Crystal structure of pokeweed antiviral protein with well-defined sugars from seeds at 1.8A resolution.
The crystal structure of pokeweed antiviral protein from seeds of Phytolacca americana (PAP-S) was solved at 1.8A. PAP-S is a one-chain ribosome-inactivating protein (RIP) and distinctively contains three well-defined N-acetylglucosamines, each covalently linked to an asparagine residue at positions, 10, 44, and 255, respectively. The high-resolution structure clearly shows the three mono-sugars to have either an alpha- or a beta-conformation. Two of sugars are located on the same side of the molecule with the active pocket. Except one hydrogen bond, there are no intermolecular interactions between the polypeptide chain and the sugars. Instead the sugar conformations appear to be stabilized by intermolecular interactions. The sugar structure defined at high resolution provides a structural basis for understanding their possible biological activity. The structural comparisons of PAP-S with other PAPs reveal that the major disparity of these homologous molecules is the different charge distribution on the upper right side of the front side near the active pocket. Based on the available structure of the 50S ribosomal subunit, the possible interactions between PAPs and the ribosome are discussed.
Zeng
Zong-Hao
ZH
Center for Molecular Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
He
Xiao-Lin
XL
Li
Hong-Min
HM
Hu
Zhong
Z
Wang
Da-Cheng
DC
D000117:Acetylglucosamine / Q000737:chemistry; D000595:Amino Acid Sequence; D001216:Asparagine / Q000737:chemistry; D002241:Carbohydrates / Q000737:chemistry*; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009699:N-Glycosyl Hydrolases; D010940:Plant Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D011487:Protein Conformation; D054789:Ribosome Inactivating Proteins, Type 1; D012270:Ribosomes / Q000737:chemistry / Q000648:ultrastructure; D012639:Seeds / Q000648:ultrastructure*; D017386:Sequence Homology, Amino Acid
D002241:Carbohydrates; D010940:Plant Proteins; D054789:Ribosome Inactivating Proteins, Type 1; D001216:Asparagine; D009699:N-Glycosyl Hydrolases; C024275:pokeweed antiviral protein; D000117:Acetylglucosamine