scholarly journals The role of conserved surface hydrophobic residues in the carbapenemase activity of the class D β-lactamases

2017 ◽  
Vol 73 (8) ◽  
pp. 692-701 ◽  
Author(s):  
Marta Toth ◽  
Clyde A. Smith ◽  
Nuno T. Antunes ◽  
Nichole K. Stewart ◽  
Lauren Maltz ◽  
...  
Keyword(s):  
Water Molecule ◽  
Active Site ◽  
Clinical Importance ◽  
Catalytic Efficiency ◽  
Structural Data ◽  
Molecular Surface ◽  
Water Molecules ◽  
Hydrophobic Residues ◽  
Class D ◽  
Life Threatening

Carbapenem-hydrolyzing class D β-lactamases (CHDLs) produce resistance to the last-resort carbapenem antibiotics and render these drugs ineffective for the treatment of life-threatening infections. Here, it is shown that among the clinically important CHDLs, OXA-143 produces the highest levels of resistance to carbapenems and has the highest catalytic efficiency against these substrates. Structural data demonstrate that acylated carbapenems entirely fill the active site of CHDLs, leaving no space for water molecules, including the deacylating water. Since the entrance to the active site is obstructed by the acylated antibiotic, the deacylating water molecule must take a different route for entry. It is shown that in OXA-143 the movement of a conserved hydrophobic valine residue on the surface opens a channel to the active site of the enzyme, which would not only allow the exchange of water molecules between the active site and the milieu, but would also create extra space for a water molecule to position itself in the vicinity of the scissile bond of the acyl-enzyme intermediate to perform deacylation. Structural analysis of the OXA-23 carbapenemase shows that in this enzyme movement of the conserved leucine residue, juxtaposed to the valine on the molecular surface, creates a similar channel to the active site. These data strongly suggest that all CHDLs may employ a mechanism whereupon the movement of highly conserved valine or leucine residues would allow a water molecule to access the active site to promote deacylation. It is further demonstrated that the 6α-hydroxyethyl group of the bound carbapenem plays an important role in the stabilization of this channel. The recognition of a universal deacylation mechanism for CHDLs suggests a direction for the future development of inhibitors and novel antibiotics for these enzymes of utmost clinical importance.

scholarly journals Analysis of β-lactone formation by clinically observed carbapenemases informs on a novel antibiotic resistance mechanism

2020 ◽  
Vol 295 (49) ◽  
pp. 16604-16613
Author(s):  
Kristina M. J. Aertker ◽  
H. T. Henry Chan ◽  
Christopher T. Lohans ◽  
Christopher J. Schofield
Keyword(s):  
Antibiotic Resistance ◽  
Recent Work ◽  
Active Site ◽  
Resistance Mechanism ◽  
Methyl Substituent ◽  
Nmr Studies ◽  
Hydrophobic Residues ◽  
Hydrolysis Products ◽  
Class D ◽  
Enzyme Complexes

An important mechanism of resistance to β-lactam antibiotics is via their β-lactamase–catalyzed hydrolysis. Recent work has shown that, in addition to the established hydrolysis products, the reaction of the class D nucleophilic serine β-lactamases (SBLs) with carbapenems also produces β-lactones. We report studies on the factors determining β-lactone formation by class D SBLs. We show that variations in hydrophobic residues at the active site of class D SBLs (i.e. Trp105, Val120, and Leu158, using OXA-48 numbering) impact on the relative levels of β-lactones and hydrolysis products formed. Some variants, i.e. the OXA-48 V120L and OXA-23 V128L variants, catalyze increased β-lactone formation compared with the WT enzymes. The results of kinetic and product studies reveal that variations of residues other than those directly involved in catalysis, including those arising from clinically observed mutations, can alter the reaction outcome of class D SBL catalysis. NMR studies show that some class D SBL variants catalyze formation of β-lactones from all clinically relevant carbapenems regardless of the presence or absence of a 1β-methyl substituent. Analysis of reported crystal structures for carbapenem-derived acyl-enzyme complexes reveals preferred conformations for hydrolysis and β-lactone formation. The observation of increased β-lactone formation by class D SBL variants, including the clinically observed carbapenemase OXA-48 V120L, supports the proposal that class D SBL-catalyzed rearrangement of β-lactams to β-lactones is important as a resistance mechanism.

scholarly journals Class D β-Lactamases: Are They All Carbapenemases?

