title: Structure prediction and functional analysis of KdsD, an enzyme involved in lipopolysaccharide biosynthesis.
abstract: Lipopolysaccharide is an essential component of the outer membrane of Gram-negative bacteria and consists of three elements: lipid A, the core oligosaccharide and the O-antigen. The inner core region is highly conserved and contains at least one residue of 3-deoxy-D-manno-octulosonate (Kdo). The first committed step of Kdo biosynthesis is the aldol-keto isomerisation of d-ribulose 5-phosphate to d-arabinose 5-phosphate catalyzed by arabinose 5-phosphate isomerase encoded in Escherichia coli by the kdsD gene. KdsD contains an N-terminal sugar isomerase (SIS) domain commonly found in phosphosugar isomerases but its three-dimensional structure is unknown. The structure of the KdsD SIS domain has been predicted by homology modeling using the hypothetical 3etn protein as a template. Moreover by sequence alignments, comparison with other sugar isomerases structurally related to KdsD, and site-directed mutagenesis we implicated four residues in KdsD activity or substrate recognition. A possible role of these residues in the catalysis is discussed.
authors: Dipartimento di Biotecnologie e Bioscienze, Piazza della Scienza 2, Università di Milano-Bicocca, 20126 Milan, Italy.
authors: Silvia
authors: S
authors: Sommaruga
authors: Luca De
authors: LD
authors: Gioia
authors: Paolo
authors: P
authors: Tortora
authors: Alessandra
authors: A
authors: Polissi
mesh_terms: D019747:Aldose-Ketose Isomerases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000595:Amino Acid Sequence; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006639:Histidine / Q000737:chemistry / Q000235:genetics; D008070:Lipopolysaccharides / Q000096:biosynthesis*; D008239:Lysine / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D009154:Mutation; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D013400:Sugar Acids / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; D008070:Lipopolysaccharides; D013400:Sugar Acids; D006639:Histidine; D019747:Aldose-Ketose Isomerases; C477520:D-arabinose 5-phosphate isomerase, E coli; D008239:Lysine; C120356:3-deoxy-manno-oct-2-ulopyranosonic acid