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Crystals
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Crystallography of Enzymes
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Crystallography of Enzymes

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

Deadline for manuscript submissions: 20 August 2024 | Viewed by 4339

Special Issue Editors

Dr. Bo Liang

E-Mail Website
Guest Editor
Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
Interests: biochemistry; structural biology; RNA biology; virology; neurobiology; cancer biology
Dr. Houfu Guo

E-Mail Website
Guest Editor
Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, USA
Interests: protein biochemistry; structural biology; collagen; post-translational modifications; cancer biology; matrix biology

Special Issue Information

Dear Colleagues,

Enzymes are proteins or RNA molecules that act as biological catalysts for accelerating biochemical reactions by lowering their activation energies. Enzymes catalyze more than 5,000 known types of biochemical reactions; however, how enzymes carry out such diverse functions is still not fully understood. Since enzymes' unique three-dimensional (3D) structural architectures allow them to act on substrates and convert them to products, determining enzymes' structure is critical in elucidating their diverse functions. Just as Francis Crick, one of the greatest biologists, once said: "If you want to understand the function, study structure." Currently, X-ray crystallography remains the favored technique for determining enzyme structures. X-ray crystallography has been widely utilized to elucidate the atomic details of catalytic mechanisms and conformational changes in enzymes, such as active site binding to substrates or inhibitors. Such structural insights inform biology and biomedicine. Although many enzyme structures have been determined in the past several decades, more remain to be elucidated. Thus, we welcome structural biologists and biochemists to provide their views and perspectives on the crystallography of interesting and novel enzymes.

Dr. Bo Liang
Dr. Houfu Guo
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Crystals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • enzyme
  • structure
  • function
  • X-ray crystallography
  • crystal
  • crystallization
  • catalytic mechanism
  • antagonist

Published Papers (4 papers)

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Research

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14 pages, 4767 KiB  
Article
Structural Flexibility of the Monomeric Red Fluorescent Protein DsRed
by Ki Hyun Nam
Crystals 2024, 14(1), 62; https://doi.org/10.3390/cryst14010062 - 02 Jan 2024
Viewed by 954
Abstract
The monomeric red fluorescent protein DsRed (mDsRed) is widely used as an optical probe for multicolor applications in flow cytometry or fluorescence microscopy. Understanding the structure and dynamics of mDsRed provides fundamental information for its practical applications. The mDsRed crystal structure has been [...] Read more.
The monomeric red fluorescent protein DsRed (mDsRed) is widely used as an optical probe for multicolor applications in flow cytometry or fluorescence microscopy. Understanding the structure and dynamics of mDsRed provides fundamental information for its practical applications. The mDsRed crystal structure has been reported, but the structural dynamics have not been fully elucidated. Herein, the crystal structure of mDsRed was determined at 2.9 Å resolution, and the molecular flexibility was analyzed. mDsRed contains a solvent-accessible hole between the β7-strand and β9-α10 loop, which is connected to the chromophore. A partial disorder was present in the electron density map of the tyrosine-ring group of the mDsRed chromophore, indicating a flexible conformation of the chromophore. The refined mDsRed chromophore displayed a cis-conformation with a nonplanar configuration between the tyrosine and imidazoline rings of the chromophore. Temperature factor analysis indicated that the β-barrel fold of mDsRed is rigid, while the loops at the top and bottom of the β-barrel are relatively flexible. The β-barrel surface of mDsRed was closer to the native conformation compared with the previously reported Zn-bound state of mDsRed. These structural findings extend our understanding of the molecular flexibility of mDsRed. Full article
(This article belongs to the Special Issue Crystallography of Enzymes)
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13 pages, 7480 KiB  
Article
Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Porphyromonas gingivalis
by Jisub Hwang, Hackwon Do, Youn-Soo Shim and Jun Hyuck Lee
Crystals 2023, 13(8), 1274; https://doi.org/10.3390/cryst13081274 - 18 Aug 2023
Viewed by 860
Abstract
Aspartate semialdehyde dehydrogenase (ASADH) catalyzes the biosynthesis of several essential amino acids, including lysine, methionine, and threonine, and bacterial cell components. Thus, ASADH is a crucial target for developing new antimicrobial agents that can potentially disrupt the biosynthesis of essential amino acids, thereby [...] Read more.
Aspartate semialdehyde dehydrogenase (ASADH) catalyzes the biosynthesis of several essential amino acids, including lysine, methionine, and threonine, and bacterial cell components. Thus, ASADH is a crucial target for developing new antimicrobial agents that can potentially disrupt the biosynthesis of essential amino acids, thereby inhibiting the growth of pathogens. Herein, the crystal structures of ASADH obtained from Porphyromonas gingivalis (PgASADH, UniProtKB code A0A1R4DY25) were determined in apo- and adenosine-2′-5′-diphosphate (2′,5′-ADP)-bound complex forms at a resolution of 1.73 Å. The apo- and 2′,5′-ADP-complexed crystals of PgASADH belonged to the space groups of I212121 and C2221, respectively. Analytical size-exclusion chromatography showed a stable PgASADH dimer in a solution. Clustering analysis and structural comparison studies performed on PgASADH and previously known ASADHs revealed that ASADHs, including PgASADH, can be classified into three types depending on sequential and structural differences at the α-helical subdomain region. These findings provide valuable insights into developing structure-based species-specific new antibacterial drugs against the oral pathogen P. gingivalis. Full article
(This article belongs to the Special Issue Crystallography of Enzymes)
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11 pages, 4004 KiB  
Article
Crystal Structure and Functional Characterization of an S-Formylglutathione Hydrolase (BuSFGH) from Burkholderiaceae sp.
by Jisub Hwang, Hackwon Do, Youn-Soo Shim and Jun Hyuck Lee
Crystals 2023, 13(4), 621; https://doi.org/10.3390/cryst13040621 - 04 Apr 2023
Viewed by 969
Abstract
S-formylglutathione hydrolases (SFGHs) catalyze the hydrolysis of S-formylglutathione to formate and glutathione using the conserved serine hydrolase catalytic triad residues (Ser-His-Asp). SFGHs have broad substrate specificity, including, for example, ester bond-containing substrates. Here, we report the crystal structure of Burkholderiaceae sp. SFGH ( [...] Read more.
S-formylglutathione hydrolases (SFGHs) catalyze the hydrolysis of S-formylglutathione to formate and glutathione using the conserved serine hydrolase catalytic triad residues (Ser-His-Asp). SFGHs have broad substrate specificity, including, for example, ester bond-containing substrates. Here, we report the crystal structure of Burkholderiaceae sp. SFGH (BuSFGH) at 1.73 Å resolution. Structural analysis showed that the overall structure of BuSFGH has a typical α/β hydrolase fold, with a central β-sheet surrounded by α-helices. Analytical ultracentrifugation analysis showed that BuSFGH formed a stable dimer in solution. The enzyme activity assay indicated that BuSFGH has a high preference for short-chain p-nitrophenyl esters, such as p-nitrophenyl acetate. The activity of BuSFGH toward p-nitrophenyl acetate was five times higher than that of p-nitrophenyl butylate. Molecular modeling studies on the p-nitrophenyl acetate-bound BuSFGH structure indicate that Gly52, Leu53, Trp96, His147, Ser148, Trp182, Phe228, and His259 residues may be crucial for substrate binding. Collectively, these results are useful for understanding the substrate-binding mechanism and substrate specificity of BuSFGH. They can also provide useful insights for designing modified BuSFGHs with different substrate specificities. Full article
(This article belongs to the Special Issue Crystallography of Enzymes)
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Review