2014 ◽  
Vol 58 (4) ◽  
pp. 2119-2125 ◽  
Author(s):  
Nuno T. Antunes ◽  
Toni L. Lamoureaux ◽  
Marta Toth ◽  
Nichole K. Stewart ◽  
Hilary Frase ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Clinical Importance ◽  
Kinetic Studies ◽  
Resistance Pattern ◽  
Content Type ◽  
Narrow Spectrum ◽  
Class D ◽  
Life Threatening

ABSTRACTCarbapenem-hydrolyzing class D β-lactamases (CHDLs) are enzymes of the utmost clinical importance due to their ability to produce resistance to carbapenems, the antibiotics of last resort for the treatment of various life-threatening infections. The vast majority of these enzymes have been identified inAcinetobacterspp., notably inAcinetobacter baumannii. The OXA-2 and OXA-10 enzymes predominantly occur inPseudomonas aeruginosaand are currently classified as narrow-spectrum class D β-lactamases. Here we demonstrate that when OXA-2 and OXA-10 are expressed inEscherichia colistrain JM83, they produce a narrow-spectrum antibiotic resistance pattern. When the enzymes are expressed inA. baumanniiATCC 17978, however, they behave as extended-spectrum β-lactamases and confer resistance to carbapenem antibiotics. Kinetic studies of OXA-2 and OXA-10 with four carbapenems have demonstrated that their catalytic efficiencies with these antibiotics are in the same range as those of some recognized class D carbapenemases. These results are in disagreement with the classification of the OXA-2 and OXA-10 enzymes as narrow-spectrum β-lactamases, and they suggest that other class D enzymes that are currently regarded as noncarbapenemases may in fact be CHDLs.

scholarly journals VERY LOW H–O–H BENDING FREQUENCIES. VI. VIBRATIONAL SPECTRA OF CdCl2·H2O

2017 ◽  
Vol 38 (1) ◽  
pp. 91
Author(s):  
Viktor Stefov ◽  
Metodija Najdoski ◽  
Bernward Engelen ◽  
Zlatko Ilievski ◽  
Adnan Cahil
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Gas Phase ◽  
Raman Spectra ◽  
Structural Data ◽  
Liquid Nitrogen Temperature ◽  
Water Molecules ◽  
Deuterium Content ◽  
Infrared And Raman Spectra ◽  
The Difference

The infrared and Raman spectra of CdCl2·H2O as well as those of a series of its partially deuterated analogues were recorded at room and at liquid-nitrogen temperature (RT and LNT, respectively). The combined results from the analysis of the spectra were used to assign the observed bands. In the difference IR spectrum of the compound with low deuterium content (≈ 4 % D) recorded at RT, one broad bands is observed at around 2590 cm–1 while in the LNT spectrum two bands appear (at 2584 cm–1 and 2575 cm–1). The appearance in the LNT spectrum of these two bands which are due to the stretching OD modes of the isotopically isolated HDO molecules points to the existance of two crystallographically different hydrogen bonds and is in accordance with the structural data for this compound. In the LNT infrared and Raman spectra of the protiated compound, one band, at 1583 cm-1, is observed in the region of the bending НОН vibrations with a frequency that is decreasing with lowering the temperature. An interesting finding related to this band is that its frequency is lower than that for the water molecule in the gas phase (1594 cm–1). In the RT and LNT IR spectra, only one strong band (at 560 cm–1) is observed in the region of the librations of water molecules (700 cm–1 – 400 cm–1).

scholarly journals Crystal Structure of Carbapenemase OXA-58 from Acinetobacter baumannii

2014 ◽  
Vol 58 (4) ◽  
pp. 2135-2143 ◽  
Author(s):  
Clyde A. Smith ◽  
Nuno Tiago Antunes ◽  
Marta Toth ◽  
Sergei B. Vakulenko
Keyword(s):  
Water Molecule ◽  
Acinetobacter Baumannii ◽  
Active Site ◽  
Bacterial Infections ◽  
Surrounding Medium ◽  
Active Site Residues ◽  
Content Type ◽  
Class D ◽  
Enzyme Complexes ◽  
Wide Dissemination

