Preprint Communication Version 1 This version is not peer-reviewed

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

Version 1 : Received: 10 August 2019 / Approved: 11 August 2019 / Online: 11 August 2019 (08:37:08 CEST)

A peer-reviewed article of this Preprint also exists.

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

Journal reference: Crystals 2019, 9, 444
DOI: 10.3390/cryst9090444

Abstract

Various peptides or non-structural amino acids are recognized by their specific target proteins and perform 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 substrate recognition of peptide-recognizing enzyme, X-ray crystallographic studies were performed using triglycine (Gly-Gly-Gly) as main-chain of peptide. The crystal structure of Parengyodontium album Proteinase K in complex with triglcyine was determined at 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 main-chain. One of the triglycine-binding conformations was identical with the binding mode of a peptide-based inhibitor from a previously reported crystal structure of Proteinase K. Triglycine has potential application X-ray crystallography to identify substrate recognition sites in peptide binding enzymes.

Subject Areas

protein-protein interaction; protein-peptide interaction; triglycine; substrate binding site; peptide; inhibitor; Proteinase K

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