scholarly journals Crystal structure of UbiX, an aromatic acid decarboxylase from the psychrophilic bacterium Colwellia psychrerythraea that undergoes FMN-induced conformational changes

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Hackwon Do ◽  
Soo Jin Kim ◽  
Chang Woo Lee ◽  
Han-Woo Kim ◽  
Hyun Ho Park ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Aromatic Acid ◽  
Acid Decarboxylase ◽  
Psychrophilic Bacterium ◽  
Colwellia Psychrerythraea

scholarly journals Purification, crystallization and preliminary X-ray crystallographic studies of FMN-bound and FMN-free forms of aromatic acid decarboxylase (CpsUbiX) from the psychrophilic bacteriumColwellia psychrerythraea34H

2014 ◽  
Vol 70 (2) ◽  
pp. 215-220 ◽  
Author(s):  
Hackwon Do ◽  
Chang Woo Lee ◽  
Se Jong Han ◽  
Sung Gu Lee ◽  
Hak Jun Kim ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Aromatic Acid ◽  
Diffusion Method ◽  
Flavin Mononucleotide ◽  
Acid Decarboxylase ◽  
Data Sets ◽  
Single Mutation ◽  
Homologous Proteins ◽  
Space Group

TheubiXgene (UniProtKB code Q489U8) ofColwellia psychrerythraeastrain 34H has been annotated as a putative flavin mononucleotide (FMN)-dependent aromatic acid decarboxylase. Based on previous studies of homologous proteins, CpsUbiX is thought to catalyze the decarboxylation of 3-octaprenyl-4-hydroxybenzoate to produce 2-polyprenylphenol in the ubiquinone-biosynthesis pathway using a noncovalently bound FMN molecule as a cofactor. However, the detailed mechanisms of this important enzyme are not yet clear and need to be further elucidated. In this study, it was found that the V47S single mutation resulted in a loss of FMN binding, resulting in the production of FMN-free CpsUbiX protein. This mutation is likely to destabilize FMN–protein interactions without affecting the overall structural folding. To fully characterize the conformational changes upon FMN binding and the enzymatic mechanism at the molecular level, the wild-type (FMN-bound) and V47S mutant (FMN-free) CpsUbiX proteins were purified and crystallized using the sitting-drop vapour-diffusion method. Furthermore, complete diffraction data sets for FMN-bound (space groupC2221) and FMN-free (space groupP23) forms were obtained to 2.0 and 1.76 Å resolution, respectively.

Improved resolution crystal structure of Acanthamoeba actophorin reveals structural plasticity not induced by microgravity

2021 ◽  
Vol 77 (12) ◽  
Author(s):  
Stephen Quirk ◽  
Raquel L. Lieberman
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Actin Filaments ◽  
Space Station ◽  
Acanthamoeba Castellanii ◽  
Test Case ◽  
Molecular Replacement ◽  
International Space ◽  
Microgravity Conditions ◽  
Turn Region

Actophorin, a protein that severs actin filaments isolated from the amoeba Acanthamoeba castellanii, was employed as a test case for crystallization under microgravity. Crystals of purified actophorin were grown under microgravity conditions aboard the International Space Station (ISS) utilizing an interactive crystallization setup between the ISS crew and ground-based experimenters. Crystals grew in conditions similar to those grown on earth. The structure was solved by molecular replacement at a resolution of 1.65 Å. Surprisingly, the structure reveals conformational changes in a remote β-turn region that were previously associated with actophorin phosphorylated at the terminal residue Ser1. Although crystallization under microgravity did not yield a higher resolution than crystals grown under typical laboratory conditions, the conformation of actophorin obtained from solving the structure suggests greater flexibility in the actophorin β-turn than previously appreciated and may be beneficial for the binding of actophorin to actin filaments.

scholarly journals Crystal structure of SARS-CoV-2 main protease in complex with a Chinese herb inhibitor shikonin

2020 ◽  
Author(s):  
Jian Li ◽  
Xuelan Zhou ◽  
Yan Zhang ◽  
Fanglin Zhong ◽  
Cheng Lin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Drug Targets ◽  
Chinese Herb ◽  
Binding Modes ◽  
High Potency ◽  
Main Protease ◽  
Covalent Inhibitors ◽  
Catalytic Dyad ◽  
Important Drug

AbstractMain protease (Mpro, also known as 3CLpro) has a major role in the replication of coronavirus life cycle and is one of the most important drug targets for anticoronavirus agents. Here we report the crystal structure of main protease of SARS-CoV-2 bound to a previously identified Chinese herb inhibitor shikonin at 2.45 angstrom resolution. Although the structure revealed here shares similar overall structure with other published structures, there are several key differences which highlight potential features that could be exploited. The catalytic dyad His41-Cys145 undergoes dramatic conformational changes, and the structure reveals an unusual arrangement of oxyanion loop stabilized by the substrate. Binding to shikonin and binding of covalent inhibitors show different binding modes, suggesting a diversity in inhibitor binding. As we learn more about different binding modes and their structure-function relationships, it is probable that we can design more effective and specific drugs with high potency that can serve as effect SARS-CoV-2 anti-viral agents.

