Expression, purification, and characterization of blasticidin S deaminase (BSD) from Aspergillus terreus: the role of catalytic zinc in enzyme structure

We established an efficient overproduction-purification system for blasticidin S deaminase (BSD) using the cDNA cloned from Aspergillus terreus. The estimated molecular mass of the purified enzyme indicated BSD was a tetramer. This tetrameric form was very resistant to denaturation by SDS and showed heat-modifiable behavior on SDS-PAGE; i.e., BSD migrated much slower (as a single band of 36 kDa) in its active conformation than its completely denatured polypeptide (13 kDa) if heat treatment in 2% SDS was not performed before electrophoresis. As predicted from the presence of the catalytic zinc-coordinating sequence motif conserved in the cytosine nucleoside/nucleotide deaminase family, BSD also contained one zinc per deaminase subunit. However, the predicted catalytic function appeared not to be the only role of this zinc in the enzyme. First, titration of the zinc-chelating -SH groups with p-hydroxymercuriphenylsulfonate led to dissociation of the BSD tetramer into unstable monomers or dimers. Second, depletion of zinc on reconstitution of chemically denatured BSD (with either guanidine-HCl or acidic pH) resulted in improper folding of the polypeptide. These results suggest that zinc also plays a structural role in maintenance of the protein structure. When we introduced mutations at Glu-56 (the proposed active site) and Cys-91 (a proposed catalytic zinc-binding Cys) in BSD, none of the resulting mutants (E56D, E56Q, C91A, C91S, and C91H) showed any detectable activity, as judged with the spectrophotometric assay. Replacements of Cys-91 resulted in gross perturbation of the enzyme structure although the catalytically essential Glu-56 was not necessarily required for proper folding of the enzyme. These results further support our proposal that the catalytic zinc coordinated by the conserved sequence motif is also structural in BSD.     

Cloning of the blasticidin S deaminase gene (BSD) from Aspergillus terreus and its use as a selectable marker for Schizosaccharomyces pombe and Pyricularia oryzae

Aspergillus terreus produces a unique enzyme, blasticidin S deaminase, which catalyzes the deamination of blasticidin S (BS), and in consequence confers high resistance to the antibiotic. A cDNA clone derived from the structural gene for BS deaminase (BSD) was isolated by transforming Escherichia coli with an Aspergillus cDNA expression library and directly selecting for the ability to grow in the presence of the antibiotic. The complete nucleotide sequene of BSD was determined and proved to contain an open reading frame of 393 bp, encoding a polypeptide of 130 amino acids. Comparison of its nulceotide sequence with that of bsr, the BS deaminase gene isolated from Bacillus cereus, indicated no homology and a large difference in codon usage. The activity of BSD expressed in E. coli was easily quantified by an assay based on spectrophotometric recording. The BSD gene was placed in a shuttle vector for Schizosaccharomyces pombe, downstream of the SV40 early region promoter, and this allowed direct selection with BS at high frequency, following transformation into the yeast. The BSD gene was also employed as a selectable marker for Pyricularia oryzae, which could not be transformed to BS resistance by bsr. These results promise that the BSD gene will be useful as a new dominant selectable marker for eukaryotes.     

A new transformation system of Saccharomyces cerevisiae with blasticidin S deaminase gene

A new method for transformation of Saccharomyces cerevisiae that allows selection was developed. As the frequency of spontaneous blasticidin S resistant mutants from diploid type yeast strain (X-2180AB) was 5.2×10^–6, which was a thousandfold less than that from haploid type yeast strain (X-2180B), it was considered that the mechanism of spontaneous blasticidin S resistant mutations was related to recessive gene. Industrial yeasts, which were diploid, were transformed with blasticidin S deaminase gene from Aspergillus terreus to blasticidin S resistance. Expression of blasticidin S deaminase gene allowed selection of transformants from industrial yeasts.     

