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Crystallization and X-ray diffraction analysis of an L -arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate dehydratase from Caulobacter crescentus
DOI:
10.1107/S2053230X16010311
Authors:
Mohammad Mubinur
Rahman
(University of Eastern Finland)
,
Martina
Andberg
(VTT Technical Research Centre of Finland Ltd)
,
Anu
Koivula
(VTT Technical Research Centre of Finland Ltd)
,
Juha
Rouvinen
(University of Eastern Finland)
,
Nina
Hakulinen
(University of Eastern Finland)
Co-authored by industrial partner:
No
Type:
Journal Paper
Journal:
Acta Crystallographica Section F Structural Biology Communications
, VOL 72
, PAGES 604 - 608
State:
Published (Approved)
Published:
August 2016
Diamond Proposal Number(s):
8030
,
10291

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 VM 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, [beta] = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a VM value of 4.0 Å3 Da-1 and a solvent content of 69%.
Journal Keywords: L-arabinonate dehydratase; D-xylonate dehydratase; IlvD/EDD enzymes; [Fe–S] cluster; Rhizobium leguminosarum bv. trifolii; Caulobacter crescentus
Diamond Keywords: Bacteria; Enzymes
Subject Areas:
Chemistry,
Biology and Bio-materials
Instruments:
I04-Macromolecular Crystallography
Other Facilities: ID14-2 at ESRF
Added On:
01/09/2016 12:08
Discipline Tags:
Biotechnology
Biochemistry
Catalysis
Chemistry
Structural biology
Engineering & Technology
Life Sciences & Biotech
Technical Tags:
Diffraction
Macromolecular Crystallography (MX)