scholarly journals MMOD-induced structural changes of hydroxylase in soluble methane monooxygenase

2019 ◽  
Vol 5 (10) ◽  
pp. eaax0059
Author(s):  
Hanseong Kim ◽  
Sojin An ◽  
Yeo Reum Park ◽  
Hara Jang ◽  
Heeseon Yoo ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Methane Monooxygenase ◽  
Regulatory Protein ◽  
Access Route ◽  
Inhibitory Mechanism ◽  
Ambient Conditions ◽  
Soluble Methane Monooxygenase ◽  
Auxiliary Protein ◽  
Binding Component

Soluble methane monooxygenase in methanotrophs converts methane to methanol under ambient conditions. The maximum catalytic activity of hydroxylase (MMOH) is achieved through the interplay of its regulatory protein (MMOB) and reductase. An additional auxiliary protein, MMOD, functions as an inhibitor of MMOH; however, its inhibitory mechanism remains unknown. Here, we report the crystal structure of the MMOH-MMOD complex from Methylosinus sporium strain 5 (2.6 Å). Its structure illustrates that MMOD associates with the canyon region of MMOH where MMOB binds. Although MMOD and MMOB recognize the same binding site, each binding component triggers different conformational changes toward MMOH, which then respectively lead to the inhibition and activation of MMOH. Particularly, MMOD binding perturbs the di-iron geometry by inducing two major MMOH conformational changes, i.e., MMOH β subunit disorganization and subsequent His147 dissociation with Fe1 coordination. Furthermore, 1,6-hexanediol, a mimic of the products of sMMO, reveals the substrate access route.

scholarly journals MMOD-induced structural changes of hydroxylase in soluble methane monooxygenase

2018 ◽  
Author(s):  
Hanseong Kim ◽  
Sojin An ◽  
Yeo Reum Park ◽  
Hara Jang ◽  
Sang Ho Park ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Activity ◽  
Structural Changes ◽  
Methane Monooxygenase ◽  
Regulatory Protein ◽  
Inhibitory Mechanism ◽  
Ambient Conditions ◽  
Soluble Methane Monooxygenase ◽  
Access Channel ◽  
Hydrocarbon Substrates

SummarySoluble methane monooxygenase in methanotrophs converts methane to methanol under ambient conditions1-3. The maximum catalytic activity of hydroxylase (MMOH) is achieved via interplay of its regulatory protein (MMOB) and reductase4-6. An additional auxiliary protein, MMOD, is believed to function as an inhibitor of the catalytic activity of MMOH; however, the mechanism of its action remains unknown7,8. Herein, we report the crystal structure of MMOH–MMOD complex fromMethylosinus sporiumstrain 5 (2.6 Å), which illustrates that two molecules of MMOD associate symmetrically with the canyon region of MMOH in a manner similar to MMOB, indicating that MMOD competes with MMOB for MMOH recognition. Further, MMOD binding disrupts the geometry of the di-iron centre and opens the substrate access channel. Notably, the electron density of 1,6-hexanediol at the substrate access channel mimics products of sMMO in hydrocarbon oxidation. The crystal structure of MMOH–MMOD unravels the inhibitory mechanism by which MMOD suppresses the MMOH catalytic activity, and reveals how hydrocarbon substrates/products access to the di-iron centre.

scholarly journals Structure of the soluble methane monooxygenase regulatory protein B

1999 ◽  
Vol 96 (14) ◽  
pp. 7877-7882 ◽  
Author(s):  
K. J. Walters ◽  
G. T. Gassner ◽  
S. J. Lippard ◽  
G. Wagner
Keyword(s):  
Methane Monooxygenase ◽  
Regulatory Protein ◽  
Soluble Methane Monooxygenase ◽  
Protein B

scholarly journals Crystal structure of unliganded TRAP: implications for dynamic allostery

2011 ◽  
Vol 434 (3) ◽  
pp. 427-434 ◽  
Author(s):  
Ali D. Malay ◽  
Masahiro Watanabe ◽  
Jonathan G. Heddle ◽  
Jeremy R. H. Tame
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Structural Changes ◽  
Bacillus Stearothermophilus ◽  
Rna Binding ◽  
Regulatory Protein ◽  
Protein A ◽  
Feedback System ◽  
Vibrational Modes ◽  
Specific Mrna

Allostery is vital to the function of many proteins. In some cases, rather than a direct steric effect, mutual modulation of ligand binding at spatially separated sites may be achieved through a change in protein dynamics. Thus changes in vibrational modes of the protein, rather than conformational changes, allow different ligand sites to communicate. Evidence for such an effect has been found in TRAP (trp RNA-binding attenuation protein), a regulatory protein found in species of Bacillus. TRAP is part of a feedback system to modulate expression of the trp operon, which carries genes involved in tryptophan synthesis. Negative feedback is thought to depend on binding of tryptophan-bound, but not unbound, TRAP to a specific mRNA leader sequence. We find that, contrary to expectations, at low temperatures TRAP is able to bind RNA in the absence of tryptophan, and that this effect is particularly strong in the case of Bacillus stearothermophilus TRAP. We have solved the crystal structure of this protein with no tryptophan bound, and find that much of the structure shows little deviation from the tryptophan-bound form. These data support the idea that tryptophan may exert its effect on RNA binding by TRAP through dynamic and not structural changes, and that tryptophan binding may be mimicked by low temperature.

Protein-induced conformational changes in 16S rRNA during assembly of the Escherichia Coli 30S ribosomal subunit: A STEM study

1987 ◽  
Vol 45 ◽  
pp. 910-911
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
16S Rrna ◽  
Conformational Changes ◽  
Ribosomal Proteins ◽  
Structural Changes ◽  
Ribosomal Subunit ◽  
Compact Structure ◽  
E Coli ◽  
Freeze Dried ◽  
16S Rna ◽  
30S Subunit

The aim of this study is to understand the mechanism of 16S rRNA folding into the compact structure of the small 30S subunit of E. coli ribosome. The assembly of the 30S E. coli ribosomal subunit is a sequence of specific interactions of 16S rRNA with 21 ribosomal proteins (S1-S21). Using dedicated high resolution STEM we have monitored structural changes induced in 16S rRNA by the proteins S4, S8, S15 and S20 which are involved in the initial steps of 30S subunit assembly. S4 is the first protein to bind directly and stoichiometrically to 16S rRNA. Direct binding also occurs individually between 16S RNA and S8 and S15. However, binding of S20 requires the presence of S4 and S8. The RNA-protein complexes are prepared by the standard reconstitution procedure, dialyzed against 60 mM KCl, 2 mM Mg(OAc)2, 10 mM-Hepes-KOH pH 7.5 (Buffer A), freeze-dried and observed unstained in dark field at -160°.

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