The Crystal Structure and Characteristics of Enzymes

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Biomolecular Crystals".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 754

Special Issue Editors


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Guest Editor
Department of Chemistry, Soongsil University, Seoul 06978, Republic of Korea
Interests: structural biology; enzyme characterization; nitrogenase assembly
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Guest Editor
Diamond Light Source, Didcot OX110DE, UK
Interests: structural biology; macromolecular crystallography; synchrotron radiation; beamline instrumentation; crystal handling

Special Issue Information

Dear Colleagues,

Enzymes are the molecular workhorses of life, orchestrating countless biochemical reactions within cells. Understanding their structure and unique characteristics is essential for unravelling the intricate mechanisms that govern biological processes. Delving into the world of enzymes, this Special Issue embarks on a journey to explore the enigmatic intricacies hidden within the structure. The structure provides windows into the heart of enzymatic activity, revealing the precise arrangement of amino acids and cofactors that allow enzymes to carry out their functions. By uncovering these structural secrets, researchers gain a deeper comprehension of how enzymes interact with substrates, how they facilitate reactions, and how they can be manipulated for various applications. However, enzymes are not just passive spectators in the biological arena. They possess distinctive attributes that make them the true stars of the show. Their remarkable efficiency, selectivity, and ability to function under specific conditions set them apart. Some enzymes can accelerate reactions millions of times faster than they would occur in their absence, while others exhibit astounding substrate specificity, ensuring that the right reactions happen at the right place and time. Enzymes can also adapt to a wide range of environmental conditions, making them versatile tools that can be harnessed for diverse applications, from biotechnology to medical therapies. In this Special Issue, we embrace the fascinating world of enzymes, a world where these tiny but mighty structures orchestrate the symphony of life. We will explore the mysteries of enzymatic catalysis, investigate their evolution and divergence, and witness the marvel of enzyme engineering. With a deep understanding of enzymes and their structures, we can unlock the doors to unprecedented opportunities in science and technology, ultimately leading to innovations that can revolutionize various fields and improve the quality of life for all.

Dr. Wonchull Kang
Dr. Armin Wagner
Guest Editors

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Keywords

  • structure
  • X-ray crystallography
  • crystallization
  • enzyme
  • engineering
  • direct evolution

Published Papers (1 paper)

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Research

12 pages, 6839 KiB  
Article
Recognition of a Single β-D-Xylopyranose Molecule by Xylanase GH11 from Thermoanaerobacterium saccharolyticum
by Ki Hyun Nam
Crystals 2024, 14(5), 402; https://doi.org/10.3390/cryst14050402 - 26 Apr 2024
Cited by 1 | Viewed by 504
Abstract
The endo-β-1,4-xylanase glycosyl hydrolase (GH11) decomposes the backbone of xylan into xylooligosaccharides or xylose. These enzymes are important for industrial applications in the production of biofuel, feed, food, and value-added materials. β-D-xylopyranose (XYP, also known as β-D-xylose) is the fundamental unit of the [...] Read more.
The endo-β-1,4-xylanase glycosyl hydrolase (GH11) decomposes the backbone of xylan into xylooligosaccharides or xylose. These enzymes are important for industrial applications in the production of biofuel, feed, food, and value-added materials. β-D-xylopyranose (XYP, also known as β-D-xylose) is the fundamental unit of the substrate xylan, and understanding its recognition is fundamental for the initial steps of GH11’s molecular mechanism. However, little is known about the recognition of a single XYP molecule by GH11. In this study, the crystal structures of GH11 from Thermoanaerobacterium saccharolyticum (TsaGH11) complexed with an XYP molecule were determined at a resolution of 1.7–1.9 Å. The XYP molecule binds to subsite −2 of the substrate-binding cleft. The XYP molecule is mainly stabilized by a π–π interaction with the conserved Trp36 residue. The O2 and O3 atoms of XYP are stabilized by hydrogen bond interactions with the hydroxyl groups of Tyr96 and Tyr192. The conformation of the thumb domain of TsaGH11 does not play a critical role in XYP binding, and XYP binding induces a shift in the thumb domain of TsaGH11 toward the XYP molecule. A structural comparison of TsaGH11 with other GH11 xylanases revealed that the XYP molecule forms π–π stacking with the center between the phenyl and indoline ring of Trp36, whereas the XYP molecule unit from xylobiose or xylotetraose forms π–π stacking with the indoline of Trp36, which indicates that the binding modes of the substrate and XYP differ. These structural results provide a greater understanding of the recognition of XYP by the GH11 family. Full article
(This article belongs to the Special Issue The Crystal Structure and Characteristics of Enzymes)
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