Defluorination Capability of <scp>l</scp>‐2‐Haloacid Dehalogenases in the HAD‐Like Hydrolase Superfamily Correlates with Active Site Compactness

Chan, P.W.Y.; Chakrabarti, Nilmadhab; Ing, Christopher; Halgas, Ondrej; To, Terence; Wälti, Marielle A.; Petit, Alain; Tran, Christopher; Savchenko, Alexei; Yakunin, Alexander F.; Edwards, Elizabeth A.; Pomès, Régis; Pai, E.F.

doi:10.1002/cbic.202100414

Cited by 19 publications

(33 citation statements)

References 47 publications

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“…The defluorination of fluorotelomer compounds by Pseudomonas (Kim et al ., 2012) is chemically an elimination reaction (Tucker and Mecozzi, 2013), catalysed by lyase enzymes that do not require oxygen. The well‐studied defluorination of fluoroacetate, first demonstrated with a Pseudomonas enzyme (Goldman, 1965), is catalysed by a member of the haloalkane dehalogenase superfamily (Chan et al ., 2022), an enzyme class common in Pseudomonas and many other bacteria.…”

Section: Extensive Data On Pseudomonas Genomes Metabolism Enzymes And...mentioning

confidence: 99%

Pseudomonas: versatile biocatalysts for PFAS

Wackett

2022

Environmental Microbiology

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Section: Extensive Data On Pseudomonas Genomes Metabolism Enzymes And...mentioning

confidence: 99%

Pseudomonas: versatile biocatalysts for PFAS

Wackett

2022

Environmental Microbiology

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“…This sequence motif (Gly-Xaa-His) forms redox-active nickel coordination complexes [23]. Moreover, a nickel affinity column was used for purification [3], and the Gly-Xaa-His motif can capture Ni 2+ ions from these columns [24][25][26]. The resulting square planar nickel complexes catalyze the decomposition of hydrogen peroxide to other ROS such as hydroxyl radicals [23].…”

Section: A Known Source Of Reactive Oxygen Species Contacts the Unexp...mentioning

confidence: 99%

The μ opioid receptor crystal structure with BU72 is a covalent adduct

Munro

2022

Preprint

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Background The first crystal structure of the active μ opioid receptor (μOR) exhibited several unexplained features. The ligand BU72 exhibited many extreme deviations from ideal geometry, along with unexplained electron density around the benzylic carbon. I previously showed that inverting the benzylic configuration resolved these problems, establishing revised stereochemistry of BU72 and its analog BU74. However, another problem remains unresolved: additional unexplained electron density contacts both BU72 and a histidine residue in the N-terminus. Results Here I show that these short contacts and uninterrupted density are inconsistent with non-covalent interactions. Therefore, BU72 and μOR form a covalent adduct through an unmodeled atom, and the published model as two separate entities is incorrect. A subsequently proposed magnesium complex is also inconsistent with multiple lines of evidence. However, oxygen fits the unexplained density well. While the structure I propose is tentative, similar oxygen-bridged adducts have been reported previously in the presence of reactive oxygen species. Moreover, known sources of reactive oxygen species were present: HEPES buffer, nickel ions, and a sequence motif that forms redox-active nickel complexes. This motif contacts the unexplained density. The adduct exhibits severe strain, and the tethered N-terminus forms contacts with adjacent residues. These forces, along with the nanobody used as a G protein substitute, would be expected to influence the receptor conformation. Consistent with this, the intracellular end of the structure differs markedly from subsequent structures of active μOR bound to Gi protein. Conclusions Later Gi-bound structures are likely to be more accurate templates for docking and molecular dynamics simulations of active μOR. The possibility of reactions like this should be considered in the choice of protein truncation sites and purification conditions, and in the interpretation of excess or unexplained density.

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“…A search of PDBeMotif ( 27) revealed eight protein structures in which square planar Gly-Xaa-His-Ni 2+ complexes were resolved: PDB entries 1JVN, 1XMK, 2RJ2, 3RDH, 3UM9, 3ZUC, 4I71, and 4OMO. In three cases, the nickel was not added during crystallization, but unexpectedly captured during affinity chromatography: 1JVN (24), 3UM9 (25), and 3ZUC (26). Intriguingly, in 1JVN the electron density was not consistent with the expected ligand structure; no density supported several of the atoms, suggesting partial decomposition (24).…”

Section: A Known Source Of Reactive Oxygen Species Contacts the Unexp...mentioning

confidence: 99%

The μ opioid receptor crystal structure with BU72 is a covalent adduct

Munro

2022

Preprint

View full text Add to dashboard Cite

The first crystal structure of the active μ opioid receptor (μOR) exhibited several unexplained features. The ligand BU72 exhibited many extreme deviations from ideal geometry, along with unexplained electron density around the benzylic carbon. I previously showed that inverting the benzylic configuration resolved these problems, establishing revised stereochemistry of BU72 and its analog BU74. However, another problem remains unresolved: additional unexplained electron density contacts both BU72 and a histidine residue in the N-terminus. Here I show that these short contacts and uninterrupted density are inconsistent with non-covalent interactions. Therefore, BU72 and μOR form a covalent adduct through an unmodeled atom, and the published model as two separate entities is incorrect. A subsequently proposed magnesium complex is also inconsistent with multiple lines of evidence. However, oxygen fits the unexplained density well. While the proposed structure is tentative, similar oxygen-bridged adducts have been reported previously in the presence of reactive oxygen species. Moreover, known sources of reactive oxygen species were present: HEPES buffer, nickel ions, and a sequence motif that forms redox-active nickel complexes. This motif contacts the unexplained density. The adduct exhibits severe strain, and the tethered N-terminus forms contacts with adjacent residues. These forces, along with the nanobody used as a G-protein substitute, would be expected to influence the receptor conformation. Consistent with this, the intracellular end of the structure differs markedly from subsequent structures of active μOR bound to Gi protein. These later structures are likely to be more accurate templates for docking and molecular dynamics simulations. The possibility of reactions like this should be considered in the choice of protein truncation sites and purification conditions, and in the interpretation of excess or unexplained density.

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Defluorination Capability of l‐2‐Haloacid Dehalogenases in the HAD‐Like Hydrolase Superfamily Correlates with Active Site Compactness

Cited by 19 publications

References 47 publications

Pseudomonas: versatile biocatalysts for PFAS

Pseudomonas: versatile biocatalysts for PFAS

The μ opioid receptor crystal structure with BU72 is a covalent adduct

The μ opioid receptor crystal structure with BU72 is a covalent adduct

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