2ZR1

Agglutinin from Abrus Precatorius

Summary for 2ZR1

• Entry DOI: 10.2210/pdb2zr1/pdb
• Related: 1ABR 2Q3N
• Descriptor: Agglutinin-1 chain A, Agglutinin-1 chain B, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: ribosome-inactivating protein, immunotoxin, agglutinin abrin, glycoprotein, hydrolase, lectin, plant defense, protein synthesis inhibitor, pyrrolidone carboxylic acid, toxin, plant protein
• Biological source: Abrus precatorius (Indian licorice); More
• Total number of polymer chains: 4
• Total formula weight: 118006.00

Authors

Cheng, J.,Lu, T.H.,Liu, C.L.,Lin, J.Y. (deposition date: 2008-08-22, release date: 2009-08-25, Last modification date: 2024-10-30)

Primary citation

Cheng, J.,Lu, T.H.,Liu, C.L.,Lin, J.Y.
A biophysical elucidation for less toxicity of Agglutinin than Abrin-a from the Seeds of Abrus Precatorius in consequence of crystal structure
J.Biomed.Sci., 17:34-34, 2010

PubMed Abstract: 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.

PubMed: 20433687
DOI: 10.1186/1423-0127-17-34

Experimental method

X-RAY DIFFRACTION (2.6 Å)