title: Modeling studies with Helicobacter pylori octaprenyl pyrophosphate synthase reveal the enzymatic mechanism of trans-prenyltransferases.
abstract: Octaprenyl pyrophosphate synthase (OPPs), an enzyme belonging to the trans-prenyltransferases family, is involved in the synthesis of C40 octaprenyl pyrophosphate (OPP) by reacting farnesyl pyrophosphate (FPP) with five isopentenyl pyrophosphates (IPP). It has been reported that OPPs is essential for bacteria's normal growth and is a potential target for novel antibacterial drug design. Here we report the crystal structure of OPPs from Helicobacter pylori, determined by MAD method at 2.8 Å resolution and refined to 2.0 Å resolution. The substrate IPP was docked into HpOPPs structure and residues involved in IPP recognition were identified. The other substrate FPP, the intermediate GGPP and a nitrogen-containing bisphosphonate drug were also modeled into the structure. The resulting model shed some lights on the enzymatic mechanism, including (1) residues Arg87, Lys36 and Arg39 are essential for IPP binding; (2) residues Lys162, Lys224 and Gln197 are involved in FPP binding; (3) the second DDXXD motif may involve in FPP binding by Mg(2+) mediated interactions; (4) Leu127 is probably involved in product chain length determination in HpOPPs and (5) the intermediate products such as GGPP need a rearrange to occupy the binding site of FPP and then IPP is reloaded. Our results also indicate that the nitrogen-containing bisphosphonate drugs are potential inhibitors of FPPs and other trans-prenyltransferases aiming at blocking the binding of FPP.
authors.affiliation: Department of Clinical Microbiology and Immunology, College of Medical Laboratory, Third Military Medical University, Chongqing, China.
authors.forename: Jinyong
authors.initials: J
authors.lastname: Zhang
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Zhang
authors.forename: Rui
authors.initials: R
authors.lastname: Zhang
authors.forename: Chao
authors.initials: C
authors.lastname: Wu
authors.forename: Ying
authors.initials: Y
authors.lastname: Guo
authors.forename: Xuhu
authors.initials: X
authors.lastname: Mao
authors.forename: Gang
authors.initials: G
authors.lastname: Guo
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhang
authors.forename: Da-Cheng
authors.initials: DC
authors.lastname: Wang
authors.forename: Defeng
authors.initials: D
authors.lastname: Li
authors.forename: Quanming
authors.initials: Q
authors.lastname: Zou
mesh_terms: D019883:Alkyl and Aryl Transferases / Q000737:chemistry* / Q000235:genetics; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D020134:Catalytic Domain; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D016480:Helicobacter pylori / Q000201:enzymology*; D045782:Hemiterpenes / Q000737:chemistry; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009943:Organophosphorus Compounds / Q000737:chemistry; D011106:Polyisoprenyl Phosphates / Q000737:chemistry; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D012717:Sesquiterpenes / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D045782:Hemiterpenes; D009943:Organophosphorus Compounds; D011106:Polyisoprenyl Phosphates; D012717:Sesquiterpenes; C004809:isopentenyl pyrophosphate; C004808:farnesyl pyrophosphate; D019883:Alkyl and Aryl Transferases; C048987:octaprenyl pyrophosphate synthetase