X‐ray structure of a novel l‐ribose isomerase acting on a non‐natural sugar l‐ribose as its ideal substrate. (6th June 2014)

• Record Type: Journal Article
• Authors: Yoshida, Hiromi; Yoshihara, Akihide; Teraoka, Misa; Terami, Yuji; Takata, Goro; Izumori, Ken; Kamitori, Shigehiro
• Is Part Of: FEBS journal. Volume 281:Number 14(2014)
• Page Start: 3150
• Page End: 3164
• Publication Date: 2014-06-06
• Subjects: Biochemistry -- Periodicals; Molecular biology -- Periodicals; Pathology, Molecular -- Periodicals; 572
• DOI: 10.1111/febs.12850
• Languages: English
• ISSNs: 1742-464X

Abstract

<abstract abstract-type="main" id="febs12850-abs-0001"> <title> <x xml:space="preserve">Abstract</x> </title> <sec id="febs12850-sec-0001" sec-type="section"> <p> <sc>l</sc>‐Ribose, a pentose, is not known to exist in nature. Although organisms typically do not have a metabolic pathway that uses <sc>l</sc>‐ribose as a carbon source, prokaryotes use various sugars as carbon sources for survival. <italic>Acinetobacter</italic> sp. DL‐28 has been shown to express the novel enzyme, <sc>l</sc>‐ribose isomerase (AcL‐RbI), which catalyzes reversible isomerization between <sc>l</sc>‐ribose and <sc>l</sc>‐ribulose. AcL‐RbI showed the highest activity to <sc>l</sc>‐ribose, followed by <sc>d</sc>‐lyxose with 47% activity, and had no significant amino acid sequence similarity to structure‐known proteins, except for weak homology with the <sc>d</sc>‐lyxose isomerases from <italic>Escherichia coli</italic> O157 : H7 (18%) and <italic>Bacillus subtilis</italic> strain (19%). Thus, AcL‐RbI is expected to have the unique three‐dimensional structure to recognize <sc>l</sc>‐ribose as its ideal substrate. The X‐ray structures of AcL‐RbI in complexes with substrates were determined. AcL‐RbI had a cupin‐type β‐barrel structure, and the catalytic site was found between two large β‐sheets with a bound metal ion. The catalytic site structures clearly showed that AcL‐RbI adopted a <italic>cis</italic>‐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.</p> </sec> <sec id="febs12850-sec-0002" sec-type="section"> <title>Database</title> <p>The atomic coordinates and structure factors of AcL‐RbI/<sc>l</sc>‐ribose, AcL‐RbI/<sc>l</sc>‐ribulose, AcL‐RbI/ribitol, E204Q/<sc>l</sc>‐ribose and E204Q/<sc>l</sc>‐ribulose have been deposited in the Protein Data Bank under accession codes, <ext-link ext-link-type="uri" xlink:href="http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4Q0P" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">4Q0P</ext-link>, <ext-link ext-link-type="uri" xlink:href="http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4Q0Q" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">4Q0Q</ext-link>, <ext-link ext-link-type="uri" xlink:href="http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4Q0S" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">4Q0S</ext-link>, <ext-link ext-link-type="uri" xlink:href="http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4Q0U" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">4Q0U</ext-link> and <ext-link ext-link-type="uri" xlink:href="http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4Q0V" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">4Q0V</ext-link>.</p> </sec> <sec id="febs12850-sec-0003" sec-type="section"> <title>Structured digital abstract</title> <p> <ext-link ext-link-type="uri" xlink:href="http://www.uniprot.org/uniprot/Q93UQ5" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">AcL-RbI</ext-link> and <ext-link ext-link-type="uri" xlink:href="http://www.uniprot.org/uniprot/Q93UQ5" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">AcL-RbI</ext-link><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0407" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">bind</ext-link> by <ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0114" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">x-ray crystallography</ext-link> (<ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/intact/interaction/EBI-9524805" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">View interaction</ext-link>).</p> </sec> </abstract>