Comparison of CryoEM and X-ray structures of dimethylformamidase

Vinothkumar, Kutti R.; Arya, Chetan Kumar; Ramanathan, G.; Subramanian, Ramaswamy

doi:10.1016/j.pbiomolbio.2020.06.008

Cited by 3 publications

(1 citation statement)

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“…To discard the possibility that the MVM capsid might be an unusual complex for which those limiting factors had no significant effect on dynamics-related parameters, we tested the same approach for other viral and cellular protein complexes from the PDB (Berman et al, 2000) and EMDB (Lawson et al, 2016) repositories. Four different assemblies solved to atomic or near atomic resolution by both X-ray crystallography and cryo-EM were selected: β-galactosidase (Bartesaghi et al, 2018; Juers et al, 2000), dimethylformamidase [DMFase, (Arya et al, 2020; Vinothkumar, Arya, Ramanathan, & Subramanian, 2021)], apoferritin (Masuda, Goto, Yoshihara, & Mikami, 2010; Yip, Fischer, Paknia, Chari, & Stark, 2020) and porcine circovirus-2 [PCV-2, (Liu, Guo, Wang, Li, & Jiang, 2016; Mo et al, 2019)]. For every macromolecular complex a clear correlation between LR values and relative B-factors was found (Fig.…”

Section: Discussionmentioning

confidence: 99%

Equilibrium dynamics of a biomolecular complex analyzed at single-amino acid resolution by cryo-electron microscopy

Luque

Ortega-Esteban

Valbuena

et al. 2022

Preprint

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The biological function of macromolecular complexes depends not only on large-scale transitions between conformations, but also on small-scale conformational fluctuations at equilibrium. This study shows that detailed information on the equilibrium dynamics of a biocomplex obtained from local resolution (LR) data in cryo-electron microscopy (cryo-EM) density maps matches the information obtained in solution by hydrogen-deuterium exchange mass-spectrometry. The structure of the minute virus of mice (MVM) capsid as a model system was determined by cryo-EM, and LR values were found to correlate with both crystallographic B-factors and hydrogen-deuterium exchange values. Once validated, the cryo-EM LR-based approach was used to compare the equilibrium dynamics of wild-type and two mutant MVM capsids. The results revealed a linkage between mechanical stiffening and impaired equilibrium dynamics in a biocomplex. Cryo-EM is emerging as a powerful approach for simultaneously acquiring information on the atomic structure and local equilibrium dynamics of biomolecular complexes.

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Section: Discussionmentioning

confidence: 99%

Equilibrium dynamics of a biomolecular complex analyzed at single-amino acid resolution by cryo-electron microscopy

Luque

Ortega-Esteban

Valbuena

et al. 2022

Preprint

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Dimethylformamidase with a Unique Iron Center

Arya¹,

Ramanathan²,

Vinothkumar³

et al. 2022

Encyclopedia of Inorganic and Bioinorganic Chemistry

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N, N ‐Dimethylformamide is an abundant and one of the most used solvents in the chemical industry. The enzyme dimethylformamidase catalyzes the hydrolytic cleavage of the highly stable formamide bond. Sequence analysis of the enzyme suggested that it does not belong to the known family of amidohydrolases. The enzyme in its smallest form, is a tetramer made of two large and two small subunits. It is a very halotolerant enzyme that oligomerizes to form a dimer of tetramers with increasing salt concentration. The domain that contains the active site is a new fold. The active site is a Fe(III) center coordinated by two tyrosines and glutamic acid. Site‐directed mutagenesis shows that glutamic acid, histidine, and asparagine around the active site are critical for the catalysis by the enzyme. The evolution of the enzyme to break down the man‐made dimethylformamide is still a mystery.

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