Crystal structures of Vibrio harveyi chitinase A complexed with chitooligosaccharides: implications for the catalytic mechanism

This research describes four X-ray structures of Vibrio harveyi chitinase A and its catalytically inactive mutant (E315M) in the presence and absence of substrates. The overall structure of chitinase A is that of a typical family-18 glycosyl hydrolase comprising three distinct domains: (i) the amino-terminal chitin-binding domain; (ii) the main catalytic (α/β)₈ TIM-barrel domain; and (iii) the small (α + β) insertion domain. The catalytic cleft of chitinase A has a long, deep groove, which contains six chitooligosaccharide ring-binding subsites (−4)(−3)(−2)(−1)(+1)(+2). The binding cleft of the ligand-free E315M is partially blocked by the C-terminal (His)₆-tag. Structures of E315M-chitooligosaccharide complexes display a linear conformation of pentaNAG, but a bent conformation of hexaNAG. Analysis of the final 2F_o − F_c omit map of E315M-NAG6 reveals the existence of the linear conformation of the hexaNAG at a lower occupancy with respect to the bent conformation. These crystallographic data provide evidence that the interacting sugars undergo conformational changes prior to hydrolysis by the wild-type enzyme.     

Crystal structures of arginine deiminase with covalent reaction intermediates; implications for catalytic mechanism

Arginine deiminase (ADI), an enzyme that hydrolyzes arginine to generate energy in many parasitic microorganisms, has potent anticancer activities and can halt growth of solid tumors. We determined the crystal structure of ADI from Mycoplasma arginini in two different forms (1.6 and 2.0 A resolution) using multiple isomorphous replacement. ADI shares common structural features with the arginine-catabolizing enzymes Arg:Gly amidinotransferase and dimethylarginine dimethyl-aminohydrolase; ADI contains an additional domain of five helices. The scissile C-N bonds of the substrates and the catalytic triads (Cys398-His269-Glu213 of ADI) for the three enzymes superimpose on each other. The ADI structure from form I crystals corresponds to a tetrahedral intermediate with four heteroatoms (1S, 2N, 1O) covalently bonded to the reaction-center carbon. The structure from form II crystals represents an amidino-enzyme complex; the reaction-center carbon is covalently bonded to Cys398 sulfur and two nitrogens, and the reacting water molecule is only 2.54 A away.     

Expression of the blasticidin S deaminase gene (bsr) in tobacco: Fungicide tolerance and a new selective marker for transgenic plants

Summary Blasticidin S (BS), a fungicide of microbial origin, is used for the practical control of rice blast disease. It has broad antimicrobial activity but occasionally exhibits adverse phytotoxic effects on some dicot plants. An inactivating enzyme, BS deaminase, was discovered in the BS resistant strain, Bacillus cereus K55-S1, and the structural gene, bsr, for the enzyme has been cloned. We introduced the bsr gene into tobacco plants using the Ti plasmid vector system and demonstrated that the bsr gene conferred a BS resistant phenotype to the plants. Thus the bsr gene could be useful as a selective marker for plant transformation and provides an example for a new approach to the solution of phytotoxicity problems associated with the use of some types of fungicide.     

Crystal structure of unliganded TRAP: implications for dynamic allostery

Allostery is vital to the function of many proteins. In some cases, rather than a direct steric effect, mutual modulation of ligand binding at spatially separated sites may be achieved through a change in protein dynamics. Thus changes in vibrational modes of the protein, rather than conformational changes, allow different ligand sites to communicate. Evidence for such an effect has been found in TRAP (trp RNA-binding attenuation protein), a regulatory protein found in species of Bacillus. TRAP is part of a feedback system to modulate expression of the trp operon, which carries genes involved in tryptophan synthesis. Negative feedback is thought to depend on binding of tryptophan-bound, but not unbound, TRAP to a specific mRNA leader sequence. We find that, contrary to expectations, at low temperatures TRAP is able to bind RNA in the absence of tryptophan, and that this effect is particularly strong in the case of Bacillus stearothermophilus TRAP. We have solved the crystal structure of this protein with no tryptophan bound, and find that much of the structure shows little deviation from the tryptophan-bound form. These data support the idea that tryptophan may exert its effect on RNA binding by TRAP through dynamic and not structural changes, and that tryptophan binding may be mimicked by low temperature.     

Crystal structures of catalytic core domain of BIV integrase: implications for the interaction between integrase and target DNA

Integrase plays a critical role in the recombination of viral DNA into the host genome. Therefore, over the past decade, it has been a hot target of drug design in the fight against type 1 human immunodeficiency virus (HIV-1). Bovine immunodeficiency virus (BIV) integrase has the same function as HIV-1 integrase. We have determined crystal structures of the BIV integrase catalytic core domain (CCD) in two different crystal forms at a resolution of 2.45? and 2.2?, respectively. In crystal form I, BIV integrase CCD forms a back-to-back dimer, in which the two active sites are on opposite sides. This has also been seen in many of the CCD structures of HIV-1 integrase that were determined previously. However, in crystal form II, BIV integrase CCD forms a novel face-to-face dimer in which the two active sites are close to each other. Strikingly, the distance separating the two active sites is approximately 20 ?, a distance that perfectly matches a 5-base pair interval. Based on these data, we propose a model for the interaction of integrase with its target DNA, which is also supported by many published biochemical data. Our results provide important clues for designing new inhibitors against HIV-1.     

