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Open AccessCommunication

Triglycine-Based Approach for Identifying the Substrate Recognition Site of an Enzyme

by Ki Hyun Nam 1,2
1
Division of Biotechnology, Korea University, Seoul 02481, Korea
2
Institute of Life Science and Natural Resources, Korea University, Seoul 02481, Korea
Crystals 2019, 9(9), 444; https://doi.org/10.3390/cryst9090444
Received: 10 August 2019 / Revised: 23 August 2019 / Accepted: 24 August 2019 / Published: 26 August 2019
(This article belongs to the Special Issue Crystallographic Studies of Enzymes)
Various peptides or non-structural amino acids are recognized by their specific target proteins, and perform a biological role in various pathways in vivo. Understanding the interactions between target protein and peptides (or non-structural amino acids) provides key information on the molecular interactions, which can be potentially translated to the development of novel drugs. However, it is experimentally challenging to determine the crystal structure of protein–peptide complexes. To obtain structural information on the substrate recognition of the peptide-recognizing enzyme, X-ray crystallographic studies were performed using triglycine (Gly-Gly-Gly) as the main-chain of the peptide. The crystal structure of Parengyodontium album Proteinase K in complex with triglcyine was determined at a 1.4 Å resolution. Two different bound conformations of triglycine were observed at the substrate recognition site. The triglycine backbone forms stable interactions with β5-α4 and α5-β6 loops of the main-chain. One of the triglycine-binding conformations was identical to the binding mode of a peptide-based inhibitor from a previously reported crystal structure of Proteinase K. Triglycine has potential application in X-ray crystallography in order to identify the substrate recognition sites in the peptide binding enzymes. View Full-Text
Keywords: protein–protein interaction; protein–peptide interaction; triglycine; substrate binding site; peptide; inhibitor; Proteinase K protein–protein interaction; protein–peptide interaction; triglycine; substrate binding site; peptide; inhibitor; Proteinase K
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MDPI and ACS Style

Nam, K.H. Triglycine-Based Approach for Identifying the Substrate Recognition Site of an Enzyme. Crystals 2019, 9, 444.

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