4E2T

Crystal Structures of RadA intein from Pyrococcus horikoshii

Summary for 4E2T

• Entry DOI: 10.2210/pdb4e2t/pdb
• Related: 2LQM 4E2U
• Descriptor: Pho radA intein, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, GLYCEROL, ... (4 entities in total)
• Functional Keywords: intein, hint-fold, unknown function
• Biological source: Pyrococcus horikoshii
• Total number of polymer chains: 2
• Total formula weight: 40443.78

Authors

Oeemig, J.S.,Zhou, D.,Kajander, T.,Wlodawer, A.,Iwai, H. (deposition date: 2012-03-09, release date: 2012-05-16, Last modification date: 2023-09-13)

Primary citation

Oeemig, J.S.,Zhou, D.,Kajander, T.,Wlodawer, A.,Iwai, H.
NMR and Crystal Structures of the Pyrococcus horikoshii RadA Intein Guide a Strategy for Engineering a Highly Efficient and Promiscuous Intein.
J.Mol.Biol., 421:85-99, 2012

PubMed Abstract: In protein splicing, an intervening protein sequence (intein) in the host protein excises itself out and ligates two split host protein sequences (exteins) to produce a mature host protein. Inteins require the involvement for the splicing of the first residue of the extein that follows the intein (which is Cys, Ser, or Thr). Other extein residues near the splicing junctions could modulate splicing efficiency even when they are not directly involved in catalysis. Mutual interdependence between this molecular parasite (intein) and its host protein (exteins) is not beneficial for intein spread but could be advantageous for intein survival during evolution. Elucidating extein-intein dependency has increasingly become important since inteins are recognized as useful biotechnological tools for protein ligation. We determined the structures of one of inteins with high splicing efficiency, the RadA intein from Pyrococcus horikoshii (PhoRadA). The solution NMR structure and the crystal structures elucidated the structural basis for its high efficiency and directed our efforts of engineering that led to rational design of a functional minimized RadA intein. The crystal structure of the minimized RadA intein also revealed the precise interactions between N-extein and the intein. We systematically analyzed the effects at the -1 position of N-extein and were able to significantly improve the splicing efficiency of a less robust splicing variant by eliminating the unfavorable extein-intein interactions observed in the structure. This work provides an example of how unveiling structure-function relationships of inteins offer a promising way of improving their properties as better tools for protein engineering.

PubMed: 22560994
DOI: 10.1016/j.jmb.2012.04.029

Experimental method

X-RAY DIFFRACTION (1.75 Å)