ABSTRACTClass D β-lactamases capable of hydrolyzing last-resort carbapenem antibiotics represent a major challenge for treatment of bacterial infections. Wide dissemination of these enzymes inAcinetobacter baumanniielevated this pathogen to the category of most deadly and difficult to treat. We present here the structure of the OXA-58 β-lactamase, a major class D carbapenemase ofA. baumannii, determined to 1.30-Å resolution. Unlike two otherAcinetobactercarbapenemases, OXA23 and OXA-24, the OXA-58 enzyme lacks the characteristic hydrophobic bridge over the active site, despite conservation of the residues which participate in its formation. The active-site residues in OXA-58 are spatially conserved in comparison to those in other class D β-lactamases. Lys86, which activates water molecules during the acylation and deacylation steps, is fully carboxylated in the OXA-58 structure. In the absence of a substrate, a water molecule is observed in the active site of the enzyme and is positioned in the pocket that is usually occupied by the 6α-hydroxyethyl moiety of carbapenems. A water molecule in this location would efficiently deacylate good substrates, such as the penicillins, but in the case of carbapenems, it would be expelled by the 6α-hydroxyethyl moiety of the antibiotics and a water from the surrounding medium would find its way to the vicinity of the carboxylated Lys86 to perform deacylation. Subtle differences in the position of this water in the acyl-enzyme complexes of class D β-lactamases could ultimately be responsible for differences in the catalytic efficiencies of these enzymes against last-resort carbapenem antibiotics.

scholarly journals HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fa-Hui Sun ◽  
Peng Zhao ◽  
Nan Zhang ◽  
Lu-Lu Kong ◽  
Catherine C. L. Wong ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Active Site ◽  
Negative Charge ◽  
Structural Data ◽  
Dna Breaks ◽  
Adp Ribosylation ◽  
Local Conformation ◽  
Key Residues ◽  
Structural Insights

AbstractUpon binding to DNA breaks, poly(ADP-ribose) polymerase 1 (PARP1) ADP-ribosylates itself and other factors to initiate DNA repair. Serine is the major residue for ADP-ribosylation upon DNA damage, which strictly depends on HPF1. Here, we report the crystal structures of human HPF1/PARP1-CAT ΔHD complex at 1.98 Å resolution, and mouse and human HPF1 at 1.71 Å and 1.57 Å resolution, respectively. Our structures and mutagenesis data confirm that the structural insights obtained in a recent HPF1/PARP2 study by Suskiewicz et al. apply to PARP1. Moreover, we quantitatively characterize the key residues necessary for HPF1/PARP1 binding. Our data show that through salt-bridging to Glu284/Asp286, Arg239 positions Glu284 to catalyze serine ADP-ribosylation, maintains the local conformation of HPF1 to limit PARP1 automodification, and facilitates HPF1/PARP1 binding by neutralizing the negative charge of Glu284. These findings, along with the high-resolution structural data, may facilitate drug discovery targeting PARP1.

scholarly journals Fe(2)OG: an integrated HMM profile-based web server to predict and analyze putative non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenase function in protein sequences

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Siddhartha Kundu
Keyword(s):  
Amino Acid ◽  
Water Molecule ◽  
Active Site ◽  
Ferrous Iron ◽  
Web Server ◽  
Protein Sequences ◽  
Diverse Group ◽  
And Function ◽  
Functionally Diverse ◽  
Haem Iron

Abstract Objective Non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenases (i2OGdd), are a taxonomically and functionally diverse group of enzymes. The active site comprises ferrous iron in a hexa-coordinated distorted octahedron with the apoenzyme, 2-oxoglutarate and a displaceable water molecule. Current information on novel i2OGdd members is sparse and relies on computationally-derived annotation schema. The dissimilar amino acid composition and variable active site geometry thereof, results in differing reaction chemistries amongst i2OGdd members. An additional need of researchers is a curated list of sequences with putative i2OGdd function which can be probed further for empirical data. Results This work reports the implementation of $$Fe\left(2\right)OG$$ F e 2 O G , a web server with dual functionality and an extension of previous work on i2OGdd enzymes $$\left(Fe\left(2\right)OG\equiv \{H2OGpred,DB2OG\}\right)$$ F e 2 O G ≡ { H 2 O G p r e d , D B 2 O G } . $$Fe\left(2\right)OG$$ F e 2 O G , in this form is completely revised, updated (URL, scripts, repository) and will strengthen the knowledge base of investigators on i2OGdd biochemistry and function. $$Fe\left(2\right)OG$$ F e 2 O G , utilizes the superior predictive propensity of HMM-profiles of laboratory validated i2OGdd members to predict probable active site geometries in user-defined protein sequences. $$Fe\left(2\right)OG$$ F e 2 O G , also provides researchers with a pre-compiled list of analyzed and searchable i2OGdd-like sequences, many of which may be clinically relevant. $$Fe(2)OG$$ F e ( 2 ) O G , is freely available (http://204.152.217.16/Fe2OG.html) and supersedes all previous versions, i.e., H2OGpred, DB2OG.

