Special Issue "Crystallographic Studies of Enzymes"

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

Deadline for manuscript submissions: 31 October 2019.

Special Issue Editors

Guest Editor
Prof. Dr. Kyeong Kyu Kim Website E-Mail
SungKyunKwan University, School of Medicine, Department of Molecular and Cellular Biology, Suwon 16419, South Korea
Interests: enzymes; structures; esterase; deubiquitinase; noncanonical DNA
Guest Editor
Prof. Dr. T. Doohun Kim Website E-Mail
Sookmyung Women's University, College of Natural Science, Department of Chemistry, Seoul, 04310, South Korea
Interests: protein-ligand interactions; enzyme structures; assay development; immobilization of enzymes

Special Issue Information

Dear Colleagues,

Enzymes play a major role in control of key biological processes, including metabolism and signalling, by accelerating chemical processes. Therefore, examining their structures and reaction mechanisms is essential for understanding not only the biological processes at a molecule level but also their application in various fields such as protein engineering and drug development. Indeed, enzymes such as protein kinases or proteases can be considered major drug targets for many diseases. Although cryoEM and NMR provide useful structural information, X-ray crystallography is the best because it elucidates the atomic structure of enzymes, which can be used as a frame for structure-based protein engineering or drug development. In these aspects, enzyme crystallography can be considered a door leading to a new world.

In this Special Issue, we intend to collect research manuscripts on enzyme crystallography. However, since the goal of this Issue is to provide rich resources on enzymes regarding their structural and functional aspects, we also encourage manuscript submissions of studies on the structure, function, and application of enzymes, which would provide complementary information for enzyme crystallography.  

Prof. Dr. Kyeong Kyu Kim
Prof. Dr. T. Doohun Kim
Guest Editors

Manuscript Submission Information

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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 1400 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

  • crystallography
  • enzymes
  • structure
  • function
  • drug target
  • protein engineering

Published Papers (5 papers)

