X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with FMN at 1.8 A resolution

Structure. 2000 Jul 15;8(7):751-62. doi: 10.1016/s0969-2126(00)00162-3.

Abstract

Background: Escherichia coli pyridoxine 5'-phosphate oxidase (PNPOx) catalyzes the terminal step in the biosynthesis of pyridoxal 5'-phosphate (PLP), a cofactor used by many enzymes involved in amino acid metabolism. The enzyme oxidizes either the 4'-hydroxyl group of pyridoxine 5'-phosphate (PNP) or the 4'-primary amine of pyridoxamine 5'-phosphate (PMP) to an aldehyde. PNPOx is a homodimeric enzyme with one flavin mononucleotide (FMN) molecule non-covalently bound to each subunit. A high degree of sequence homology among the 15 known members of the PNPOx family suggests that all members of this group have similar three-dimensional folds.

Results: The crystal structure of PNPOx from E. coli has been determined to 1.8 A resolution. The monomeric subunit folds into an eight-stranded beta sheet surrounded by five alpha-helical structures. Two monomers related by a twofold axis interact extensively along one-half of each monomer to form the dimer. There are two clefts at the dimer interface that are symmetry-related and extend from the top to the bottom of the dimer. An FMN cofactor that makes interactions with both subunits is located in each of these two clefts.

Conclusions: The structure is quite similar to the recently deposited 2.7 A structure of Saccharomyces cerevisiae PNPOx and also, remarkably, shares a common structural fold with the FMN-binding protein from Desulfovibrio vulgaris and a domain of chymotrypsin. This high-resolution E. coli PNPOx structure permits predictions to be made about residues involved in substrate binding and catalysis. These predictions provide testable hypotheses, which can be answered by making site-directed mutants.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Chymotrypsin / chemistry
  • Crystallography, X-Ray
  • Desulfovibrio vulgaris / enzymology
  • Dimerization
  • Electron Transport
  • Escherichia coli / enzymology*
  • Flavin Mononucleotide / chemistry*
  • Flavin Mononucleotide / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Phosphates / metabolism
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Secondary
  • Pyridoxaminephosphate Oxidase / chemistry*
  • Pyridoxaminephosphate Oxidase / metabolism
  • Recombinant Fusion Proteins / chemistry
  • Saccharomyces cerevisiae / enzymology
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Species Specificity

Substances

  • Bacterial Proteins
  • Phosphates
  • Recombinant Fusion Proteins
  • Flavin Mononucleotide
  • Pyridoxaminephosphate Oxidase
  • Chymotrypsin

Associated data

  • PDB/1DNL