Crystal structure of the stromelysin catalytic domain at 2.0 Å resolution: inhibitor-induced conformational changes 1 1Edited by R. Huber

1999 ◽  
Vol 293 (3) ◽  
pp. 545-557 ◽  
Author(s):  
Longyin Chen ◽  
Timothy J Rydel ◽  
Fei Gu ◽  
C.Michelle Dunaway ◽  
Stanislaw Pikul ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Catalytic Domain

Synthesis, crystal structure and properties of two ternary rare earth complexes with aromatic acid and 1,10-phenanthroline

2008 ◽  
Vol 463 (1-2) ◽  
pp. 338-342 ◽  
Author(s):  
Na Zhao ◽  
Shu-Ping Wang ◽  
Rui-Xia Ma ◽  
Zhi-Hua Gao ◽  
Rui-Fen Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Rare Earth ◽  
Aromatic Acid ◽  
Rare Earth Complexes ◽  
Structure And Properties

Cloning, Expression, and Characterization of a Cold-Adapted Shikimate Kinase from the Psychrophilic Bacterium Colwellia psychrerythraea 34H

2016 ◽  
Vol 26 (12) ◽  
pp. 2087-2097 ◽  
Author(s):  
Wahyu Sri Kunto Nugroho ◽  
Dong-Woo Kim ◽  
Jong-Cheol Han ◽  
Young Baek Hur ◽  
Soo-Wan Nam ◽  
...  
Keyword(s):  
Psychrophilic Bacterium ◽  
Shikimate Kinase ◽  
Cold Adapted ◽  
Colwellia Psychrerythraea

scholarly journals Binding of cardiotonic steroids to Na+,K+-ATPase in the E2P state

2020 ◽  
Vol 118 (1) ◽  
pp. e2020438118
Author(s):  
Ryuta Kanai ◽  
Flemming Cornelius ◽  
Haruo Ogawa ◽  
Kanna Motoyama ◽  
Bente Vilsen ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Conformational Changes ◽  
Ground State ◽  
Sodium Pump ◽  
Structural Features ◽  
Animal Cells ◽  
Inhibitory Potency ◽  
New Members ◽  
Wide Range

The sodium pump (Na+, K+-ATPase, NKA) is vital for animal cells, as it actively maintains Na+ and K+ electrochemical gradients across the cell membrane. It is a target of cardiotonic steroids (CTSs) such as ouabain and digoxin. As CTSs are almost unique strong inhibitors specific to NKA, a wide range of derivatives has been developed for potential therapeutic use. Several crystal structures have been published for NKA-CTS complexes, but they fail to explain the largely different inhibitory properties of the various CTSs. For instance, although CTSs are thought to inhibit ATPase activity by binding to NKA in the E2P state, we do not know if large conformational changes accompany binding, as no crystal structure is available for the E2P state free of CTS. Here, we describe crystal structures of the BeF3− complex of NKA representing the E2P ground state and then eight crystal structures of seven CTSs, including rostafuroxin and istaroxime, two new members under clinical trials, in complex with NKA in the E2P state. The conformations of NKA are virtually identical in all complexes with and without CTSs, showing that CTSs bind to a preformed cavity in NKA. By comparing the inhibitory potency of the CTSs measured under four different conditions, we elucidate how different structural features of the CTSs result in different inhibitory properties. The crystal structures also explain K+-antagonism and suggest a route to isoform specific CTSs.

scholarly journals Recognition of an α-helical hairpin in P22 large terminase by a synthetic antibody fragment

2020 ◽  
Vol 76 (9) ◽  
pp. 876-888
Author(s):  
Ravi K. Lokareddy ◽  
Ying-Hui Ko ◽  
Nathaniel Hong ◽  
Steven G. Doll ◽  
Marcin Paduch ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Recombinant Antibody ◽  
Antibody Fragment ◽  
Genome Packaging ◽  
Synthetic Antibody ◽  
High Affinity ◽  
N Terminus ◽  
Helical Hairpin ◽  
Accessible Surface

The genome-packaging motor of tailed bacteriophages and herpesviruses is a multisubunit protein complex formed by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal protein vertex of an empty precursor capsid to power the energy-dependent packaging of viral DNA. Both the ATPase and nuclease activities associated with genome packaging reside in TerL. Structural studies of TerL from bacteriophage P22 have been hindered by the conformational flexibility of this enzyme and its susceptibility to proteolysis. Here, an unbiased, synthetic phage-display Fab library was screened and a panel of high-affinity Fabs against P22 TerL were identified. This led to the discovery of a recombinant antibody fragment, Fab4, that binds a 33-amino-acid α-helical hairpin at the N-terminus of TerL with an equilibrium dissociation constant K d of 71.5 nM. A 1.51 Å resolution crystal structure of Fab4 bound to the TerL epitope (TLE) together with a 1.15 Å resolution crystal structure of the unliganded Fab4, which is the highest resolution ever achieved for a Fab, elucidate the principles governing the recognition of this novel helical epitope. TLE adopts two different conformations in the asymmetric unit and buries as much as 1250 Å2 of solvent-accessible surface in Fab4. TLE recognition is primarily mediated by conformational changes in the third complementarity-determining region of the Fab4 heavy chain (CDR H3) that take place upon epitope binding. It is demonstrated that TLE can be introduced genetically at the N-terminus of a target protein, where it retains high-affinity binding to Fab4.

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