Stable transformation of trypanosomatids through targeted chromosomal integration of the selectable marker gene encoding blasticidin S deaminase

The susceptibilities of the protozoan parasites Leishmania mexicana and Trypanosoma brucei to the nucleoside antibiotic blasticidin S were assessed. A concentration of 10 microg ml(-1) was sufficient to cause cell death within 72 h of L. mexicana promastigotes and bloodstream forms of T. brucei in vitro. The gene encoding blasticidin S deaminase (BSD) was therefore incorporated into cassettes for targeting to the cysteine proteinase C locus of L. mexicana (CPC::BSD) and the tubulin locus of T. brucei (tub::RAD51-BSR). Following transfection of mutant parasites that contained other well-established selectable marker genes (HYG, NEO, BLE, PAC and SAT), clones resistant to 10 microg ml(-1) blasticidin S were shown by PCR and Southern blotting to have integrated the cassettes by homologous recombination. The results confirm that BSD can be used as a selectable marker gene for targeted chromosomal integration during genetic manipulations of trypanosomatids.     

Crystal structures and catalytic activities of Zn(II) compounds containing btp ligands

The structures of new compounds containing Zn(II) ions and btp (2,6-bis(N′-1,2,4-triazolyl)pyridine) ligands have been determined. With coordinating chloride and bromide anions, Zn(II) produces chains 2 and 3 containing C-H?X(Cl or Br) weak interactions to build crystal structures and they are face-to-face aligned. With non-coordinating anions, Zn(II) produces monomeric compounds 4 and 5 containing H-bonds between anions and water ligands and face-to-face π-π interactions to build crystal structures. The previously reported polymeric compound 1 containing [Zn(NO₃)(H₂O)₂(btp)₂]⁺ units bridged by btp ligands was found to carry out the catalytic transesterification of a range of esters with methanol at room temperature under mild conditions, whereas it did not catalyze the ring opening of epoxide (easier reaction) with methanol. These results indicate that the polymeric compound 1 shows selective reactivity. In addition, the catalyst 1 has shown even better catalytic activity than the corresponding Zn(NO₃)₂ salt.     

Crystal structures of substrate-free and nitrosyl cytochrome p450cin: implications for o(2) activation

The crystal structure of the P450cin substrate-bound nitric oxide complex and the substrate-free form have been determined revealing a substrate-free structure that adopts an open conformation relative to the substrate-bound structure. The region of the I helix that forms part of the O(2) binding pocket shifts from an α helix in the substrate-free form to a π helix in the substrate-bound form. Unique to P450cin is an active site residue, Asn242, in the I helix that H-bonds with the substrate. In most other P450s this residue is a Thr and plays an important role in O(2) activation by participating in an H-bonding network required for O(2) activation. The π/α I helix transition results in the carbonyl O atom of Gly238 moving in to form an H-bond with the water/hydroxide ligand in the substrate-free form. The corresponding residue, Gly248, in the substrate-free P450cam structure experiences a similar motion. Most significantly, in the oxy-P450cam complex Gly248 adopts a position midway between the substrate-free and -bound states. A comparison between these P450cam and the new P450cin structures provides insights into differences in how the two P450s activate O(2). The structure of P450cin complexed with nitric oxide, a close mimic of the O(2) complex, shows that Gly238 is likely to form tighter interactions with ligands than the corresponding Gly248 in P450cam. Having a close interaction between an H-bond acceptor, the Gly238 carbonyl O atom, and the distal oxygen atom of O(2) will promote protonation and hence further reduction of the oxy complex to the hydroperoxy intermediate resulting in heterolytic cleavage of the peroxide O-O bond and formation of the active ferryl intermediate required for substrate hydroxylation.     