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Research

Open AccessArticle
Comparison of Candida Albicans Fatty Acid Amide Hydrolase Structure with Homologous Amidase Signature Family Enzymes
Crystals 2019, 9(9), 472; https://doi.org/10.3390/cryst9090472 - 10 Sep 2019
Abstract
Fatty acid amide hydrolase (FAAH) is a well-characterized member of the amidase signature (AS) family of serine hydrolases. The membrane-bound FAAH protein is responsible for the catabolism of neuromodulatory fatty acid amides, including anandamide and oleamide, that regulate a wide range of mammalian [...] Read more.
Fatty acid amide hydrolase (FAAH) is a well-characterized member of the amidase signature (AS) family of serine hydrolases. The membrane-bound FAAH protein is responsible for the catabolism of neuromodulatory fatty acid amides, including anandamide and oleamide, that regulate a wide range of mammalian behaviors, including pain perception, inflammation, sleep, and cognitive/emotional state. To date, limited crystal structures of FAAH and non-mammalian AS family proteins have been determined and used for structure-based inhibitor design. In order to provide broader structural information, the crystal structure of FAAH from the pathogenic fungus Candida albicans was determined at a resolution of 2.2 Å. A structural comparison with a brown rat Rattus norvegicus FAAH as well as with other bacterial AS family members, MAE2 and PAM, showed overall similarities but there were several discriminative regions found: the transmembrane domain and the hydrophobic cap of the brown rat FAAH were completely absent in the fungal FAAH structure. Along with these results, a phylogenetic analysis of 19 species within the AS family showed that fungal FAAHs diverged from a common ancestor before the separation of eukarya and prokarya. Taken together, this study provides insights into developing more potent inhibitors of FAAH as well as expanding our knowledge of the relationships between AS family members. Full article
(This article belongs to the Special Issue Crystallographic Studies of Enzymes)
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Open AccessArticle
Crystal Structure of NADPH-Dependent Methylglyoxal Reductase Gre2 from Candida Albicans
Crystals 2019, 9(9), 471; https://doi.org/10.3390/cryst9090471 - 10 Sep 2019
Abstract
Gre2 is a key enzyme in the methylglyoxal detoxification pathway; it uses NADPH or NADH as an electron donor to reduce the cytotoxic methylglyoxal to lactaldehyde. This enzyme is a member of the short-chain dehydrogenase/reductase (SDR) superfamily whose members catalyze this type of [...] Read more.
Gre2 is a key enzyme in the methylglyoxal detoxification pathway; it uses NADPH or NADH as an electron donor to reduce the cytotoxic methylglyoxal to lactaldehyde. This enzyme is a member of the short-chain dehydrogenase/reductase (SDR) superfamily whose members catalyze this type of reaction with a broad range of substrates. To elucidate the structural features, we determined the crystal structures of the NADPH-dependent methylglyoxal reductase Gre2 from Candida albicans (CaGre2) for both the apo-form and NADPH-complexed form at resolutions of 2.8 and 3.02 Å, respectively. The CaGre2 structure is composed of two distinct domains: the N-terminal cofactor-binding domain and the C-terminal substrate-binding domain. Extensive comparison of CaGre2 with its homologous structures reveals conformational changes in α12 and β3′ of the NADPH-complex forms. This study may provide insights into the structural and functional variation of SDR family proteins. Full article
(This article belongs to the Special Issue Crystallographic Studies of Enzymes)
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Open AccessCommunication
Triglycine-Based Approach for Identifying the Substrate Recognition Site of an Enzyme
Crystals 2019, 9(9), 444; https://doi.org/10.3390/cryst9090444 - 26 Aug 2019
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Crystallographic Studies of Enzymes)
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Open AccessArticle
Structural Analyses of Helicobacter Pylori FolC Conducting Glutamation in Folate Metabolism
Crystals 2019, 9(8), 429; https://doi.org/10.3390/cryst9080429 - 19 Aug 2019
Abstract
FolC plays important roles in the folate metabolism of cells by attaching l-Glu to dihydropteroate (DHP) and folate, which are known activities of dihydrofolate synthetase (DHFS) and folylpolyglutamate synthetase (FPGS), respectively. Here, we determined the crystal structure of Helicobacter pylori FolC ( [...] Read more.
FolC plays important roles in the folate metabolism of cells by attaching l-Glu to dihydropteroate (DHP) and folate, which are known activities of dihydrofolate synthetase (DHFS) and folylpolyglutamate synthetase (FPGS), respectively. Here, we determined the crystal structure of Helicobacter pylori FolC (HpFolC) at 1.95 Å resolution using the single-wavelength anomalous diffraction method. HpFolC has globular N- and C-terminal domains connected by a single loop, and a binding site for ATP is located between the two domains. Apo-HpFolC was crystallized in the presence of citrate in a crystallization solution, which was held in the ATP-binding site. Structural motifs such as the P-loop and Ω-loop of HpFolC for binding of ATP and two magnesium ions are well conserved in spite of the low overall sequence similarity to other FolC/FPGSs. The Ω-loop would also recognize a folate molecule, and the DHP-binding loop of HpFolC is expected to exhibit a unique recognition mode on DHP, compared with other FolCs. Because human FolC is known to only exhibit FPGS activity, the DHFS activity of bacterial FolC is an attractive target for the eradication of pathogenic bacteria. Consequently, our structural analyses of HpFolC provide a valuable foundation for a universal antibacterial strategy against H. pylori as well as other pathogenic bacteria. Full article
(This article belongs to the Special Issue Crystallographic Studies of Enzymes)
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Open AccessArticle
Crystal Structure of Chaperonin GroEL from Xanthomonas oryzae pv. oryzae
Crystals 2019, 9(8), 399; https://doi.org/10.3390/cryst9080399 - 02 Aug 2019
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a plant pathogen that causes bacterial blight of rice, with outbreaks occurring in most rice-growing countries. Thus far, there is no effective pesticide against bacterial blight. Chaperones in bacterial pathogens are important for the stabilization [...] Read more.
Xanthomonas oryzae pv. oryzae (Xoo) is a plant pathogen that causes bacterial blight of rice, with outbreaks occurring in most rice-growing countries. Thus far, there is no effective pesticide against bacterial blight. Chaperones in bacterial pathogens are important for the stabilization and delivery of effectors into host cells to cause disease. In bacteria, GroEL/GroES complex mediates protein folding and protects proteins against misfolding and aggregation caused by environmental stress. We determined the crystal structure of GroEL from Xanthomonas oryzae pv. oryzae (XoGroEL) at 3.2 Å resolution, which showed the open form of two conserved homoheptameric rings stacked back-to-back. In the open form structure, the apical domain of XoGroEL had a higher B factor than the intermediate and equatorial domains, indicating that the apical domain had a flexible conformation before the binding of substrate unfolded protein and ATP. The XoGroEL structure will be helpful in understanding the function and catalytic mechanism of bacterial chaperonin GroELs. Full article
(This article belongs to the Special Issue Crystallographic Studies of Enzymes)
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