title: Crystal structure of PotD, the primary receptor of the polyamine transport system in Escherichia coli.
abstract: PotD protein is a periplasmic binding protein and the primary receptor of the polyamine transport system, which regulates the polyamine content in Escherichia coli. The crystal structure of PotD in complex with spermidine has been solved at 2.5-A resolution. The PotD protein consists of two domains with an alternating beta-alpha-beta topology. The polyamine binding site is in a central cleft lying in the interface between the domains. In the cleft, four acidic residues recognize the three positively charged nitrogen atoms of spermidine, while five aromatic side chains anchor the methylene backbone by van der Waals interactions. The overall fold of PotD is similar to that of other periplasmic binding proteins, and in particular to the maltodextrin-binding protein from E. coli, despite the fact that sequence identity is as low as 20%. The comparison of the PotD structure with the two maltodextrin-binding protein structures, determined in the presence and absence of the substrate, suggests that spermidine binding rearranges the relative orientation of the PotD domains to create a more compact structure.
authors.affiliation: Protein Engineering Research Institute, Suita, Osaka, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Sugiyama
authors.forename: D G
authors.initials: DG
authors.lastname: Vassylyev
authors.forename: M
authors.initials: M
authors.lastname: Matsushima
authors.forename: K
authors.initials: K
authors.lastname: Kashiwagi
authors.forename: K
authors.initials: K
authors.lastname: Igarashi
authors.forename: K
authors.initials: K
authors.lastname: Morikawa
mesh_terms: D018528:ATP-Binding Cassette Transporters; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D002352:Carrier Proteins / Q000737:chemistry*; D003196:Computer Graphics; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins; D046911:Macromolecular Substances; D058619:Maltose-Binding Proteins; D026901:Membrane Transport Proteins; D008958:Models, Molecular; D008961:Models, Structural; D008969:Molecular Sequence Data; D009004:Monosaccharide Transport Proteins; D033902:Periplasmic Binding Proteins; D011073:Polyamines / Q000378:metabolism; D017433:Protein Structure, Secondary; D013095:Spermidine
chemical_list: D018528:ATP-Binding Cassette Transporters; D001426:Bacterial Proteins; D002352:Carrier Proteins; D029968:Escherichia coli Proteins; D046911:Macromolecular Substances; C461619:MalE protein, E coli; D058619:Maltose-Binding Proteins; D026901:Membrane Transport Proteins; D009004:Monosaccharide Transport Proteins; D033902:Periplasmic Binding Proteins; D011073:Polyamines; C099274:PotD protein, E coli; C461599:maltose transport system, E coli; D013095:Spermidine