scholarly journals The Crystal Structure of Nα-p-tosyl-lysyl Chloromethylketone-Bound Oligopeptidase B from Serratia Proteamaculans Revealed a New Type of Inhibitor Binding

Crystals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1438
Author(s):  
Vladimir I. Timofeev ◽  
Dmitry E. Petrenko ◽  
Yulia K. Agapova ◽  
Anna V. Vlaskina ◽  
David M. Karlinsky ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Pocket ◽  
Catalytic Triad ◽  
Inhibitor Binding ◽  
Inhibitor Molecule ◽  
Covalent Bonds ◽  
Catalytic Residues ◽  
Serratia Proteamaculans ◽  
Oligopeptidase B ◽  
New Type

A covalent serine protease inhibitor—Na-p-tosyl-lysyl chloromethylketone (TCK) is a modified lysine residue tosylated at the N-terminus and chloromethylated at the C-terminus, one molecule of which is capable of forming two covalent bonds with both Ser and His catalytic residues, was co-crystallized with modified oligopeptidase B (OpB) from Serratia proteomaculans (PSPmod). The kinetics study, which preceded crystallization, shows that the stoichiometry of TCK-dependent inhibition of PSPmod was 1:2 (protein:inhibitor). The crystal structure of the PSPmod-TCK complex, solved at a resolution of 2.3 Å, confirmed a new type of inhibitor binding. Two TCK molecules were bound to one enzyme molecule: one with the catalytic Ser, the other with the catalytic His. Due to this mode of binding, the intermediate state of PSPmod and the disturbed conformation of the catalytic triad were preserved in the PSPmod-TCK complex. Nevertheless, the analysis of the amino acid surroundings of the inhibitor molecule bound to the catalytic Ser and its comparison with that of antipain-bound OpB from Trypanosoma brucei provided an insight in the structure of the PSPmod substrate-binding pocket. Supposedly, the new type of binding is typical for the interaction of chloromethylketone derivatives with two-domain OpBs. In the open conformational state that these enzymes are assumed in solution, the disordered configuration of the catalytic triad prevents simultaneous interaction of one inhibitor molecule with two catalytic residues.

Activity modulation of the oligopeptidase B from Serratia proteamaculans by site-directed mutagenesis of amino acid residues surrounding catalytic triad histidine

Biochimie ◽  
2017 ◽  
Vol 139 ◽  
pp. 125-136 ◽  
Author(s):  
Anna G. Mikhailova ◽  
Tatiana V. Rakitina ◽  
Vladimir I. Timofeev ◽  
David M. Karlinsky ◽  
Dmitry A. Korzhenevskiy ◽  
...  
Keyword(s):  
Amino Acid ◽  
Catalytic Triad ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Serratia Proteamaculans ◽  
Oligopeptidase B

scholarly journals Structure-function studies of CrmK, an oxidase involved in Caerulomycin A biosynthesis

2014 ◽  
Vol 70 (a1) ◽  
pp. C1669-C1669
Author(s):  
Marie-Ève Picard ◽  
Julie Barma ◽  
Yiguang Zhu ◽  
Xavier Murphy Després ◽  
Jean-Baptiste Duvignaud ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Pocket ◽  
Antimicrobial Activities ◽  
Active Site Residues ◽  
Covalent Bonds ◽  
Protein Residues ◽  
Function Relationship ◽  
Structure And Function Relationship ◽  
And Function ◽  
Relationship Of

Caerulomycin A (CRM A) is an immunosupressive agent that has a unique 2,2'-bipyridine core structure. Isolated from a marine-derived Actinoalloteichus cyanogriseus, this natural product exhibits antifungal, anti-amoebic, antitumor, and antimicrobial activities. Its biosynthetic pathway consists of more than 20 enzymes, at least seven of which are putatively involved in post-PKS/NRPS modifications of the scaffold. Among these, CrmK is a flavin-dependent oxidase. We have determined the crystal structure of CrmK bound to its flavin adenin dinucleotide (FAD) cofactor at 1.9 Å resolution. FAD linkage to CrmK is observed via two covalent bonds with protein residues His64 and Cys124. This crystal structure, combined with the activity analysis of both wild-type CrmK and a series of mutants, has revealed the role of active site residues lining the substrate and FAD binding pocket. Our studies add additional molecular insights into the structure and function relationship of the bicovalently flavinylated oxidases.

scholarly journals Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9965 ◽  
Author(s):  
Valentina L. Kouznetsova ◽  
Aidan Zhang ◽  
Mahidhar Tatineni ◽  
Mark A. Miller ◽  
Igor F. Tsigelny
Keyword(s):  
Crystal Structure ◽  
Pharmacophore Model ◽  
Binding Pocket ◽  
Free Energies ◽  
Inhibitor Binding ◽  
Drug List ◽  
Approved Drugs ◽  
Docking Interaction ◽  
Potential Inhibitors ◽  
Fda Approved Drugs

