Structural Study of Metal Binding and Coordination in Ancient Metallo-ß-Lactamase PNGM-1 Variants.

The increasing incidence of community- and hospital-acquired infections with multidrug-resistant (MDR) bacteria poses a critical threat to public health and the healthcare system. Although ß-lactam antibiotics are effective against most bacterial infections, some bacteria are resistant to ß-lactam antibiotics by producing ß-lactamases. Among ß-lactamases, metallo-ß-lactamases (MBLs) are especially worrisome as only a few inhibitors have been developed against them. In MBLs, the metal ions play an important role as they coordinate a catalytic water molecule that hydrolyzes ß-lactam rings. We determined the crystal structures of different variants of PNGM-1, an ancient MBL with additional tRNase Z activity. The variants were generated by site-directed mutagenesis targeting metal-coordinating residues. In PNGM-1, both zinc ions are coordinated by six coordination partners in an octahedral geometry, and the zinc-centered octahedrons share a common face. Structures of the PNGM-1 variants confirm that the substitution of a metal-coordinating residue causes the loss of metal binding and ß-lactamase activity. Compared with PNGM-1, subclass B3 MBLs lack one metal-coordinating residue, leading to a shift in the metal-coordination geometry from an octahedral to tetrahedral geometry. Our results imply that a subtle change in the metal-binding site of MBLs can markedly change their metal-coordination geometry and catalytic activity.

Characterization of HemY-type protoporphyrinogen IX oxidase genes from cyanobacteria and their functioning in transgenic Arabidopsis.

KEY MESSAGE: We investigated the functions of two cyanobacterial HemY protoporphyrinogen IX oxidase (PPO) genes with in vitro and in vivo assays and evaluated their applicability as resistance traits to PPO-inhibiting herbicides. We isolated HemY-type protoporphyrinogen IX oxidase (PPO) genes from cyanobacteria, OnPPO gene from Oscillatoria nigro-viridis PCC7112 and HaPPO gene from Halothece sp. PCC7418. The alignment of amino acid sequences as well as phylogenetic analyses conducted showed that OnPPO and HaPPO are classified as HemY-type PPO and are more closely related to plastidic PPOs than to mitochondrial PPOs. The PPO-deficient Escherichia coli BT3 strain, which requires heme supplementation, could obtain normal growth in the absence of heme supplementation when complemented with OnPPO and HaPPO. The enzyme assays of OnPPO, HaPPO, and Arabidopsis thaliana PPO1 (AtPPO1) proteins each revealed different kinetic properties in terms of catalytic efficiency, substrate affinity, and the degree of inhibition by PPO inhibitors. In particular, the catalytic efficiencies (kcat/Km) of OnPPO and HaPPO were approximately twofold higher than that of AtPPO1. The elution profiles of all three PPOs, acquired by size-exclusion chromatography, showed only a single peak with a molecular weight of approximately 52-54 kDa, which corresponds to a monomeric form. Moreover, functional complementation with OnPPO and HaPPO in AtPPO1-silenced Arabidopsis resulted in restored growth, whereas AtPPO1-silenced wild type Arabidopsis suffered necrotic death. In addition, we observed that overexpression of OnPPO and HaPPO in Arabidopsis conferred resistance to the PPO-inhibiting herbicides tiafenacil and saflufenacil. These results suggest that two HemY-type PPOs of cyanobacteria can functionally substitute for plastidic PPO activity in Arabidopsis and can enhance resistance to tiafenacil and saflufenacil.

Biochemical and physiological mode of action of tiafenacil, a new protoporphyrinogen IX oxidase-inhibiting herbicide.

We conducted biochemical and physiological experiments to investigate the mode of action of tiafenacil (Terrad'or™), a new protoporphyrinogen IX oxidase (PPO)-inhibiting pyrimidinedione herbicide. Analysis of the half-maximal inhibitory concentration (IC50) against recombinant PPO enzymes from various plant species, including amaranth (Amaranthus tuberculatus), soybean (Glycine max), arabidopsis (Arabidopsis thaliana), and rapeseed (Brassica napus), showed that tiafenacil had an IC50 of 22 to 28 nM, similar to the pyrimidinedione herbicides butafenacil and saflufenacil and the N-phenylphthalimide herbicide flumioxazin. By contrast, tiafenacil exhibited 3- to 134-fold lower IC50 values than the diphenyl ether herbicides fomesafen, oxyfluorfen, and acifluorfen. Tiafenacil is non-selective and is herbicidal to both dicots and monocots, such as the weeds velvetleaf (Abutilon theophrasti), amaranth, and barnyardgrass (Echinochloa crus-galli) as well as the crops soybean, rapeseed, rice (Oryza sativa), and maize (Zea mays) at concentrations ranging from 1 to 50 µM. Treatment of plant tissue with tiafenacil in darkness resulted in the accumulation of protoporphyrin IX. Subsequent exposure to light increased the content of malondialdehyde and significantly decreased the Fv/Fm values of chlorophyll fluorescence. The results suggest that tiafenacil is a new PPO-inhibiting pyrimidinedione herbicide.

