Structural properties of the nickel ions in urease: novel insights into the catalytic and inhibition mechanisms

A structure-based proposal for the catalytic mechanism of the bacterial acid phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases

The Escherichia coli gene aphA codes for a periplasmic acid phosphatase called AphA, belonging to class B bacterial phosphatases, which is part of the DDDD superfamily of phosphohydrolases. After our first report about its crystal structure, we have started a series of crystallographic studies aimed at understanding of the catalytic mechanism of the enzyme. Here, we report three crystal structures of the AphA enzyme in complex with the hydrolysis products of nucleoside monophosphate substrates and a fourth with a proposed intermediate analogue that appears to be covalently bound to the enzyme. Comparison with the native enzyme structure and with the available X-ray structures of different phosphatases provides clues about the enzyme chemistry and allows us to propose a catalytic mechanism for AphA, and to discuss it with respect to the mechanism of other bacterial and human phosphatases.

Effect of Zn⋅⋅⋅Zn Separation on the Hydrolytic Activity of Model Dizinc Phosphodiesterases

From the study of highly preorganized model systems, experimental support has been obtained for a possible functional role of the Zn-(H)O...HO(H)-Zn motif in oligozinc hydrolases. The mechanistic relevance of such an array, which may be described as a hydrated form of a pseudo-terminal Zn-bound hydroxide, has recently been supported by DFT calculations on various metallohydrolase active sites. In the present targeted approach, the Zn...Zn distance in two related dizinc complexes has been controlled through the use of multifunctional pyrazolate-based ligand scaffolds, giving either a tightly bridged Zn-O(H)-Zn or a more loosely bridged Zn-(H)O...HO(H)-Zn species in the solid state. Zn-bound water has been found to exhibit comparable acidity irrespective of whether the resulting hydroxide is supported by strong hydrogen-bonding in the O(2)H(3) moiety or is in a bridging position between two zinc ions, indicating that water does not necessarily have to adopt a bridging position in order for its pK(a) to be sufficiently lowered so as to provide a Zn-bound hydroxide at physiological pH. Comparative reactivity studies on the cleavage of bis(4-nitrophenyl)phosphate (BNPP) mediated by the two dizinc complexes have revealed that the system with the larger Zn...Zn separation is hydrolytically more potent, both in the hydrolysis and the transesterification of BNPP. The extent of active site inhibition by the reaction products has also been found to be governed by the Zn...Zn distance, since phosphate diester coordination in a bridging mode within the clamp of two zinc ions is only favored for Zn...Zn distances well above 4 A. Different binding affinities are rationalized in terms of the structural characteristics of the product-inhibited complexes for the two different ligand scaffolds, with dimethyl phosphate found as a bridging ligand within the bimetallic pocket.

Nickel trafficking: insights into the fold and function of UreE, a urease metallochaperone

UreE is a metallo-chaperone assisting the incorporation of two adjacent Ni(2+) ions in the active site of urease. This study describes an attempt to distill general information on this protein using a computational post-genomic approach for the understanding of the structural details of the molecular function of UreE in nickel trafficking. The two crystal structures recently determined for UreE from Bacillus pasteurii (BpUreE) and Klebsiella aerogenes (KaUreE) were comparatively analyzed. This analysis provided insights into the protein structural and conformational features. A structural database of UreE proteins from a large number of different genomes was built using homology modeling. All available sequences of UreE were retrieved from protein and cDNA databases, and their structures were modeled on the crystal structures of BpUreE and KaUreE. A self-consistent iterative protocol was devised for multiple sequence alignment optimization involving secondary structure prediction and evaluation of the energy features of the obtained modeled structures. The quality of all models was tested using standard assessment procedures. The final optimized structure-based multiple alignment and the derived model structures provided insightful information on the evolutionary conservation of key residues in the protein sequence and surface patches presumably involved in protein recognition during the urease active site assembly.

Urea decomposition facilitated by a urease model complex: a theoretical investigation

Density functional theory calculations were used to examine the role of the urease model complex [Ni2(bdptz)(micro-OH)(micro-H2O)(H2O)2](OTs)3(bdptz=1,4-bis(2,2'-dipyridylmethyl)-phthalazine; OTs=tosylate) in the degradation of urea. An elimination mechanism that converts urea to ammonium cyanate was investigated in detail. The lowest energy pathway involves urea coordination through the oxygen atom to a Ni center followed by protonation of a urea NH2 group by the bridging water ligand. Subsequent rotation of the protonated urea, followed by deprotonation of the NH2 by a bridging OH ligand generates the bound, disproportionated urea substrate, HNCONH3, from which ammonium cyanate was produced.

