q0V. STRUCTURED DIGITAL ABSTRACT: * AcL-RbI and AcL-RbI bind by x-ray crystallography (View interaction).
X-ray structure of a novel l-ribose isomerase acting on a non-natural sugar l-ribose as its ideal substrate.,Yoshida H, Yoshihara A, Teraoka M, Terami Y, Takata G, Izumori K, Kamitori S FEBS J. 2014 May 20. doi: 10.1111/febs.12850. PMID:24846739[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yoshida H, Yoshihara A, Teraoka M, Terami Y, Takata G, Izumori K, Kamitori S. X-ray structure of a novel l-ribose isomerase acting on a non-natural sugar l-ribose as its ideal substrate. FEBS J. 2014 May 20. doi: 10.1111/febs.12850. PMID:24846739 doi:http://dx.doi.org/10.1111/febs.12850
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