Structure of ginseng major latex-like protein 151 and its proposed lysophosphatidic acid-binding mechanism.

Lysophosphatidic acid (LPA) is a phospholipid growth factor with myriad effects on biological systems. LPA is usually present bound to animal plasma proteins such as albumin or gelsolin. When LPA complexes with plasma proteins, it binds to its cognate receptors with higher affinity than when it is free. Recently, gintonin from ginseng was found to bind to LPA and to activate mammalian LPA receptors. Gintonin contains two components: ginseng major latex-like protein 151 (GLP) and ginseng ribonuclease-like storage protein. Here, the crystal structure of GLP is reported, which belongs to the plant Bet v 1 superfamily, and a model is proposed for how GLP binds LPA. Amino-acid residues of GLP recognizing LPA were identified using site-directed mutagenesis and isothermal titration calorimetry. The resulting GLP mutants were used to study the activation of LPA receptor-dependent signalling pathways. In contrast to wild-type GLP, the H147A mutant did not bind LPA, elicit intracellular Ca(2+) transients in neuronal cells or activate Ca(2+)-dependent Cl(-) channels in Xenopus oocytes. Based on these results, a mechanism by which GLP recognizes LPA and its requirement to activate G protein-coupled LPA receptors to elicit diverse biological responses were proposed.

PLP undergoes conformational changes during the course of an enzymatic reaction.

Numerous enzymes, such as the pyridoxal 5'-phosphate (PLP)-dependent enzymes, require cofactors for their activities. Using X-ray crystallography, structural snapshots of the L-serine dehydratase catalytic reaction of a bacterial PLP-dependent enzyme were determined. In the structures, the dihedral angle between the pyridine ring and the Schiff-base linkage of PLP varied from 18° to 52°. It is proposed that the organic cofactor PLP directly catalyzes reactions by active conformational changes, and the novel catalytic mechanism involving the PLP cofactor was confirmed by high-level quantum-mechanical calculations. The conformational change was essential for nucleophilic attack of the substrate on PLP, for concerted proton transfer from the substrate to the protein and for directing carbanion formation of the substrate. Over the whole catalytic cycle, the organic cofactor catalyzes a series of reactions, like the enzyme. The conformational change of the PLP cofactor in catalysis serves as a starting point for identifying the previously unknown catalytic roles of organic cofactors.

Structure of ADC-68, a novel carbapenem-hydrolyzing class C extended-spectrum ß-lactamase isolated from Acinetobacter baumannii.

Outbreaks of multidrug-resistant bacterial infections have become more frequent worldwide owing to the emergence of several different classes of ß-lactamases. In this study, the molecular, biochemical and structural characteristics of an Acinetobacter-derived cephalosporinase (ADC)-type class C ß-lactamase, ADC-68, isolated from the carbapenem-resistant A. baumannii D015 were investigated. The blaADC-68 gene which encodes ADC-68 was confirmed to exist on the chromosome via Southern blot analysis and draft genome sequencing. The catalytic kinetics of ß-lactams and their MICs (minimum inhibitory concentrations) for A. baumannii D015 and purified ADC-68 (a carbapenemase obtained from this strain) were assessed: the strain was resistant to penicillins, narrow-spectrum and extended-spectrum cephalosporins, and carbapenems, which were hydrolyzed by ADC-68. The crystal structure of ADC-68 was determined at a resolution of 1.8 Å. The structure of ADC-68 was compared with that of ADC-1 (a non-carbapenemase); differences were found in the central part of the Ω-loop and the C-loop constituting the edge of the R1 and R2 subsites and are close to the catalytic serine residue Ser66. The ADC-68 C-loop was stabilized in the open conformation of the upper R2 subsite and could better accommodate carbapenems with larger R2 side chains. Furthermore, a wide-open conformation of the R2-loop allowed ADC-68 to bind to and hydrolyze extended-spectrum cephalosporins. Therefore, ADC-68 had enhanced catalytic efficiency against these clinically important ß-lactams (extended-spectrum cephalosporins and carbapenems). ADC-68 is the first reported enzyme among the chromosomal class C ß-lactamases to possess class C extended-spectrum ß-lactamase and carbapenemase activities.

Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli.

YmfB from Escherichia coli is the Nudix hydrolase involved in the metabolism of thiamine pyrophosphate, an important compound in primary metabolism and a cofactor of many enzymes. In addition, it hydrolyzes (d)NTPs to (d)NMPs and inorganic orthophosphates in a stepwise manner. The structures of YmfB alone and in complex with three sulfates and two manganese ions determined by X-ray crystallography, when compared with the structures of other Nudix hydrolases such as MutT, Ap4Aase and DR1025, provide insight into the unique hydrolysis mechanism of YmfB. Mass-spectrometric analysis confirmed that water attacks the terminal phosphates of GTP and GDP sequentially. Kinetic analysis of binding-site mutants showed that no individual residue is absolutely required for catalytic activity, suggesting that protein residues do not participate in the deprotonation of the attacking water. Thermodynamic integration calculations show that a hydroxyl ion bound to two divalent metal ions attacks the phosphate directly without the help of a nearby catalytic base.

Expression, crystallization and preliminary X-ray crystallographic analysis of alcohol dehydrogenase (ADH) from Kangiella koreensis.

Alcohol dehydrogenases (ADHs) are a group of dehydrogenase enzymes that facilitate the interconversion between alcohols and aldehydes or ketones with the reduction of NAD(+) to NADH. In bacteria, some alcohol dehydrogenases catalyze the opposite reaction as part of fermentation to ensure a constant supply of NAD(+). The adh gene from Kangiella koreensis was cloned and the protein (KkADH) was expressed, purified and crystallized. A KkADH crystal diffracted to 2.5 Šresolution and belonged to the monoclinic space group P2(1), with unit-cell parameters a = 94.1, b = 80.9, c = 115.6 Å, ß = 111.9°. Four monomers were present in the asymmetric unit, with a corresponding VM of 2.55 Å(3) Da(-1) and a solvent content of 51.8%.

Expression, crystallization and preliminary X-ray crystallographic analysis of peptide deformylase from Campylobacter jejuni.

Campylobacter jejuni is one of the major foodborne pathogens causing human infection. Peptide deformylase, a metallohydrolase, catalyzes the deformylation of N-formylated methionine in newly synthesized polypeptides in prokaryotes and some eukaryotic organelles. The deformylation process is an essential step in protein synthesis and has attracted much attention as a potential target for the development of novel antibacterial agents. Here, the cloned codon-optimized def gene from C. jejuni was synthesized and the protein was expressed, purified and crystallized. C. jejuni peptide deformylase crystals obtained at pH 7.0 and pH 6.5 diffracted to 2.9 Šresolution and belonged to the trigonal space group R3, with unit-cell parameters a=b=105.7, c=58.0 Å. One monomer existed in the asymmetric unit, with a corresponding VM of 3.1 Å3 Da(-1) and a solvent content of 60.4%.

Expression, crystallization and preliminary X-ray crystallographic analysis of cellobiose 2-epimerase from Dictyoglomus turgidum DSM 6724.

Cellobiose 2-epimerase epimerizes and isomerizes ß-1,4- and α-1,4-gluco-oligosaccharides. N-Acyl-D-glucosamine 2-epimerase (DT_epimerase) from Dictyoglomus turgidum has an unusually high catalytic activity towards its substrate cellobiose. DT_epimerase was expressed, purified and crystallized. Crystals were obtained of both His-tagged DT_epimerase and untagged DT_epimerase. The crystals of His-tagged DT_epimerase diffracted to 2.6 Šresolution and belonged to the monoclinic space group P21, with unit-cell parameters a=63.9, b=85.1, c=79.8 Å, ß=110.8°. With a Matthews coefficient VM of 2.18 Å3 Da(-1), two protomers were expected to be present in the asymmetric unit with a solvent content of 43.74%. The crystals of untagged DT_epimerase diffracted to 1.85 Šresolution and belonged to the orthorhombic space group P212121, with unit-cell parameters a=55.9, b=80.0, c=93.7 Å. One protomer in the asymmetric unit was expected, with a corresponding VM of 2.26 Å3 Da(-1) and a solvent content of 45.6%.

