Abstract
Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the transfer of the aminopropyl group from S-adenosylmethionine (dcSAM) to putrescine, leading to form spermindine and 5’-deoxy-5’-methylthioadenosine (MTA). The structure of Helicobacter pylori spermidine synthase (HpPAPT) was solved by our lab previously, using multiwavelengh anomalous dispersion (MAD) from selenomethionine (SeMet)-containing crystals. HpPAPT consisted of two domains, an N-terminal β-strand domain including 6β-strands, and a C-terminal Rossmann-like domain. Moreover, the substrate binding site might locate in a deep binding pocket between the N- and C- terminal domains. Structural comparison with other PAPTs showed that HpPAPT has a unique binding pocket between two domains, numerous non-conserved residues, a less acidic electrostatic surface potential, and a large buried space within the structure. We used the substrate analogue S-adenosylmethionine (SAM) and the potent inhibitor 5’-deoxy-5’-methylthioadenosine (MTA) in complex with HpPAPT. Two complex crystals, HpPAPT-SAM and HpPAPT-MTA, were determined at 2.1 and 2.0 □, respectively. The binding site and orientation of the two bound substrate/product of the HpPAPT are very similar. But there is difference between the shifted binding site and the putative active site, which included three parts, adenosyl moiety binding residues (N29, Q101, A102, H128, L146, Q147, E148, and P149), aminopropyl group binding residues (E58, S59, D83) and putrescine binding residues (M44, L49, D80, G81, S206, and I211)1. This shifted binding pocket is located in aminopropyl group and putrescine binding part, which is close to Rossmann-like domain, and only two residues, E58 and D83 are corresponding to the putative active site. There are other residues, F51, F54, R203 and L205 involved in SAM or MTA binding site. In addition, PAPTs are essential for bacterial cell viability, HpPAPT can be a potential drug target for H. pylori by the complex structural information.