SbnG, a citrate synthase in Staphylococcus aureus: a new fold on an old enzyme

J Biol Chem. 2014 Dec 5;289(49):33797-807. doi: 10.1074/jbc.M114.603175. Epub 2014 Oct 21.

Abstract

In response to iron deprivation, Staphylococcus aureus produces staphyloferrin B, a citrate-containing siderophore that delivers iron back to the cell. This bacterium also possesses a second citrate synthase, SbnG, that is necessary for supplying citrate to the staphyloferrin B biosynthetic pathway. We present the structure of SbnG bound to the inhibitor calcium and an active site variant in complex with oxaloacetate. The overall fold of SbnG is structurally distinct from TCA cycle citrate synthases yet similar to metal-dependent class II aldolases. Phylogenetic analyses revealed that SbnG forms a separate clade with homologs from other siderophore biosynthetic gene clusters and is representative of a metal-independent subgroup in the phosphoenolpyruvate/pyruvate domain superfamily. A structural superposition of the SbnG active site to TCA cycle citrate synthases and site-directed mutagenesis suggests a case for convergent evolution toward a conserved catalytic mechanism for citrate production.

Keywords: Citrate Synthase; Convergent Evolution; Crystal Structure; Iron; Siderophore; Staphylococcus aureus (S. aureus); Tricarboxylic Acid Cycle (TCA Cycle) (Krebs Cycle).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / classification
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Citrate (si)-Synthase / chemistry*
  • Citrate (si)-Synthase / classification
  • Citrate (si)-Synthase / genetics
  • Citrate (si)-Synthase / metabolism
  • Citrates / biosynthesis
  • Citric Acid Cycle / genetics
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Evolution, Molecular
  • Gene Expression
  • Iron / metabolism*
  • Iron-Regulatory Proteins / chemistry*
  • Iron-Regulatory Proteins / classification
  • Iron-Regulatory Proteins / genetics
  • Iron-Regulatory Proteins / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Oxaloacetic Acid / metabolism
  • Phosphoenolpyruvate / metabolism
  • Phylogeny
  • Protein Folding
  • Protein Structure, Quaternary
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Pyruvic Acid / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / classification
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Sequence Alignment
  • Staphylococcus aureus / chemistry*
  • Staphylococcus aureus / enzymology

Substances

  • Bacterial Proteins
  • Citrates
  • Iron-Regulatory Proteins
  • Recombinant Proteins
  • staphyloferrin B
  • Oxaloacetic Acid
  • Phosphoenolpyruvate
  • Pyruvic Acid
  • Iron
  • Citrate (si)-Synthase

Associated data

  • PDB/1D8C
  • PDB/1DXE
  • PDB/1IZC
  • PDB/1N8W
  • PDB/1PKY
  • PDB/1Z6K
  • PDB/2H12
  • PDB/2HWG
  • PDB/2V5J
  • PDB/2VWS
  • PDB/2WQD
  • PDB/3QLL
  • PDB/3QQW
  • PDB/3QZ6
  • PDB/4CTS
  • PDB/4TV5
  • PDB/4TV6