Using the crystal structure of SARS-CoV-2 papain-like protease (PLpro) as a template, we developed a pharmacophore model of functional centers of the PLpro inhibitor-binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. This search identified 147 compounds that can be potential inhibitors of SARS-CoV-2 PLpro. The conformations of these compounds underwent 3D fingerprint similarity clusterization, followed by docking of possible conformers to the binding pocket of PLpro. Docking of random compounds to the binding pocket of protease was also done for comparison. Free energies of the docking interaction for the selected compounds were lower than for random compounds. The drug list obtained includes inhibitors of HIV, hepatitis C, and cytomegalovirus (CMV), as well as a set of drugs that have demonstrated some activity in MERS, SARS-CoV, and SARS-CoV-2 therapy. We recommend testing of the selected compounds for treatment of COVID-19

Crystal structure of an inclusion complex between chiral monoaza-15-crown-5 and S(–)-1-phenyl-ethyl ammonium percholorate

2003 ◽  
Vol 218 (5) ◽  
Author(s):  
Süheyla Özbey ◽  
F. B. Kaynak ◽  
M. Toğrul ◽  
N. Demirel ◽  
H. Hoşgören
Keyword(s):  
Crystal Structure ◽  
Inclusion Complex ◽  
Single Crystal ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
New Type

AbstractA new type of inclusion complex, S(–)-1 phenyl ethyl ammonium percholorate complex of R-(–)-2-ethyl - N - benzyl - 4, 7, 10, 13 - tetraoxa -1- azacyclopentadecane, has been prepared and studied by NMR, IR and single crystal X-ray diffraction techniques. The compound crystallizes in space group

Structural Insights into Azole-based Inhibitors of Heme Oxygenase-1: Development of Selective Compounds for Therapeutic Applications

2019 ◽  
Vol 25 (42) ◽  
pp. 5803-5821 ◽  
Author(s):  
Mona N. Rahman ◽  
Dragic Vukomanovic ◽  
Jason Z. Vlahakis ◽  
Walter A. Szarek ◽  
Kanji Nakatsu ◽  
...  
Keyword(s):  
Heme Oxygenase ◽  
Competitive Inhibition ◽  
Cytochromes P450 ◽  
Structural Similarity ◽  
Binding Pocket ◽  
Initial Study ◽  
Structural Basis ◽  
Heme Oxygenase 1 ◽  
Design Strategies ◽  
Inhibitor Binding

The development of isozyme-selective heme oxygenase (HO) inhibitors promises powerful pharmacological tools to elucidate the regulatory characteristics of the HO system. It is already known that HO has cytoprotective properties with a role in several disease states; thus, it is an enticing therapeutic target. Historically, the metalloporphyrins have been used as competitive HO inhibitors based on their structural similarity to the substrate, heme. However, heme’s important role in several other proteins (e.g. cytochromes P450, nitric oxide synthase), results in non-selectivity being an unfortunate side effect. Reports that azalanstat and other non-porphyrin molecules inhibited HO led to a multi-faceted effort over a decade ago to develop novel compounds as potent, selective inhibitors of HO. The result was the creation of the first generation of non-porphyrin based, non-competitive inhibitors with selectivity for HO, including a subset with isozyme selectivity for HO-1. Using X-ray crystallography, the structures of several complexes of HO-1 with novel inhibitors have been elucidated and provided insightful information regarding the salient features required for inhibitor binding. This included the structural basis for non-competitive inhibition, flexibility and adaptability of the inhibitor binding pocket, and multiple, potential interaction subsites, all of which can be exploited in future drug-design strategies. Notably, HO-1 inhibitors are of particular interest for the treatment of hyperbilirubinemia and certain types of cancer. Key features based on this initial study have already been used by others to discover additional potential HO-1 inhibitors. Moreover, studies have begun to use selected compounds and determine their effects in some disease models.

A 2-D Zn(II) coordination polymer based on 4,5-imidazoledicarboxylate and bis(benzimidazole) ligands: synthesis, crystal structure and fluorescence properties

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Xinzhao Xia ◽  
Lixian Xia ◽  
Geng Zhang ◽  
Yuxuan Jiang ◽  
Fugang Sun ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Coordination Polymer ◽  
Zigzag Chain ◽  
Supramolecular Framework ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
Hydrogen Bond Interaction ◽  
X Ray ◽  
New Type ◽  
Solid State Fluorescence

Abstract In this work, a new type of zinc(II) coordination polymer {[Zn(HIDC)(BBM)0.5]·H2O} n (Zn-CP) was synthesized using 4,5-imidazoledicarboxylic acid (H3IDC) and 2,2-(1,4-butanediyl)bis-1,3-benzimidazole (BBM) under hydrothermal conditions. Its structure has been characterized by infrared spectroscopy, elemental analysis and single crystal X-ray diffraction analysis. The Zn(II) ion is linked by the HIDC2− ligand to form a zigzag chain by chelating and bridging, and then linked by BBM to form a layered network structure. Adjacent layers are further connected by hydrogen bond interaction to form a 3-D supramolecular framework. The solid-state fluorescence performance of Zn-CP shows that compared with free H3IDC ligand, its fluorescence intensity is significantly enhanced.

