scholarly journals Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: A basis for the substrate-induced conformational changes

2006 ◽  
Vol 64 (4) ◽  
pp. 1078-1082 ◽  
Author(s):  
Jun Hyuck Lee ◽  
Young Na ◽  
Hye-Eun Song ◽  
Dooil Kim ◽  
Bo-Hyun Park ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Thermus Caldophilus

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

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.

scholarly journals Crystal structure of pyrrolizidine alkaloid N-oxygenase from the grasshopper Zonocerus variegatus

2018 ◽  
Vol 74 (5) ◽  
pp. 422-432 ◽  
Author(s):  
Christian Kubitza ◽  
Annette Faust ◽  
Miriam Gutt ◽  
Luzia Gäth ◽  
Dietrich Ober ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Enzyme Activity ◽  
Conformational Changes ◽  
Pyrrolizidine Alkaloid ◽  
Chemical Defence ◽  
Kinetic Studies ◽  
Food Plants ◽  
Single Amino Acid ◽  
Dimensional Structure ◽  
Zonocerus Variegatus

The high-resolution crystal structure of the flavin-dependent monooxygenase (FMO) from the African locust Zonocerus variegatus is presented and the kinetics of structure-based protein variants are discussed. Z. variegatus expresses three flavin-dependent monooxygenase (ZvFMO) isoforms which contribute to a counterstrategy against pyrrolizidine alkaloids (PAs). PAs are protoxic compounds produced by some angiosperm lineages as a chemical defence against herbivores. N-Oxygenation of PAs and the accumulation of PA N-oxides within their haemolymph result in two evolutionary advantages for these insects: (i) they circumvent the defence mechanism of their food plants and (ii) they can use PA N-oxides to protect themselves against predators, which cannot cope with the toxic PAs. Despite a high degree of sequence identity and a similar substrate spectrum, the three ZvFMO isoforms differ greatly in enzyme activity. Here, the crystal structure of the Z. variegatus PA N-oxygenase (ZvPNO), the most active ZvFMO isoform, is reported at 1.6 Å resolution together with kinetic studies of a second isoform, ZvFMOa. This is the first available crystal structure of an FMO from class B (of six different FMO subclasses, A–F) within the family of flavin-dependent monooxygenases that originates from a more highly developed organism than yeast. Despite the differences in sequence between family members, their overall structure is very similar. This indicates the need for high conservation of the three-dimensional structure for this type of reaction throughout all kingdoms of life. Nevertheless, this structure provides the closest relative to the human enzyme that is currently available for modelling studies. Of note, the crystal structure of ZvPNO reveals a unique dimeric arrangement as well as small conformational changes within the active site that have not been observed before. A newly observed kink within helix α8 close to the substrate-binding path might indicate a potential mechanism for product release. The data show that even single amino-acid exchanges in the substrate-entry path, rather than the binding site, have a significant impact on the specific enzyme activity of the isoforms.

scholarly journals Structural organization of a major neuronal G protein regulator, the RGS7-Gβ5-R7BP complex

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Dipak N Patil ◽  
Erumbi S Rangarajan ◽  
Scott J Novick ◽  
Bruce D Pascal ◽  
Douglas J Kojetin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
G Protein ◽  
Conformational Changes ◽  
Structural Organization ◽  
Rgs Proteins ◽  
Protein Signaling ◽  
Vast Number ◽  
Precise Control ◽  
Multiple Domains ◽  
Organizational Features

Signaling by the G-protein-coupled receptors (GPCRs) plays fundamental role in a vast number of essential physiological functions. Precise control of GPCR signaling requires action of regulators of G protein signaling (RGS) proteins that deactivate heterotrimeric G proteins. RGS proteins are elaborately regulated and comprise multiple domains and subunits, yet structural organization of these assemblies is poorly understood. Here, we report a crystal structure and dynamics analyses of the multisubunit complex of RGS7, a major regulator of neuronal signaling with key roles in controlling a number of drug target GPCRs and links to neuropsychiatric disease, metabolism, and cancer. The crystal structure in combination with molecular dynamics and mass spectrometry analyses reveals unique organizational features of the complex and long-range conformational changes imposed by its constituent subunits during allosteric modulation. Notably, several intermolecular interfaces in the complex work in synergy to provide coordinated modulation of this key GPCR regulator.

scholarly journals Crystal structure and calcium‐induced conformational changes of diacylglycerol kinase α EF‐hand domains

2019 ◽  
Vol 28 (4) ◽  
pp. 694-706 ◽  
Author(s):  
Daisuke Takahashi ◽  
Kano Suzuki ◽  
Taiichi Sakamoto ◽  
Takeo Iwamoto ◽  
Takeshi Murata ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Diacylglycerol Kinase ◽  
Ef Hand

scholarly journals Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure

Virology ◽  
2009 ◽  
Vol 388 (2) ◽  
pp. 324-334 ◽  
Author(s):  
Tiancen Hu ◽  
Yu Zhang ◽  
Lianwei Li ◽  
Kuifeng Wang ◽  
Shuai Chen ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Sars Coronavirus ◽  
Dimer Interface
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