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

Research output: Contribution to journalArticleScientificpeer-review

3 Citations (Scopus)

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

Fingerprint

Caulobacter crescentus
Rhizobium leguminosarum
Hydro-Lyases
formates
Crystallization
X-Ray Diffraction
X ray diffraction analysis
pentose
sodium
crystallization
formic acid
gel chromatography
chromatography
sugars
Escherichia
cells
diffraction
dehydration
crystals
affinity

Keywords

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

Cite this

@article{07f985b394e2426aa666a4c41322e5ef,
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 {\AA} 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 {\AA}, [beta] = 90.43°. Eight RlArDHT molecules (two tetramers) in the asymmetric unit give a V M value of 3.2 {\AA}3 Da-1 and a solvent content of 62{\%}. Crystals of CcXyDHT that diffracted to 2.66 {\AA} 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 {\AA}, {\ss} = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a V M value of 4.0 {\AA}3 Da-1 and a solvent content of 69{\%}.",
keywords = "Caulobacter crescentus, d-xylonate dehydratase, IlvD/EDD enzymes, l-arabinonate dehydratase, Rhizobium leguminosarum bv. trifolii, [Fe-S] cluster",
author = "Rahman, {Mohammad Mubinur} and Martina Andberg and Anu Koivula and Juha Rouvinen and Nina Hakulinen",
year = "2016",
doi = "10.1107/S2053230X16010311",
language = "English",
volume = "72",
pages = "604--608",
journal = "Acta Crystallographica Section F: Structural Biology Communications",
issn = "2053-230X",
publisher = "International Union of Crystallography",
number = "Part 8",

}

Crystallization and X-ray diffraction analysis of an l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a d-xylonate dehydratase from Caulobacter crescentus. / Rahman, Mohammad Mubinur; Andberg, Martina; Koivula, Anu; Rouvinen, Juha; Hakulinen, Nina.

In: Acta Crystallographica Section F: Structural Biology Communications, Vol. 72, No. Part 8, 2016, p. 604-608.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Crystallization and X-ray diffraction analysis of an l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a d-xylonate dehydratase from Caulobacter crescentus

AU - Rahman, Mohammad Mubinur

AU - Andberg, Martina

AU - Koivula, Anu

AU - Rouvinen, Juha

AU - Hakulinen, Nina

PY - 2016

Y1 - 2016

N2 - 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%.

AB - 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%.

KW - Caulobacter crescentus

KW - d-xylonate dehydratase

KW - IlvD/EDD enzymes

KW - l-arabinonate dehydratase

KW - Rhizobium leguminosarum bv. trifolii

KW - [Fe-S] cluster

U2 - 10.1107/S2053230X16010311

DO - 10.1107/S2053230X16010311

M3 - Article

VL - 72

SP - 604

EP - 608

JO - Acta Crystallographica Section F: Structural Biology Communications

JF - Acta Crystallographica Section F: Structural Biology Communications

SN - 2053-230X

IS - Part 8

ER -