Expression, crystallization and preliminary X-ray crystallographic analysis of alanine racemase from Acinetobacter baumannii OXA-23.

Acinetobacter baumannii has received much attention owing to its exceptional ability to develop resistance to currently available antibiotics. Alanine racemase (ALR) catalyzes the racemization of L-alanine to D-alanine with pyridoxal 5'-phosphate (PLP) as a cofactor. The D-alanine product is an essential component of the bacterial cell wall and ALR is a potential target for the development of novel antibacterial drugs. The alr gene from A. baumannii was cloned and the protein (AbALR) was expressed, purified and crystallized. The AbALR crystal diffracted to 2.3 Šresolution and belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 55.1, b = 85.0, c = 167.7 Å. Two protomers were present in the asymmetric unit, with a corresponding V(M) value of 2.3 Å(3) Da(-1) and a solvent content of 47.5%.

Crystal structure of cytochrome P450 CYP105N1 from Streptomyces coelicolor, an oxidase in the coelibactin siderophore biosynthetic pathway.

The genome sequence of Streptomyces coelicolor contains 18 cytochrome P450 enzymes. The recombinant CYP105N1 protein has been expressed in Escherichia coli and purified, and we report the biochemical and structural characterization of CYP105N1 from S. coelicolor. The purified protein exhibited the typical CO-binding spectrum of P450 enzymes and type I binding spectra with estradiol and a coelibactin analog. The oxidation of estradiol by CYP105N1, supported by H(2)O(2), produced estriol. The crystal structure of CYP105N1 was determined at 2.9 Å resolution. An unexpected wide open binding pocket located above the heme group was identified, with a volume of approximately 4299 Å(3). These results suggest that the large open pocket to the active site may be a key feature for easy access of the peptidyl carrier protein-bound substrate to perform the hydroxylation reaction. A molecular docking model with coelibactin showed that the phenyl group of coelibactin is located <4 Å away from the heme-iron, suggesting that CYP105N1 may be involved in the hydroxylation of the phenyl ring of the coelibactin precursor during biosynthesis.

Crystallization and preliminary diffraction studies of GIM-1, a class B carbapenem-hydrolyzing ß-lactamase.

GIM-1 is a member of the class B carbapenemases (metallo-ß-lactamases; MBLs) and has a wide spectrum of activity against carbapenems, penicillins and extended-spectrum cephalosporins, but not aztreonam. GIM-1 presents an enormous challenge to infection control, particularly in the eradication of Gram-negative pathogens including Enterobacteriaceae, Pseudomonas aeruginosa, Acinetobacter baumannii and nonfermenters. There are presently few or no drugs in late-stage development for these pathogens and GIM-1 is a potential target for the development of antimicrobial agents against pathogens producing MBLs. In this study, GIM-1 was cloned, overexpressed and crystallized. The GIM-1 crystals diffracted to 1.4 Šresolution and belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 38.5, b = 67.6, c = 72.8 Å. One molecule is present in the asymmetric unit, with a corresponding V(M) of 1.69 Å(3) Da(-1) and a solvent content of 27.1%.

Crystallization and preliminary diffraction studies of SFC-1, a carbapenemase conferring antibiotic resistance.

SFC-1, a class A carbapenemase that confers antibiotic resistance, hydrolyzes the ß-lactam rings of ß-lactam antibiotics (carbapenems, cephalosporins, penicillins and aztreonam). SFC-1 presents an enormous challenge to infection control, particularly in the eradication of Gram-negative pathogens. As SFC-1 exhibits a remarkably broad substrate range, including ß-lactams of all classes, the enzyme is a potential target for the development of antimicrobial agents against pathogens producing carbapenemases. In this study, SFC-1 was cloned, overexpressed, purified and crystallized. The SFC-1 crystal diffracted to 1.6 Å resolution and belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 65.8, b = 68.3, c = 88.8 Å. Two molecules are present in the asymmetric unit, with a corresponding V(M) of 1.99 Å(3) Da(-1) and a solvent content of 38.1%.

Crystallization and preliminary diffraction studies of Nudix hydrolase YmfB from Escherichia coli K-1.

