A biophysical elucidation for less toxicity of agglutinin than abrin-a from the seeds of Abrus precatorius in consequence of crystal structure.
X-ray crystal structure determination of agglutinin from Abrus precatorius in Taiwan is presented. The crystal structure of agglutinin, a type II ribosome-inactivating protein (RIP) from the seeds of Abrus precatorius in Taiwan, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of abrin-a as the template. The structure has space group P4(1)2(1)2 with Z = 8, and been refined at 2.6 A to R-factor of 20.4%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.009 A and 1.3 degrees. Primary, secondary, tertiary and quaternary structures of agglutinin have been described and compared with those of abrin-a to a certain extent. In subsequent docking research, we found that Asn200 of abrin-a may form a critical hydrogen bond with G4323 of 28SRNA, while corresponding Pro199 of agglutinin is a kink hydrophobic residue bound with the cleft in a more compact complementary relationship. This may explain the lower toxicity of agglutinin than abrin-a, despite of similarity in secondary structure and the activity cleft of two RIPs.
Cheng
Jack
J
Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan.
Lu
Tian-Huey
TH
Liu
Chao-Lin
CL
Lin
Jung-Yaw
JY
D000036:Abrin / Q000737:chemistry* / Q000235:genetics / Q000633:toxicity*; D029912:Abrus / Q000737:chemistry* / Q000235:genetics / Q000633:toxicity*; D000595:Amino Acid Sequence; D001665:Binding Sites; D055592:Biophysical Phenomena; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D037121:Plant Lectins / Q000737:chemistry* / Q000235:genetics / Q000633:toxicity*; D011487:Protein Conformation; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D018749:RNA, Plant / Q000737:chemistry; D012339:RNA, Ribosomal, 28S / Q000737:chemistry; D012639:Seeds / Q000737:chemistry; D055672:Static Electricity
D037121:Plant Lectins; D018749:RNA, Plant; D012339:RNA, Ribosomal, 28S; C016940:abrus agglutinin; D000036:Abrin