ATOMIC STRUCTURE OF POTD-THE PRIMARY RECEPTOR OF SPERMIDINE/PUTRESCINE TRANSPORT SYSTEM IN E.COLI. D.G.Vassylyev¹, S. Sugiyama², M. Matsushima³, K. Kashiwagi⁴, K. Igarashi⁴, K. Morikawa¹, ¹Biomolecular Engineering Research Institute, 6-2-3, Furuedai, Suita, Osaka, 565, Japan, ²Kyowa Hakko Kogyo Co. Ltd., Pharmaceutical Research Laboratories, 1188 Shimotogari, Nagaizumi-cho,Sunto-gun,Shizuoka,411,Japan, ³Rational Drug Desighn Laboratories, 4-1-1 Misato, Matsukawa, Fukushima 960-12, Japan, ⁴Faculty of Pharmaceutical Sciences, Chiba Univ., 1-33 Yayoi-cho, Inage-ku, Chiba 263, Japan

The crystal structure of PotD (a periplasmic binding protein which is the primary receptor of polyamine transport system in E.coli) in complex with spermidine has been solved at 2.5Å resolution. The PotD protein (325 amino acids) consists of two domains with a deep cleft (20A long, 5A wide, 14A deep) in the interface between them. This cleft was found to be a binding site of spermidine in the complex. The three positively charged nitrogens of spermidine are recognized by four acidic side chains of PotD in the cleft while five aromatic residues anchor the spermidine methylene backbone by van der Waals interactions. The overall fold of PotD is similar to other periplasmic binding proteins despite the fact of low sequence similarity.

Crystals of the complex belong to the space group P21(a=145.3Å, b=69.1Å, c=72.5Å, [[beta]]=107.6, Z=8). The structure was solved by MIR method in combination with solvent flattening and 4-fold N.C.S. averaging and refined at 2.5Å resolution to a final R-factor of 0.199 (R-free = 0.280).