Nudix hydrolases are a family of proteins that contains the Nudix signature of the characteristic amino-acid sequence Gx(5)Ex(5) [UA]xREx(2)EExGU, where x represents any amino acid and U usually a bulky hydrophobic amino acid, such as Leu, Val, or Ile. They ubiquitously exist in more than 200 species. YmfB, a novel Nudix hydrolase found in Escherichia coli, is a nonspecific nucleoside tri- and di-phosphatase, which atypically releases inorganic orthophosphate from triphosphates instead of pyrophosphate. In this study, YmfB was cloned, overexpressed, and crystallized. Two different crystals, one belonging to an orthorhombic space group C222(1) and the other a monoclinic space group P2(1), diffracted to 2.7 A and 2.6 A resolution, and had unit cell parameters of a = 68.7 A, b = 283.1 A, c = 70.4 A and a = 69.1 A, b = 70.3 A, c = 145.6 A, beta = 103.3 degrees , respectively. For the C222(1) space group, four or five monomers exist in the asymmetric unit, with a corresponding V(m) of 2.48 or 1.99 A(3) Da(-1) and a solvent content of 50.5 or 38.2%. For the P2(1) space group, eight or nine monomers exist in the asymmetric unit, with a corresponding V(m) of 2.49 or 2.21 A(3) Da(-1) and a solvent content of 50.7 or 44.5%.

Dual activity of PNGM-1 pinpoints the evolutionary origin of subclass B3 metallo-ß-lactamases: a molecular and evolutionary study.

Resistance to ß-lactams is one of the most serious problems associated with Gram-negative infections. ß-Lactamases are able to hydrolyze ß-lactams such as cephalosporins and/or carbapenems. Evolutionary origin of metallo-ß-lactamases (MBLs), conferring critical antibiotic resistance threats, remains unknown. We discovered PNGM-1, the novel subclass B3 MBL, in deep-sea sediments that predate the antibiotic era. Here, our phylogenetic analysis suggests that PNGM-1 yields insights into the evolutionary origin of subclass B3 MBLs. We reveal the structural similarities between tRNase Zs and PNGM-1, and demonstrate that PNGM-1 has both MBL and tRNase Z activities, suggesting that PNGM-1 is thought to have evolved from a tRNase Z. We also show kinetic and structural comparisons between PNGM-1 and other proteins including subclass B3 MBLs and tRNase Zs. These comparisons revealed that the B3 MBL activity of PNGM-1 is a promiscuous activity and subclass B3 MBLs are thought to have evolved through PNGM-1 activity.

Expression, crystallization and preliminary X-ray crystallographic analysis of Xoo2316, a predicted 6-phosphogluconolactonase, from Xanthomonas oryzae pv. oryzae.

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight, which is one of the most devastating diseases of rice (Oryza sativa L.) in many rice-growing countries. The coding sequence of Xoo2316 (a predicted 6-phosphogluconolactonase; 6PGL) from Xoo was cloned and expressed in Escherichia coli. 6PGL is an enzyme that is involved in the second step of the pentose phosphate pathway, which is essential for the synthesis of nucleotide sugars and NADPH, the main source of reducing power. The protein was purified and crystallized in order to elucidate the molecular basis for its enzymatic reaction. Native crystals diffracted to 2.4 A resolution and belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 40.0, b = 65.1, c = 78.8 A. A monomer exists in the asymmetric unit with a corresponding V(M) of 1.93 A(3) Da(-1) and a solvent content of 36.5%.

The novel metallo-ß-lactamase PNGM-1 from a deep-sea sediment metagenome: crystallization and X-ray crystallographic analysis.

Metallo-ß-lactamases (MBLs) are present in major Gram-negative pathogens and environmental species, and pose great health risks because of their ability to hydrolyze the ß-lactam rings of antibiotics such as carbapenems. PNGM-1 was the first reported case of a subclass B3 MBL protein that was identified from a metagenomic library from deep-sea sediments that predate the antibiotic era. In this study, PNGM-1 was overexpressed, purified and crystallized. Crystals of native and selenomethionine-substituted PNGM-1 diffracted to 2.10 and 2.30 Šresolution, respectively. Both the native and the selenomethionine-labelled PNGM-1 crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 122, b = 83, c = 163 Å, ß = 110°. Matthews coefficient (VM) calculations suggested the presence of 6-10 molecules in the asymmetric unit, corresponding to a solvent content of ∼31-58%. Structure determination is currently in progress.

Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.

D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this reaction makes DDL an important drug target for the development of antibacterial agents. Five crystal structures of DDL from Yersinia pestis (YpDDL) were determined at 1.7-2.5 Å resolution: apo, AMP-bound, ADP-bound, adenosine 5'-(ß,γ-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the ω-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the ω-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops.

The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding.

Acinetobacter baumannii, which is emerging as a multidrug-resistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 Å. The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays.