Crystal structure of 1-deoxy-d-xylulose 5-phosphate reductoisomerase from the hyperthermophile Thermotoga maritima for insights into the coordination of conformational changes and an inhibitor binding

Vertebrate leukotriene A4 hydrolases are zinc metalloenzymes with an epoxide hydrolase and aminopeptidase activity belonging to the M1 family of aminopeptidases. Bestatin, an amino peptidase inhibitor, can inhibit both the activities. The human enzyme produces LTB4, a powerful mediator of inflammation and is implicated in a wide variety of rheumatoid diseases. The yeast homolog scLTA4H contains only a rudimentary epoxide hydrolase activity. Both the structure of the human enzyme and recently the structure of scLTA4H and have been solved to investigate the molecular architecture of the active site both with and without inhibitor Bestatin. The structure of scLTA4H shows large domain movements creating an open active site. In the human enzyme the LTA4 binding side is a narrow hydrophobic channel. Upon inhibitor a domain shifts occurs and the final binding pocket is formed. The fact that scLTA4H displays this induced fit is an interesting observation. Many members of the M1 family seem to display a certain degree of induced fit, a feature, which however, has never been observed for humLTA4H. Our recent solution SAXS studies show that humLTA4H does not make any conformational changes upon inhibitor binding which is consistent with our previous speculation that it functions by a lock and key mechanism rather than induced fit and is better suited to supply the protective and precise environment for hydrolysis of LTA4 into LTB4. On the other hand Xenopus LTA4H shows conformational change in the higher/wide angular region ( >1 nm-1) and decrease in Porod volume of approximately 20 nm3 but no change in Rg or Dmax was observed. It is also observed that like in crystal structure Xenopus LTA4H forms dimer in solution. Similarly scLTA4H forms dimer in solution, which is unlike the crystal structure, and also make conformational changes upon inhibitor binding. Taken together, Xenopus and scLTA4H makes more compact form, with decrease in flexibility, to perform it's catalytic action.

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Movement of the RecG Motor Domain upon DNA Binding Is Required for Efficient Fork Reversal

International Journal of Molecular Sciences ◽

10.3390/ijms19103049 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3049 ◽

Cited By ~ 3

Author(s):

Garrett Warren ◽

Richard Stein ◽

Hassane Mchaourab ◽

Brandt Eichman

Keyword(s):

Crystal Structure ◽

Dna Binding ◽

Conformational Changes ◽

Mutational Analysis ◽

Thermotoga Maritima ◽

Paramagnetic Resonance ◽

Chromatin Remodelers ◽

Cryo Electron Microscopy ◽

Stalled Replication Forks ◽

Electron Paramagnetic

RecG catalyzes reversal of stalled replication forks in response to replication stress in bacteria. The protein contains a fork recognition (“wedge”) domain that binds branched DNA and a superfamily II (SF2) ATPase motor that drives translocation on double-stranded (ds)DNA. The mechanism by which the wedge and motor domains collaborate to catalyze fork reversal in RecG and analogous eukaryotic fork remodelers is unknown. Here, we used electron paramagnetic resonance (EPR) spectroscopy to probe conformational changes between the wedge and ATPase domains in response to fork DNA binding by Thermotoga maritima RecG. Upon binding DNA, the ATPase-C lobe moves away from both the wedge and ATPase-N domains. This conformational change is consistent with a model of RecG fully engaged with a DNA fork substrate constructed from a crystal structure of RecG bound to a DNA junction together with recent cryo-electron microscopy (EM) structures of chromatin remodelers in complex with dsDNA. We show by mutational analysis that a conserved loop within the translocation in RecG (TRG) motif that was unstructured in the RecG crystal structure is essential for fork reversal and DNA-dependent conformational changes. Together, this work helps provide a more coherent model of fork binding and remodeling by RecG and related eukaryotic enzymes.

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Crystal Structure of Full Length Topoisomerase I from Thermotoga maritima

Journal of Molecular Biology ◽

10.1016/j.jmb.2006.03.012 ◽

2006 ◽

Vol 358 (5) ◽

pp. 1328-1340 ◽

Cited By ~ 29

Author(s):

Guido Hansen ◽

Axel Harrenga ◽

Bernd Wieland ◽

Dietmar Schomburg ◽

Peter Reinemer

Keyword(s):

Crystal Structure ◽

Topoisomerase I ◽

Thermotoga Maritima ◽

Full Length

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

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x21011419 ◽

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.

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Crystal Structure of Butyrate Kinase 2 from Thermotoga maritima, a Member of the ASKHA Superfamily of Phosphotransferases

Journal of Bacteriology ◽

10.1128/jb.00549-12 ◽

2012 ◽

Vol 194 (11) ◽

pp. 3033-3033

Author(s):

J. Diao ◽

M. S. Hasson

Keyword(s):

Crystal Structure ◽

Thermotoga Maritima ◽

Butyrate Kinase

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Molecular modeling study for conformational changes of Sirtuin 2 due to substrate and inhibitor binding

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2012.680026 ◽

2012 ◽

Vol 30 (3) ◽

pp. 235-254 ◽

Cited By ~ 12

Author(s):

Sugunadevi Sakkiah ◽

Meganathan Chandrasekaran ◽

Yuno Lee ◽

Songmi Kim ◽

Keun Woo Lee

Keyword(s):

Molecular Modeling ◽

Conformational Changes ◽

Inhibitor Binding ◽

Molecular Modeling Study ◽

Modeling Study

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

10.1101/2020.06.16.155812 ◽

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.

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THE APPLICABILITY OF THE CRYSTAL STRUCTURE OF TERMOTOGA MARITIMA 4--GLUCANOTRANSFERASE AS THE TEMPLATE FOR SULOCHRIN AS -GLUCOSIDASE INHIBITORS

Indonesian Journal of Chemistry ◽

10.22146/ijc.21520 ◽

2010 ◽

Vol 9 (3) ◽

pp. 479-486

Author(s):

Rizna Triana Dewi ◽

Yulia Anita ◽

Enade Perdana Istyastono ◽

Akhmad Darmawan ◽

Muhamad Hanafi

Keyword(s):

Crystal Structure ◽

Saccharomyces Cerevisiae ◽

Thermotoga Maritima ◽

Binding Pocket ◽

Operating Environment ◽

High Sequence Identity ◽

Glucosidase Inhibitor ◽

Glucosidase Inhibitors ◽

Docking Method ◽

Binding Residues

Interaction of sulochrin to active site of glucosidase enzyme of Termotoga maritime has been studied by employing docking method using Molecular Operating Environment (MOE), in comparison with those are reports of established inhibitor α-glucosidase such as acarbose, miglitol and voglibose, and salicinol, as reference compounds. The crystal structure T. maritima α-glucanotransferase (PDB code: 1LWJ) can be employed to serve as the template in the virtual screening of S. cerevisiae α-glucosidase. The comparison between the binding pocket residues of Thermotoga maritima α-glucanotransferase and Saccharomyces cerevisiae α-glucosidase show a high sequence identity and similarity. The result showed that sulochrin could be located in the binding pocket and formed some interactions with the binding residues. The ligands showed proper predicted binding energy (-6.74 - -4.13 kcal/mol) and predicted Ki values (0.011 - 0.939 mM). Sulochrin has a possibility to serve as a lead compound in the development of new α-glucosidase inhibitor. Keywords: Docking, sulochrin, α-glucosidase Inhibitor, Thermotoga maritime α-glucotransferase, Saccharomyces cerevisiae α-glucosidase, MOE

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