The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 Å resolution

Acta Crystallogr F Struct Biol Commun. 2016 Dec 1;72(Pt 12):885-891. doi: 10.1107/S2053230X16018525. Epub 2016 Nov 25.

Abstract

In bacteria, the second committed step in the diaminopimelate/lysine anabolic pathways is catalyzed by the enzyme dihydrodipicolinate reductase (DapB). DapB catalyzes the reduction of dihydrodipicolinate to yield tetrahydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of DapB from the human-pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are reported. Protein crystals were grown in conditions consisting of 5%(w/v) PEG 4000, 200 mM sodium acetate, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.3 Å resolution. They belonged to space group P4322, with unit-cell parameters a = 109.38, b = 109.38, c = 176.95 Å. Rr.i.m. was 0.11, Rwork was 0.177 and Rfree was 0.208. The three-dimensional structural features of the enzymes show that DapB from B. henselae is a tetramer consisting of four identical polypeptides. In addition, the substrate NADP+ was found to be bound to one monomer, which resulted in a closed conformational change in the N-terminal domain.

Keywords: Bartonella henselae; cat-scratch disease; diaminopimelate; dihydrodipicolinate reductase; lysine biosynthesis.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Bartonella henselae / chemistry*
  • Bartonella henselae / enzymology
  • Binding Sites
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Dihydrodipicolinate Reductase / chemistry*
  • Dihydrodipicolinate Reductase / genetics
  • Dihydrodipicolinate Reductase / metabolism
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Models, Molecular
  • NADP / chemistry*
  • NADP / metabolism
  • Plasmids / chemistry
  • Plasmids / metabolism
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Protein Multimerization
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Substrate Specificity

Substances

  • Bacterial Proteins
  • Recombinant Proteins
  • NADP
  • Dihydrodipicolinate Reductase