Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD

PLoS One. 2010 May 14;5(5):e10647. doi: 10.1371/journal.pone.0010647.

Abstract

As a response to high osmolality, many microorganisms synthesize various types of compatible solutes. These organic osmolytes aid in offsetting the detrimental effects of low water activity on cell physiology. One of these compatible solutes is ectoine. A sub-group of the ectoine producer's enzymatically convert this tetrahydropyrimidine into a hydroxylated derivative, 5-hydroxyectoine. This compound also functions as an effective osmostress protectant and compatible solute but it possesses properties that differ in several aspects from those of ectoine. The enzyme responsible for ectoine hydroxylation (EctD) is a member of the non-heme iron(II)-containing and 2-oxoglutarate-dependent dioxygenases (EC 1.14.11). These enzymes couple the decarboxylation of 2-oxoglutarate with the formation of a high-energy ferryl-oxo intermediate to catalyze the oxidation of the bound organic substrate. We report here the crystal structure of the ectoine hydroxylase EctD from the moderate halophile Virgibacillus salexigens in complex with Fe(3+) at a resolution of 1.85 A. Like other non-heme iron(II) and 2-oxoglutarate dependent dioxygenases, the core of the EctD structure consists of a double-stranded beta-helix forming the main portion of the active-site of the enzyme. The positioning of the iron ligand in the active-site of EctD is mediated by an evolutionarily conserved 2-His-1-carboxylate iron-binding motif. The side chains of the three residues forming this iron-binding site protrude into a deep cavity in the EctD structure that also harbours the 2-oxoglutarate co-substrate-binding site. Database searches revealed a widespread occurrence of EctD-type proteins in members of the Bacteria but only in a single representative of the Archaea, the marine crenarchaeon Nitrosopumilus maritimus. The EctD crystal structure reported here can serve as a template to guide further biochemical and structural studies of this biotechnologically interesting enzyme family.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acids / metabolism
  • Amino Acids, Diamino / chemical synthesis*
  • Amino Acids, Diamino / chemistry
  • Amino Acids, Diamino / metabolism*
  • Bacillus / enzymology*
  • Bacillus / genetics
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Crystallography, X-Ray
  • Dioxygenases / chemistry*
  • Dioxygenases / metabolism
  • Genome, Bacterial / genetics
  • Heme / metabolism*
  • Hydroxylation
  • Iron / metabolism*
  • Ketoglutaric Acids / metabolism*
  • Ligands
  • Models, Molecular
  • Pliability
  • Protein Structure, Secondary
  • Static Electricity

Substances

  • Amino Acids
  • Amino Acids, Diamino
  • Bacterial Proteins
  • Ketoglutaric Acids
  • Ligands
  • hydroxyectoine
  • Heme
  • ectoine
  • Iron
  • Dioxygenases

Associated data

  • PDB/3EMR