scholarly journals Kinetic studies and homology modeling of a dual-substrate linalool/nerolidol synthase from Plectranthus amboinicus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nur Suhanawati Ashaari ◽  
Mohd Hairul Ab. Rahim ◽  
Suriana Sabri ◽  
Kok Song Lai ◽  
Adelene Ai-Lian Song ◽  
...  
Keyword(s):  
Active Site ◽  
Catalytic Efficiency ◽  
Kinetic Studies ◽  
Homology Model ◽  
Biochemical Properties ◽  
Terpene Synthase ◽  
Monoterpene Synthase ◽  
Terminal Domain ◽  
Catalytic Active Site ◽  
Plectranthus Amboinicus

AbstractLinalool and nerolidol are terpene alcohols that occur naturally in many aromatic plants and are commonly used in food and cosmetic industries as flavors and fragrances. In plants, linalool and nerolidol are biosynthesized as a result of respective linalool synthase and nerolidol synthase, or a single linalool/nerolidol synthase. In our previous work, we have isolated a linalool/nerolidol synthase (designated as PamTps1) from a local herbal plant, Plectranthus amboinicus, and successfully demonstrated the production of linalool and nerolidol in an Escherichia coli system. In this work, the biochemical properties of PamTps1 were analyzed, and its 3D homology model with the docking positions of its substrates, geranyl pyrophosphate (C10) and farnesyl pyrophosphate (C15) in the active site were constructed. PamTps1 exhibited the highest enzymatic activity at an optimal pH and temperature of 6.5 and 30 °C, respectively, and in the presence of 20 mM magnesium as a cofactor. The Michaelis–Menten constant (Km) and catalytic efficiency (kcat/Km) values of 16.72 ± 1.32 µM and 9.57 × 10–3 µM−1 s−1, respectively, showed that PamTps1 had a higher binding affinity and specificity for GPP instead of FPP as expected for a monoterpene synthase. The PamTps1 exhibits feature of a class I terpene synthase fold that made up of α-helices architecture with N-terminal domain and catalytic C-terminal domain. Nine aromatic residues (W268, Y272, Y299, F371, Y378, Y379, F447, Y517 and Y523) outlined the hydrophobic walls of the active site cavity, whilst residues from the RRx8W motif, RxR motif, H-α1 and J-K loops formed the active site lid that shielded the highly reactive carbocationic intermediates from the solvents. The dual substrates use by PamTps1 was hypothesized to be possible due to the architecture and residues lining the catalytic site that can accommodate larger substrate (FPP) as demonstrated by the protein modelling and docking analysis. This model serves as a first glimpse into the structural insights of the PamTps1 catalytic active site as a multi-substrate linalool/nerolidol synthase.

scholarly journals Cyclooctanaminium hydrogen succinate monohydrate

2012 ◽  
Vol 68 (4) ◽  
pp. o1204-o1204 ◽  
Author(s):  
Sanaz Khorasani ◽  
Manuel A. Fernandes
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Ammonium Cation ◽  
Water Molecules ◽  
Hydrated Salt ◽  
A Chain ◽  
Hydrogen Bonded

In the title hydrated salt, C8H18N+·C4H5O4−·H2O, the cyclooctyl ring of the cation is disordered over two positions in a 0.833 (3):0.167 (3) ratio. The structure contains various O—H.·O and N—H...O interactions, forming a hydrogen-bonded layer of molecules perpendicular to thecaxis. In each layer, the ammonium cation hydrogen bonds to two hydrogen succinate anions and one water molecule. Each hydrogen succinate anion hydrogen bonds to neighbouring anions, forming a chain of molecules along thebaxis. In addition, each hydrogen succinate anion hydrogen bonds to two water molecules and the ammonium cation.

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