The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine

The following article, Alexeeva, M., Åberg, E., Engh, R.A. & Rothweiler, U. (2015). The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine. Acta Crystallographica Section D: Biological Crystallography, 71, 1207-1215, can be accessed at https://doi.org/10.1107/S1399004715005106.Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a protein kinase associated with neuronal development and brain physiology. The DYRK kinases are very unusual with respect to the sequence of the catalytic loop, in which the otherwise highly conserved arginine of the HRD motif is replaced by a cysteine. This replacement, along with the proximity of a potential disulfide-bridge partner from the activation segment, implies a potential for redox control of DYRK family activities. Here, the crystal structure of DYRK1A bound to PKC412 is reported, showing the formation of the disulfide bridge and associated conformational changes of the activation loop. The DYRK kinases represent emerging drug targets for several neurological diseases as well as cancer. The observation of distinct activation states may impact strategies for drug targeting. In addition, the characterization of PKC412 binding offers new insights for DYRK inhibitor discovery

Novel DYRK1A Inhibitor Rescues Learning and Memory Deficits in a Mouse Model of Down Syndrome

Down syndrome (DS) is a complex genetic disorder associated with substantial physical, cognitive, and behavioral challenges. Due to better treatment options for the physical co-morbidities of DS, the life expectancy of individuals with DS is beginning to approach that of the general population. However, the cognitive deficits seen in individuals with DS still cannot be addressed pharmacologically. In young individuals with DS, the level of intellectual disability varies from mild to severe, but cognitive ability generally decreases with increasing age, and all individuals with DS have early onset Alzheimer’s disease (AD) pathology by the age of 40. The present study introduces a novel inhibitor for the protein kinase DYRK1A, a key controlling kinase whose encoding gene is located on chromosome 21. The novel inhibitor is well characterized for use in mouse models and thus represents a valuable tool compound for further DYRK1A researc

Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface

Published version also available at http://dx.doi.org/10.1107/S1399004714021099DNA ligases are a structurally diverse class of enzymes which share a common catalytic core and seal breaks in the phosphodiester backbone of double-stranded DNA via an adenylated intermediate. Here, the structure and activity of a recombinantly produced ATP-dependent DNA ligase from the bacterium Psychromonas sp. strain SP041 is described. This minimal-type ligase, like its close homologues, is able to ligate singly nicked double-stranded DNA with high efficiency and to join cohesive-ended and blunt-ended substrates to a more limited extent. The 1.65 A˚ resolution crystal structure of the enzyme–adenylate complex reveals no unstructured loops or segments, and suggests that this enzyme binds the DNA without requiring full encirclement of the DNA duplex. This is in contrast to previously characterized minimal DNA ligases from viruses, which use flexible loop regions for DNA interaction. The Psychromonas sp. enzyme is the first structure available for the minimal type of bacterial DNA ligases and is the smallest DNA ligase to be crystallized to date

The crystal structure of haemoglobin from Atlantic cod

The crystal structure of haemoglobin from Atlantic cod has been solved to 2.54 Å resolution. The structure consists of two tetramers in the crystallographic asymmetric unit. The structure of haemoglobin obtained from one individual cod suggests polymorphism in the tetrameric assembly.publishedVersio

The crystal structure of the N-acetylglucosamine 2-epimerase from Nostoc sp. KVJ10 reveals the true dimer

N-Acetylglucosamine 2-epimerases (AGEs) catalyze the interconversion of N-acetylglucosamine and N-acetylmannosamine. They can be used to perform the first step in the synthesis of sialic acid from N-acetylglucosamine, which makes the need for efficient AGEs a priority. This study presents the structure of the AGE from Nostoc sp. KVJ10 collected in northern Norway, referred to as nAGE10. It is the third AGE structure to be published to date, and the first one in space group P42212. The nAGE10 monomer folds as an (α/α)6 barrel in a similar manner to that of the previously published AGEs, but the crystal did not contain the dimers that have previously been reported. The previously proposed `back-to-back' assembly involved the face of the AGE monomer where the barrel helices are connected by small loops. Instead, a `front-to-front' dimer was found in nAGE10 involving the long loops that connect the barrel helices at this end. This assembly is also present in the other AGE structures, but was attributed to crystal packing, even though the `front' interface areas are larger and are more conserved than the `back' interface areas. In addition, the front-to-front association allows a better explanation of the previously reported observations considering surface cysteines. Together, these results indicate that the `front-to-front' dimer is the most probable biological assembly for AGEs

Structure and function of a CE4 deacetylase isolated from a marine environment

Chitin, a polymer of β(1–4)-linked N-acetylglucosamine found in e.g. arthropods, is a valuable resource that may be used to produce chitosan and chitooligosaccharides, two compounds with considerable industrial and biomedical potential. Deacetylating enzymes may be used to tailor the properties of chitin and its derived products. Here, we describe a novel CE4 enzyme originating from a marine Arthrobacter species (ArCE4A). Crystal structures of this novel deacetylase were determined, with and without bound chitobiose [(GlcNAc)2], and refined to 2.1 Å and 1.6 Å, respectively. In-depth biochemical characterization showed that ArCE4A has broad substrate specificity, with higher activity against longer oligosaccharides. Mass spectrometry-based sequencing of reaction products generated from a fully acetylated pentamer showed that internal sugars are more prone to deacetylation than the ends. These enzyme properties are discussed in the light of the structure of the enzyme-ligand complex, which adds valuable information to our still rather limited knowledge on enzyme-substrate interactions in the CE4 family

Structure-based sequence alignment of CE4 deacetylases.

<p>The structure-based sequence alignment was obtained using PyMod 1.0 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187544#pone.0187544.ref043" target="_blank">43</a>]. Fully conserved residues are shown on a green background. The asterisks indicate residues involved in metal binding (blue) and in catalysis (pink). MT1-5 indicate the five conserved motifs in CE4 deacetylases. Colored horizontal bars indicate the different loops described by Andrés et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187544#pone.0187544.ref016" target="_blank">16</a>]. The deacetylases included in the alignment are: <i>Sp</i>PgdA, PDB id 2C1G [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187544#pone.0187544.ref024" target="_blank">24</a>]; <i>Cl</i>CDA, PDB id 2IW0 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187544#pone.0187544.ref034" target="_blank">34</a>]; <i>An</i>CDA, PDB id 2Y8U [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187544#pone.0187544.ref015" target="_blank">15</a>]; <i>Sl</i>CE4, PDB id 2CC0 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187544#pone.0187544.ref033" target="_blank">33</a>]; <i>Bs</i>PdaA, PDB id 1W17 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187544#pone.0187544.ref044" target="_blank">44</a>]; <i>Vc</i>CDA, PDB id 4NY2 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187544#pone.0187544.ref016" target="_blank">16</a>]. For clarity, the alignment only shows the sequence area of the five motifs and the loops. Sequence numbering is based on the primary gene product, including the signal peptide for the proteins harboring a signal peptide.</p

Activity of <i>Ar</i>CE4A against different substrates.

<p>Activity of <i>Ar</i>CE4A against different substrates.</p