Crystallization and X-ray diffraction analysis of an l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a d-xylonate dehydratase from Caulobacter crescentus

Mohammad Mubinur Rahman, Martina Andberg, Anu Koivula, Juha Rouvinen, Nina Hakulinen

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    Abstract

    l-Arabinonate dehydratase (EC 4.2.1.25) and d-xylonate dehydratase (EC 4.2.1.82) are two enzymes that are involved in a nonphosphorylative oxidation pathway of pentose sugars. l-Arabinonate dehydratase converts l-arabinonate into 2-dehydro-3-deoxy-l-arabinonate, and d-xylonate dehydratase catalyzes the dehydration of d-xylonate to 2-dehydro-3-deoxy-d-xylonate. l-Arabinonate and d-xylonate dehydratases belong to the IlvD/EDD family, together with 6-phosphogluconate dehydratases and dihydroxyacid dehydratases. No crystal structure of any l-arabinonate or d-xylonate dehydratase is available in the PDB. In this study, recombinant l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT) and d-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) were heterologously expressed in Escherichia coli and purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals of RlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space group P21, with unit-cell parameters a = 106.07, b = 208.61, c = 147.09 Å, [beta] = 90.43°. Eight RlArDHT molecules (two tetramers) in the asymmetric unit give a V M value of 3.2 Å3 Da-1 and a solvent content of 62%. Crystals of CcXyDHT that diffracted to 2.66 Å resolution were obtained using sodium formate and polyethylene glycol 3350. They belonged to space group C2, with unit-cell parameters a = 270.42, b = 236.13, c = 65.17 Å, ß = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a V M value of 4.0 Å3 Da-1 and a solvent content of 69%.
    Original languageEnglish
    Pages (from-to)604-608
    JournalActa Crystallographica Section F: Structural Biology Communications
    Volume72
    Issue numberPart 8
    DOIs
    Publication statusPublished - 2016
    MoE publication typeA1 Journal article-refereed

    Keywords

    • Caulobacter crescentus
    • d-xylonate dehydratase
    • IlvD/EDD enzymes
    • l-arabinonate dehydratase
    • Rhizobium leguminosarum bv. trifolii
    • [Fe-S] cluster

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