scholarly journals Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yufei Han ◽  
Qian Zhuang ◽  
Bo Sun ◽  
Wenping Lv ◽  
Sheng Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Biochemical Characterization ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Substrate Binding Pocket ◽  
Transmembrane Segments ◽  
Therapeutic Molecules ◽  
Binding Cavity ◽  
Immune System Regulation ◽  
Mediated Reduction

AbstractSteroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-Δ4 structure, such as testosterone or progesterone, are catalyzed by steroid 5α-reductases (SRD5As) to generate their corresponding 3-oxo-5α steroids, which are essential for multiple physiological and pathological processes. SRD5A2 is already a target of clinically relevant drugs. However, the detailed mechanism of SRD5A-mediated reduction remains elusive. Here we report the crystal structure of PbSRD5A from Proteobacteria bacterium, a homolog of both SRD5A1 and SRD5A2, in complex with the cofactor NADPH at 2.0 Å resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic substrate binding cavity, whereas TM5-7 coordinate cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with biochemical characterization, define the substrate binding pocket of SRD5As, explain the properties of disease-related mutants and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-Δ4 reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible.

scholarly journals Characterization of the Acetate Binding Pocket in the Methanosarcina thermophila Acetate Kinase

2005 ◽  
Vol 187 (7) ◽  
pp. 2386-2394 ◽  
Author(s):  
Cheryl Ingram-Smith ◽  
Andrea Gorrell ◽  
Sarah H. Lawrence ◽  
Prabha Iyer ◽  
Kerry Smith ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Binding Pocket ◽  
Acetate Kinase ◽  
Phosphoryl Group ◽  
Acetyl Phosphate ◽  
Hydrophobic Pocket ◽  
Methanosarcina Thermophila ◽  
Methyl Group ◽  
Substrate Binding Sites

ABSTRACT Acetate kinase catalyzes the reversible magnesium-dependent synthesis of acetyl phosphate by transfer of the ATP γ-phosphoryl group to acetate. Inspection of the crystal structure of the Methanosarcina thermophila enzyme containing only ADP revealed a solvent-accessible hydrophobic pocket formed by residues Val93, Leu122, Phe179, and Pro232 in the active site cleft, which identified a potential acetate binding site. The hypothesis that this was a binding site was further supported by alignment of all acetate kinase sequences available from databases, which showed strict conservation of all four residues, and the recent crystal structure of the M. thermophila enzyme with acetate bound in this pocket. Replacement of each residue in the pocket produced variants with Km values for acetate that were 7- to 26-fold greater than that of the wild type, and perturbations of this binding pocket also altered the specificity for longer-chain carboxylic acids and acetyl phosphate. The kinetic analyses of variants combined with structural modeling indicated that the pocket has roles in binding the methyl group of acetate, influencing substrate specificity, and orienting the carboxyl group. The kinetic analyses also indicated that binding of acetyl phosphate is more dependent on interactions of the phosphate group with an unidentified residue than on interactions between the methyl group and the hydrophobic pocket. The analyses also indicated that Phe179 is essential for catalysis, possibly for domain closure. Alignments of acetate kinase, propionate kinase, and butyrate kinase sequences obtained from databases suggested that these enzymes have similar catalytic mechanisms and carboxylic acid substrate binding sites.

A New Class of Oxide Superconductor (Nd, Ce, Sr)2CuO4

1989 ◽  
Vol 156 ◽  
Author(s):  
E. Takayama-Muromachi
Keyword(s):  
Crystal Structure ◽  
Crystal Chemistry ◽  
Superconducting Phase ◽  
Type Structure ◽  
Oxide Superconductor ◽  
New Class ◽  
System 2 ◽  
New Type ◽  
System 1 ◽  
Tetragonal Cell

ABSTRACTSince the discovery of the high-Tc superconductor in the La-Ba-Cu-O system [1], a great deal of experimental and theoretical effort have been made to clarify the nature of the Cu-based oxides. In order to elucidate mechanism of the high-Tc superconductivity, discovery of a new type of superconductor is no doubt of great importance. Recently, Akimitsu et al. found a new oxide superconductor in the Nd-Ce-Sr-Cu-O system [2]. Soon after their discovery, the superconducting phase was isolated and identified [3]. It has a tetragonal cell with space group P4/nmm and has a structure closely related to but different from the K2NiF4− or T'-Nd2CuO4− -type structure. Although, Tc of the Nd-Ce-Sr-Cu oxide is not so high (ca. 20 K) compared with the 1–2–3 or Bi(Tl)-based superconductors, it has aroused interest widely due to a very simple crystal structure. In this article, I will discuss superconductivity and crystal chemistry of the Nd-Ce-Sr-Cu oxide. Also, various compounds isostructural to it will be presented.

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