3DER

Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Lys dipeptide

3DER の概要

• エントリーDOI: 10.2210/pdb3der/pdb
• 関連するPDBエントリー: 3DEQ 3DES
• 分子名称: Muconate cycloisomerase, MAGNESIUM ION, ALANINE, ... (5 entities in total)
• 機能のキーワード: dipeptide epimerase, thermotoga maritima, enzymatic function, isomerase
• 由来する生物種: Thermotoga maritima MSB8
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 155911.51

構造登録者

Fedorov, A.A.,Fedorov, E.V.,Imker, H.J.,Gerlt, J.A.,Almo, S.C. (登録日: 2008-06-10, 公開日: 2008-11-25, 最終更新日: 2024-03-13)

主引用文献

Kalyanaraman, C.,Imker, H.J.,Fedorov, A.A.,Fedorov, E.V.,Glasner, M.E.,Babbitt, P.C.,Almo, S.C.,Gerlt, J.A.,Jacobson, M.P.
Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.
Structure, 16:1668-1677, 2008

PubMed Abstract: We have developed a computational approach to aid the assignment of enzymatic function for uncharacterized proteins that uses homology modeling to predict the structure of the binding site and in silico docking to identify potential substrates. We apply this method to proteins in the functionally diverse enolase superfamily that are homologous to the characterized L-Ala-D/L-Glu epimerase from Bacillus subtilis. In particular, a protein from Thermotoga martima was predicted to have different substrate specificity, which suggests that it has a different, but as yet unknown, biological function. This prediction was experimentally confirmed, resulting in the assignment of epimerase activity for L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His, whereas the enzyme is annotated incorrectly in GenBank as muconate cycloisomerase. Subsequently, crystal structures of the enzyme were determined in complex with three substrates, showing close agreement with the computational models and revealing the structural basis for the observed substrate selectivity.

PubMed: 19000819
DOI: 10.1016/j.str.2008.08.015

実験手法

X-RAY DIFFRACTION (1.9 Å)