Structure and dynamics of solvated hydrogenoxalate and oxalate anions: a theoretical study

Kroutil, Ondřej; Minofar, Babak; Kabeláč, Martin

doi:10.1007/s00894-016-3075-0

Cited by 13 publications

(13 citation statements)

References 50 publications

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“…The dihedral angle of oxalate is somewhat larger in the bi-dentate conformation with 36.3⁰ as compared to 21.0⁰ in the mono-dentate model. This can be explained by hydrogen bonding of both free oxygen atoms in opposite directions since the oxalate anion has a low rotational barrier and is well known to adjust its dihedral O-C-C-O angle to hydrogen bonding forces (47,48). The close association between R92 and the substrate in our simulations is in agreement with the earlier mutagenesis results (8) and suggests a critical role for R92 to guide oxalate into place for catalysis.…”

Section: Figure 3: Results Of Dft Simulations Of Oxalate Binding To Tsupporting

confidence: 89%

The Structure of Oxalate Decarboxylase at its Active pH

Burg

Goodsell

Twahir

et al. 2018

Preprint

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Oxalate decarboxylase catalyzes the redox-neutral unimolecular disproportionation reaction of oxalic acid. The pH maximum for catalysis is ~4.0 and activity is negligible above pH7. Here we report on the first crystal structure of the enzyme in its active pH range at pH4.6, and at a resolution of 1.45 Å, the highest to date. The fundamental tertiary and quaternary structure of the enzyme does not change with pH. However, the low pH crystals are heterogeneous containing both a closed and open conformation of a flexible loop region which gates access to the N-terminal active site cavity. Residue E162 in the closed conformation points away from the active-site Mn ion owing to the coordination of a buffer molecule, acetate. Since the quaternary structure of the enzyme appears unaffected by pH many conclusions drawn from the structures taken at high pH remain valid. Density functional theory calculations of the possible binding modes of oxalate to the N-terminal Mn ion demonstrate that both mono-and bi-dentate coordination modes are possible in the closed conformation with an energetic preference for the bidentate binding mode. The simulations suggest that R92 plays an important role as a guide for positioning the substrate in its catalytically competent orientation. A strong hydrogen bond is seen between the bi-dentate bound substrate and E101, one of the coordinating ligands for the Nterminal Mn ion. This suggests a more direct role of E101 as a transient base during the first step of catalysis.

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Section: Figure 3: Results Of Dft Simulations Of Oxalate Binding To Tsupporting

confidence: 89%

The Structure of Oxalate Decarboxylase at its Active pH

Burg

Goodsell

Twahir

et al. 2018

Preprint

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“…The Amber ff14SB and Lipid14 forcefields were employed to describe the protein and the membrane, respectively 66,67 . The oxalate ligand in solution was described with parameters determined by the electronic continuum correction with rescaling (ECCR), based on Ab Initio Molecular Dynamic simulation, developed by Kroutil et al 41,68 . However, the oxalate ligand in the binding site of OxlT was described with parameters determined by the original RESP scheme, considering that the protein environment differs from that of water solution.…”

Section: Molecular Dynamics Simulationmentioning

confidence: 99%

Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

Jaunet-Lahary

Shimamura

Hayashi

et al. 2021

Preprint

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Oxalobacter formigenes is an oxalate-degrading bacterium in the gut microbiota that absorbs food-derived oxalate to use this as a carbon and energy source and thereby helps reduce the risk of kidney stone formation of the host animals 1–4. The bacterial oxalate transporter OxlT uptakes oxalate from the gut to bacterial cells and excrete formate as a degradation product, with a strict discrimination from other carboxylates that serve as nutrients 5–7. Nevertheless, the underlying mechanism remains unclear. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two different conformations, occluded and outward-facing states. The oxalate binding site contains two basic residues that form salt bridges with a dicarboxylate substrate while preventing the conformational switch to the occluded state without an acidic substrate, a ‘disallowed’ state for an antiporter 8, 9. The occluded ligand-binding pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the binding pocket are completely blocked by extensive interdomain hydrophobic and ionic interactions. Nevertheless, a molecular dynamics simulation showed that a flip of a single side chain neighbouring the substrate is sufficient to trigger the gate opening. The OxlT structure indicates the underlying metabolic interactions enabling favourable symbiosis at a molecular level.

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“…As mentioned previously, the oxalate anion can be regarded as a complex of a proton (H + ) and an oxalate dianion (C 2 O 4 2− ) and has been previously studied experimentally and theoretically due to its unique structure [7][8][9][10][11][12][13][14][15]. The oxalate anion has two stable minima on the potential energy surface.…”

Section: Introductionmentioning

confidence: 99%

“…The oxalate anion is a molecular system that contains CO 2 molecular units with various charge states, which are important for understanding the activation of carbon dioxide [ 6 ]. As mentioned previously, the oxalate anion can be regarded as a complex of a proton (H + ) and an oxalate dianion (C 2 O 4 2 − ) and has been previously studied experimentally and theoretically due to its unique structure [ 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 ]. The oxalate anion has two stable minima on the potential energy surface.…”

Section: Introductionmentioning

confidence: 99%

“…The other is an open-form, in which the proton in the OH bond points out of the molecular framework with an O-C-C-O angle of 90°. Quantum chemical calculations show that the closed-form is about 0.4 eV more thermodynamically stable compared with the open-form and that the isomerization barrier via rotation of the OH group measured from the closed-form energy to the open-form energy of about 0.9 eV is high [ 12 , 14 ]. Thus, Continetti et al concluded that the stable closed-form is preferentially produced under their molecular beam conditions [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

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On-the-Fly Ring-Polymer Molecular Dynamics Calculations of the Dissociative Photodetachment Process of the Oxalate Anion

et al. 2021

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The dissociative photodetachment dynamics of the oxalate anion, C2O4H− + hν → CO2 + HOCO + e−, were theoretically studied using the on-the-fly path-integral and ring-polymer molecular dynamics methods, which can account for nuclear quantum effects at the density-functional theory level in order to compare with the recent experimental study using photoelectron–photofragment coincidence spectroscopy. To reduce computational time, the force acting on each bead of ring-polymer was approximately calculated from the first and second derivatives of the potential energy at the centroid position of the nuclei beads. We find that the calculated photoelectron spectrum qualitatively reproduces the experimental spectrum and that nuclear quantum effects are playing a role in determining spectral widths. The calculated coincidence spectrum is found to reasonably reproduce the experimental spectrum, indicating that a relatively large energy is partitioned into the relative kinetic energy between the CO2 and HOCO fragments. This is because photodetachment of the parent anion leads to Franck–Condon transition to the repulsive region of the neutral potential energy surface. We also find that the dissociation dynamics are slightly different between the two isomers of the C2O4H− anion with closed- and open-form structures.

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Structure and dynamics of solvated hydrogenoxalate and oxalate anions: a theoretical study

Cited by 13 publications

References 50 publications

The Structure of Oxalate Decarboxylase at its Active pH

The Structure of Oxalate Decarboxylase at its Active pH

Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

On-the-Fly Ring-Polymer Molecular Dynamics Calculations of the Dissociative Photodetachment Process of the Oxalate Anion

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