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4q0u

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'''Unreleased structure'''
 
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The entry 4q0u is ON HOLD
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==Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase mutant E204Q in complex with L-ribose==
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<StructureSection load='4q0u' size='340' side='right'caption='[[4q0u]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4q0u]] is a 1 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=4Q0U FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</td></tr>
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<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>
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q93UQ5_9GAMM Q93UQ5_9GAMM]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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).
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Authors: Yoshida, H., Yoshihara, A., Teraoka, M., Izumori, K., Kamitori, S.
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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<ref>PMID:24846739</ref>
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Description: Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase mutant E204Q in complex with L-ribose
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4q0u" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Acinetobacter sp. DL-28]]
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[[Category: Large Structures]]
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[[Category: Izumori K]]
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[[Category: Kamitori S]]
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[[Category: Teraoka M]]
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[[Category: Yoshida H]]
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[[Category: Yoshihara A]]

Current revision

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase mutant E204Q in complex with L-ribose

PDB ID 4q0u

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