Crystal structures of the carboxyl terminal domain of rat 10-formyltetrahydrofolate dehydrogenase: implications for the catalytic mechanism of aldehyde dehydrogenases

10-Formyltetrahydrofolate dehydrogenase (FDH) catalyzes an NADP+-dependent dehydrogenase reaction resulting in conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. This reaction is a result of the concerted action of two catalytic domains of FDH, the amino-terminal hydrolase domain and the carboxyl-terminal aldehyde dehydrogenase domain. In addition to participation in the overall FDH mechanism, the C-terminal domain is capable of NADP+-dependent oxidation of short chain aldehydes to their corresponding acids. We have determined the crystal structure of the C-terminal domain of FDH and its complexes with oxidized and reduced forms of NADP. Compared to other members of the ALDH family, FDH demonstrates a new mode of binding of the 2'-phosphate group of NADP via a water-mediated contact with Gln600 that may contribute to the specificity of the enzyme for NADP over NAD. The structures also suggest how Glu673 can act as a general base in both acylation and deacylation steps of the reaction. In the apo structure, the general base Glu673 is positioned optimally for proton abstraction from the sulfur atom of Cys707. Upon binding of NADP+, the side chain of Glu673 is displaced from the active site by the nicotinamide ring and contacts a chain of highly ordered water molecules that may represent a pathway for translocation of the abstracted proton from Glu673 to the solvent. When reduced, the nicotinamide ring of NADP is displaced from the active site, restoring the contact between Cys707 and Glu673 and allowing the latter to activate the hydrolytic water molecule in deacylation.     

Crystal structures and luminescent properties of zinc(II) and cadmium(II) compounds constructed from 5-sulfoisophthalic acid and flexible bis-triazole ligands

Four new cadmium(II) and zinc(II) coordination polymers {[Zn(btrp)(SIP)][Zn_0.5(H₂O)₃]}_n (1), {[Cd_1.5(btrp)(SIP)(H₂O)₂]·2H₂O}_n (2), {[Cd_1.5(btrb)(SIP)(H₂O)₃]·2H₂O}_n (3), {[Zn_1.5(btrb)_1.5(SIP)(H₂O)₂]·2H₂O}_n (4) (btrp = 1,3-bis(1,2,4-triazol-1-yl)propane, btrb = 1,3-bis(1,2,4-triazol-1-yl)butane, NaH₂SIP = 5-sulfoisophthalic acid monosodium salt) have been synthesized under hydrothermal conditions and structurally characterized. Compound 1 possesses an infinite 1D ladder-like chain structure with [Zn(H₂O)₆]²⁺ trapped in the pores, which is further interconnected by π?π interactions to lead to a 2D supramolecular architecture. Compounds 2 and 3 features two similar 2D layer structures, and the resulting 2D structures are interconnected by hydrogen-bond interactions to lead to 3D supramolecular architectures. Compound 4 is a 2D parallel ladder structure, and through the interpenetrating btrb ligand, it constructs into 3D architectures. Luminescence analyses were performed on all the four compounds, which show strong fluorescent emissions in the solid state at room temperature.     

Ferrocenylboronates: Crystal structures and electrochemical properties

The electrochemical behavior of a series of eight previously reported monoferrocenyl- and diferrocenyl-boronates derived from tridentate ligands has been studied. Even if most mononuclear and all the dinuclear complexes examined showed to undergo slow decomposition in nonaqueous solution (releasing free ferrocenyl boronic acid), their redox activity has been investigated. It has been proved that the oxidation of the two ferrocenyl subunits in the dimeric species proceeds simultaneously, indicating that no mutual electronic interaction exists between them. Additionally, the solid-state molecular structures of two diferrocenyl complexes (2a and 2b) were studied by X-ray diffraction. The analysis confirms the formation of a [5.4.0] heterobicycle with the presence of two different boron atoms, one in a tetrahedral geometry and the other one in a trigonal geometry.     

Crystal structures and catalytic activities of Zn(II) compounds containing 1,3-bis(4-pyridyl)propane

The structures of new compounds containing Zn(II) ions and bpp (1,3-bis(4-pyridyl)propane) ligands have been determined. The coordinating halides (Br⁻ or Cl⁻) produce one-dimensional compounds 6 and 7, and intra- and inter-chain CH?X (X = Br or I) interactions play roles for building crystal structures with the flexible bpp ligands. The non-coordinating anions do not produce hydroxyl bridged zinc cations or polymeric compounds, and produce only a monomeric complex 4 containing four bpp ligands and two water ligands. Previously reported polymeric compounds 1 and 2 containing hydroxyl-bridged zinc cations [Zn₂OH] were found to carry out the catalytic transesterification of a range of esters with methanol at room temperature under the mild conditions, whereas the rest of compounds did not catalyze the transesterification reactions at all. In addition, the catalysts 1 and 2 have shown even better catalytic activity than zinc salts Zn(NO₃)₂ and Zn(OTf)₂.     

