title: Crystallization and X-ray diffraction analysis of an L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate dehydratase from Caulobacter crescentus.
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, β = 90.43°. Eight RlArDHT molecules (two tetramers) in the asymmetric unit give a VM value of 3.2 Å(3) 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, β = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a VM value of 4.0 Å(3) Da(-1) and a solvent content of 69%.
authors.affiliation: Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland.
authors.forename: Mohammad Mubinur
authors.initials: MM
authors.lastname: Rahman
authors.affiliation: VTT Technical Research Centre of Finland Ltd, PO Box 1000, FIN-02044 VTT Espoo, Finland.
authors.forename: Martina
authors.initials: M
authors.lastname: Andberg
authors.affiliation: VTT Technical Research Centre of Finland Ltd, PO Box 1000, FIN-02044 VTT Espoo, Finland.
authors.forename: Anu
authors.initials: A
authors.lastname: Koivula
authors.affiliation: Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland.
authors.forename: Juha
authors.initials: J
authors.lastname: Rouvinen
authors.affiliation: Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland.
authors.forename: Nina
authors.initials: N
authors.lastname: Hakulinen
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016935:Caulobacter crescentus / Q000737:chemistry* / Q000201:enzymology; D003001:Cloning, Molecular; D003460:Crystallization; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D005561:Formates / Q000737:chemistry; D015870:Gene Expression; D006836:Hydro-Lyases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D010957:Plasmids / Q000737:chemistry* / Q000378:metabolism; D011092:Polyethylene Glycols / Q000737:chemistry; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016961:Rhizobium leguminosarum / Q000737:chemistry* / Q000201:enzymology
chemical_list: D001426:Bacterial Proteins; D005561:Formates; D011994:Recombinant Proteins; C030544:formic acid; D011092:Polyethylene Glycols; C037004:D-xylo-aldonate dehydratase; D006836:Hydro-Lyases; C000595212:polyethylene glycol 3350
keywords: Caulobacter crescentus; IlvD/EDD enzymes; Rhizobium leguminosarum bv. trifolii; [Fe–S] cluster; d-xylonate dehydratase; l-arabinonate dehydratase