2Z53

Crystal structure of the S211A mutant of the ribosome inactivating protein PDL4 from P. dioica leaves

Summary for 2Z53

• Entry DOI: 10.2210/pdb2z53/pdb
• Related: 2QES 2QET 2z4u
• Descriptor: Ribosome-inactivating protein PD-L4, 1,2-ETHANEDIOL (3 entities in total)
• Functional Keywords: crystal, ribosome inactivating protein, hydrolase
• Biological source: Phytolacca dioica
• Total number of polymer chains: 1
• Total formula weight: 29329.25

Authors

Berisio, R.,Ruggiero, A. (deposition date: 2007-06-27, release date: 2008-02-26, Last modification date: 2024-11-06)

Primary citation

Ruggiero, A.,Chambery, A.,Di Maro, A.,Parente, A.,Berisio, R.
Atomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves
Proteins, 71:8-15, 2008

PubMed Abstract: The ribosome inactivating protein PD-L4 from Phytolacca dioica is a N-beta-glycosidase, probably involved in plant defence. The crystal structures of wild type PD-L4 and of the S211A PD-L4 mutant with significantly decreased catalytic activity were determined at atomic resolution. To determine the structural determinants for the reduced activity of S211A PD-L4, both forms have also been co-crystallized with adenine, the major product of PD-L4 catalytic reaction. In the structure of the S211A mutant, the cavity formed by the lack of the Ser hydroxyl group is filled by a water molecule; the insertion of this non-isosteric group leads to small albeit concerted changes in the tightly packed active site of the enzyme. These changes have been correlated to the different activity of the mutant enzyme. This work highlights the importance of atomic resolution studies for the deep understanding of enzymatic properties.

PubMed: 17963235
DOI: 10.1002/prot.21712

Experimental method

X-RAY DIFFRACTION (1.29 Å)