Crystal structures of engrailed homeodomain mutants: implications for stability and dynamics

We report the crystal structures and biophysical characterization of two stabilized mutants of the Drosophila Engrailed homeodomain that have been engineered to minimize electrostatic repulsion. Four independent copies of each mutant occupy the crystal lattice, and comparison of these structures illustrates variation that can be partly ascribed to networks of correlated conformational adjustments. Central to one network is leucine 26 (Leu26), which occupies alternatively two side chain rotameric conformations (-gauche and trans) and different positions within the hydrophobic core. Similar sets of conformational substates are observed in other Engrailed structures and in another homeodomain. The pattern of structural adjustments can account for NMR relaxation data and sequence co-variation networks in the wider homeodomain family. It may also explain the dysfunction associated with a P26L mutation in the human ARX homeodomain protein. Finally, we observe a novel dipolar interaction between a conserved tryptophan and a water molecule positioned along the normal to the indole ring. This interaction may explain the distinctive fluorescent properties of the homeodomain family.     

Crystal structures of cobalamin-independent methionine synthase (MetE) from Streptococcus mutans: a dynamic zinc-inversion model

Cobalamin-independent methionine synthase (MetE) catalyzes the direct transfer of a methyl group from methyltetrahydrofolate to l-homocysteine to form methionine. Previous studies have shown that the MetE active site coordinates a zinc atom, which is thought to act as a Lewis acid and plays a role in the activation of thiol. Extended X-ray absorption fine structure studies and mutagenesis experiments identified the zinc-binding site in MetE from Escherichia coli. Further structural investigations of MetE from Thermotoga maritima lead to the proposition of two models: “induced fit” and “dynamic equilibrium”, to account for the catalytic mechanisms of MetE. Here, we present crystal structures of oxidized and zinc-replete MetE from Streptococcus mutans at the physiological pH. The structures reveal that zinc is mobile in the active center and has the possibility to invert even in the absence of homocysteine. These structures provide evidence for the dynamic equilibrium model.     

Zinc(II) complexes with 1,8-naphthyridine-based ligand: Crystal structures and luminescent properties

The reactions of 2,4-dimethyl-7-(2-pyridylamino)-1,8-naphthyridine (L1) with Zn(ClO₄)₂ · 6H₂O, and bis(5,7-dimethyl-1,8-naphthyrid-2-yl)amine ligand (L2) with Zn(OAc)₂ · 2H₂O, ZnCl₂ or Zn(ClO₄)₂ · 6H₂O afforded four blue luminescent zinc(II) complexes, [Zn(L1)₂](ClO₄)₂ · 2CH₂Cl₂ (1), [Zn(L2)(OAc)₂] · CH₂Cl₂ (2), [Zn(L2)₂][ZnCl₄] · 3.5CH₂Cl₂ (3) and [Zn(L2)₂](ClO₄)₂ (4), respectively. Crystal structures of complexes 1-3 have been determined by X-ray structural analyses as mononuclear complexes with pseudo-tetrahedral geometry. The crystal packing of 1 reveals the coordination cation which is self-assembled to stair chains through aromatic π-π interactions. The intermolecular N-H?O hydrogen bond in 2 generates a centrosymmetric H-bonded dimer. However, the crystal lattice of 3 shows that the molecules are linked by extensive intermolecular hydrogen bonds between the amino groups and the anions, resulting in a one-dimensional zigzag chain. Furthermore, these molecular pairs or chains were self-assembled to two-dimensional sheets or three-dimensional networks through aromatic π-π interactions. All the zinc(II) complexes display intense intraligand ¹(π-π^∗) fluorescence with λ_max at 380 and 393 nm for 1, 385 and 404 nm for 2-4 in methanol at room temperature, respectively. Emission quantum yields of these complexes are in the range from 0.41 to 0.57. The broad emission bands in their solid-state emission spectra are attributed to intraligand ¹(π-π^∗) transition and aromatic π-π interactions as well.