Structure and Characterization of Enzymes

A special issue of Crystals (ISSN 2073-4352).

Deadline for manuscript submissions: 17 July 2026 | Viewed by 1197

Special Issue Editor


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Guest Editor
School of Food Biotechnology and Nutrition, Kyungsung University, Busan 48434, Republic of Korea
Interests: structural biology; X-ray crystallography; cryo-EM; protein engineering; biotechnology

Special Issue Information

Dear Colleagues,

Enzymes, as biocatalysts, exhibit exceptional efficiency and catalytic activity that surpass those of synthetic catalysts. By facilitating a wide range of biochemical reactions essential to life, enzymes are indispensable to biological systems. These remarkable properties have established enzymes as central subjects of research in biotechnology, biochemistry, molecular biology, and medicine. Nevertheless, despite their fascinating capabilities, the precise mechanisms by which enzymes function remain incompletely understood. Structural analysis has played a pivotal role in uncovering these mechanisms, providing critical insights into enzyme function. In recent years, advancements in research methodologies—including X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-electron microscopy (cryo-EM)—have been further enhanced by breakthroughs in structure prediction technologies powered by artificial intelligence and bioinformatics. These developments have brought about a paradigm shift in our ability to explore enzyme structure and function. Therefore, we welcome contributions from structural biologists, biochemists, and computational researchers offering novel insights and perspectives at the forefront of enzyme structure–function studies.

Prof. Dr. Jung-Min Choi
Guest Editor

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Keywords

  • enzyme structure
  • biocatalysis
  • structure–function relationship
  • X-ray crystallography
  • artificial intelligence in structural biology

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Published Papers (2 papers)

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Research

15 pages, 3325 KB  
Article
Structural Study of L-Arabinose Isomerase from Latilactobacillus sakei
by Suwon Yang, Jeonghwa Cheon and Jung-Min Choi
Crystals 2026, 16(2), 84; https://doi.org/10.3390/cryst16020084 - 25 Jan 2026
Viewed by 134
Abstract
D-Tagatose is a rare sugar of interest as a low-calorie sweetener, and enzymatic isomerization of D-galactose is a practical production route. L-arabinose isomerase (L-AI; EC 5.3.1.4) is a promising catalyst for the above process, but many characterized L-AIs perform best at alkaline pH [...] Read more.
D-Tagatose is a rare sugar of interest as a low-calorie sweetener, and enzymatic isomerization of D-galactose is a practical production route. L-arabinose isomerase (L-AI; EC 5.3.1.4) is a promising catalyst for the above process, but many characterized L-AIs perform best at alkaline pH and high temperature and often require substantial divalent metal supplementation (e.g., Mn2+/Co2+), which complicates food-grade processing. Lactic acid bacteria (LAB) are attractive sources of food-compatible enzymes, yet structural information for LAB-derived L-AIs has been limited. Here, we report the 2.6 Å X-ray crystal structure of L-AI from Latilactobacillus sakei 23K (LsAI) and define its oligomeric assembly. Although the asymmetric unit contains a single monomer, crystallographic symmetry reconstructs a D3-symmetric homohexamer composed of two face-to-face trimers, consistent with a higher-order assembly in solution. Interface analysis shows predominantly polar interaction networks, and normalized B-factor mapping reveals localized flexibility near active-site-proximal regions. These findings provide a structural basis for understanding LAB-derived L-AIs and support structure-guided engineering toward food-grade, low-metal biocatalysts for rare-sugar production. Full article
(This article belongs to the Special Issue Structure and Characterization of Enzymes)
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15 pages, 4309 KB  
Article
Interference of Sulphonate Buffering Agents with E. coli Hypoxanthine-Guanine Phosphoribosyltransferase Active Site Functioning: A Crystallographic and Enzymological Study
by Evgeniy A. Zayats, Yulia A. Abramchik, Maria A. Kostromina, Vladimir I. Timofeev, Mikhail B. Shevtsov, Alexey V. Mishin, Ilya V. Fateev, Andrey A. Karanov, Alexandra R. Sharafutdinova, Aleksandra O. Arnautova, Irina D. Konstantinova, Valentin I. Borshchevskiy and Roman S. Esipov
Crystals 2025, 15(10), 874; https://doi.org/10.3390/cryst15100874 - 8 Oct 2025
Viewed by 711
Abstract
The investigation of the structure–function relationship in hypoxanthine-guanine phosphoribosyltransferases (HGPRT) is a direction that is relevant for the development of drugs and approaches of enzymatic synthesis of modified nucleosides and nucleotides. This research paper is dedicated to the investigation of binding of sulphonate [...] Read more.
The investigation of the structure–function relationship in hypoxanthine-guanine phosphoribosyltransferases (HGPRT) is a direction that is relevant for the development of drugs and approaches of enzymatic synthesis of modified nucleosides and nucleotides. This research paper is dedicated to the investigation of binding of sulphonate molecules, such as HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) in the active sites of HGPRT and similar proteins. We report the crystal structure of HGPRT from Escherichia coli (EcoHGPRT) in a complex with HEPES. In the obtained X-ray structure, a HEPES molecule binds to the active site in a position that mimics one of the HGPRT substrates, namely phosphoribosylpyrophosphate (PRPP). Enzymological study has shown that HEPES is an inhibitor of EcoHGPRT, along with two structurally similar molecules, namely MES and PIPES. Comparison of the observed EcoHGPRT/HEPES complex to other reported structures in the context of inhibition study results provides an opportunity to explore the variety of binding modes of HEPES and similar molecules and to discuss the structure–function relationship in this enzyme and similar proteins. Full article
(This article belongs to the Special Issue Structure and Characterization of Enzymes)
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