Nickel Complexes of Carboxylate-Containing Polydentate Ligands as Models for the Active Site of Urease

Two new carboxylate-containing polydentate ligands have been synthesized, the symmetric ligand 2,6-bis[N-(N-(carboxylmethyl)-N-((1-methylimidazol)methyl)amine)methyl]-4-methylphenolate (BCIMP) and the corresponding asymmetric ligand 2-(N-isopropyl-N-((1-aminomethyl)-4-methylphenol (ICIMP). The ligands have been used to prepare model complexes for the active site of the dinuclear nickel enzyme urease, viz. [Ni(2)(BCIMP)Ac(2)](-) (6), [Ni(2)(BCIMP)(Ph(2)Ac)(2)](-) (7), [Ni(2)(ICIMP)(Ph(2)Ac)(2)] (14), [Ni(4)(ICIMP)(2)(Ph(2)Ac)(2)][ClO(4)](2) (15), [Ni(4)(ICIMP)(2)(Ph(2)Ac)(2)(DMF)(2)][ClO(4)](2) (16), and [Ni(4)(ICIMP)(2)(Ph(2)Ac)(2)(urea)(H(2)O)][ClO(4)](2) (17), where the latter complex contains urea coordinated in a unidentate fashion through the carbonyl oxygen. The N(2)O-N(2)O(2) donor set of ICIMP provides a good framework for the preparation of urease models, but in some cases tetranuclear nickel complexes are formed due to coordination of the carboxylate moiety of one dinickel-ICIMP unit to one or both of the nickels of a second Ni(2) unit. Reactivity and kinetics studies of 7 and 15 show that these model complexes catalyze hydrolysis of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) at basic pH. In this assay, complexes based on the asymmetric ligand ICIMP exhibit a significantly faster rate of hydrolysis than the corresponding BCIMP complexes. Magnetic measurements indicate that there are weak antiferromagnetic interactions between the nickel ions in complex 16.

Multi-step analysis of Hg2+ ion inhibition of jack bean urease

We performed a multi-step analysis of the inhibition of jack bean urease by Hg(2+) ions that included residual activity measurements after incubation of the enzyme with the metal ion, reactivation of Hg(2+)-inhibited urease, protection of urease with thiol reagents prior to incubation with Hg(2+), progress curve analysis, and spectroscopic assay of thiol groups in urease-Hg(2+) complexes with a cysteine selective agent 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB). Hg(2+) ions were found to form stable complexes with urease that could rapidly be reversed only by the treatment with dithiotreitol, and not by dilution or dialysis. The residual activity data interpreted in terms of the Hill equation revealed the multisite Hg(2+) inhibition of urease, and along with the DTNB thiol-assay they demonstrated the involvement in the reaction with Hg(2+) of six cysteine residues per enzyme subunit, including the active-site flap cysteine. The molar ratios of the inhibitor and enzyme imply that the inhibition consists of the formation of RSHgX complexes, X being a water molecule or an anion. The time-dependent Hg(2+) inhibitory action on urease determined in the system without enzyme preincubation was best described by slow-binding mechanism with the steady-state inhibition constant K(i) = 1.9 nM (+/-10%).

Structural Characterization of the Nickel-binding Properties of Bacillus pasteurii Urease Accessory Protein (Ure)E in Solution

Urease activation is critical to the virulence of many human and animal pathogens. Urease possesses multiple, nickel-containing active sites, and UreE, the only nickel-binding protein among the urease accessory proteins, activates urease by transporting nickel ions. We performed NMR experiments to investigate the solution structure and the nickel-binding properties of Bacillus pasteurii (Bp) UreE. The secondary structures and global folds of BpUreE were determined for its metal-free and nickel-bound forms. The results indicated that no major structural change of BpUreE arises from the nickel binding. In addition to the previously identified nickel-binding site (Gly(97)-Cys(103)), the C-terminal tail region (Lys(141)-His(147)) was confirmed for the first time to be involved in the nickel binding. The C-terminally conserved sequence ((144)GHQH(147)) was confirmed to have an inherent nickel-binding ability. Nickel addition to 1.6 mm subunit, a concentration where BpUreE predominantly forms a tetramer upon the nickel binding, induced a biphasic spectral change consistent with binding of up to at least three nickel ions per tetrameric unit. In contrast, nickel addition to 0.1 mm subunit, a concentration at which the protein is primarily a dimer, caused a monophasic spectral change consistent with more than 1 equivalent per dimeric unit. Combined with the equilibrium dialysis results, which indicated 2.5 nickel equivalents binding per dimer at a micromolar protein concentration, the nickel-binding stoichiometry of BpUreE at a physiological concentration could be three nickel ions per dimer. Altogether, the present results provide the first detailed structural data concerning the nickel-binding properties of intact, wild-type BpUreE in solution.

X-ray structure of a dihydropyrimidinase from Thermus sp. at 1.3 A resolution

Dihydropyrimidinases (hydantoinases) catalyse the reversible hydrolytic ring-opening of cyclic diamides such as dihydropyrimidines in the catabolism of pyrimidines. In biotechnology, these enzymes find application in the enantiospecific production of amino acids from racemic hydantoins. The crystal structure of a D-enantio-specific dihydropyrimidinase from Thermus sp. (D-hydantoinase) was solved de novo by multiwavelength anomalous diffraction phasing. In spite of a large unit cell the D-hydantoinase crystals exhibit excellent diffraction properties. The structure was subsequently refined at 1.30 A resolution against native data. The core of D-hydantoinase consists of a (alpha/beta)(8)-barrel, which is flanked by a beta-sheet domain and some additional helices. In the active site, a carboxylated lysine residue and the catalytically active hydroxide ion bridge a binuclear zinc centre. The tertiary structure and shape of the active site show strong homology to that of ureases, dihydroorotases, and phosphotriesterases. The homology of the active site was exploited for in silicio docking of substrates in the active site. This could shed light both on the substrate binding in hydantoinases and on the recently highly discussed origin of the proton in the course of hydantoinase catalysis.