PDBsum entry 2zr1

Plant protein

PDB id: 2zr1

Contents

Protein chains

250 a.a. *

263 a.a. *

Ligands

NAG ×3

Waters ×169

* Residue conservation analysis

PDB id:

2zr1

Name:

Plant protein

Title:

Agglutinin from abrus precatorius

Structure:

Agglutinin-1 chain a. Chain: a, c. Synonym: agglutinin i, aag-a. Agglutinin-1 chain b. Chain: b, d. Synonym: agglutinin i, aag-b

Source:

Abrus precatorius. Indian licorice. Organism_taxid: 3816. Organism_taxid: 3816

Resolution:

2.60Å R-factor: 0.199 R-free: 0.227

Authors:

J.Cheng,T.H.Lu,C.L.Liu,J.Y.Lin

Key ref:

J.Cheng et al. (2010). 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. PubMed id: 20433687

Date:

22-Aug-08 Release date: 25-Aug-09

Protein chains

Q9M6E9  (AGGL_ABRPR) -  Agglutinin-1 from Abrus precatorius

Seq: 547 a.a.

Struc: 250 a.a.

Protein chains

Q9M6E9  (AGGL_ABRPR) -  Agglutinin-1 from Abrus precatorius

Seq: 547 a.a.

Struc: 263 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.3.2.2.22 - rRNA N-glycosylase.
• Reaction: Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.

J Biomed Sci 17:34-34 (2010)

PubMed id: 20433687

A biophysical elucidation for less toxicity of agglutinin than abrin-a from the seeds of Abrus precatorius in consequence of crystal structure.

J.Cheng, T.H.Lu, C.L.Liu, J.Y.Lin.

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.