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14 pages, 14944 KiB  
Review
Structural Aspects of the ROS1 Kinase Domain and Oncogenic Mutations
by Juliana F. Vilachã, Tsjerk A. Wassenaar and Siewert J. Marrink
Crystals 2024, 14(2), 106; https://doi.org/10.3390/cryst14020106 - 23 Jan 2024
Viewed by 1130
Abstract
Protein kinases function as pivotal regulators in biological events, governing essential cellular processes through the transfer of phosphate groups from ATP molecules to substrates. Dysregulation of kinase activity is frequently associated with cancer, ocasionally arising from chromosomal translocation events that relocate genes encoding [...] Read more.
Protein kinases function as pivotal regulators in biological events, governing essential cellular processes through the transfer of phosphate groups from ATP molecules to substrates. Dysregulation of kinase activity is frequently associated with cancer, ocasionally arising from chromosomal translocation events that relocate genes encoding kinases. Fusion proteins resulting from such events, particularly those involving the proto-oncogene tyrosine-protein kinase ROS (ROS1), manifest as constitutively active kinases, emphasizing their role in oncogenesis. Notably, the chromosomal reallocation of the ros1 gene leads to fusion of proteins with the ROS1 kinase domain, implicated in various cancer types. Despite their prevalence, targeted inhibition of these fusion proteins relies on repurposed kinase inhibitors. This review comprehensively surveys experimentally determined ROS1 structures, emphasizing the pivotal role of X-ray crystallography in providing high-quality insights. We delve into the intricate interactions between ROS1 and kinase inhibitors, shedding light on the structural basis for inhibition. Additionally, we explore point mutations identified in patients, employing molecular modeling to elucidate their structural impact on the ROS1 kinase domain. By integrating structural insights with in vitro and in silico data, this review advances our understanding of ROS1 kinase in cancer, offering potential avenues for targeted therapeutic strategies. Full article
(This article belongs to the Special Issue Crystallography of Enzymes)
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