Ca2+ and its substitutes have two different binding sites and roles in soluble, quinoprotein (pyrroloquinoline-quinone-containing) glucose dehydrogenase

PQQ-GDH - Structure, function and application in bioelectrochemistry

This review summarizes the basic features of the PQQ-GDH enzyme as one of the sugar converting biocatalysts. Focus is on the membrane -bound and the soluble form. Furthermore, the main principles of enzymatic catalysis as well as studies on the physiological importance are reviewed. A short overview is given on developments in protein engineering. The major part, however, deals with the different fields of application in bioelectrochemistry. This includes approaches for enzyme-electrode communication such as direct electron transfer, mediator-based systems, redox polymers or conducting polymers and holoenzyme reconstitution, and covers applied areas such as biosensing, biofuel cells, recycling schemes, enzyme competition, light-directed sensing, switchable detection schemes, logical operations by enzyme electrodes and immune sensing.

Mechanism of Reconstitution/Activation of the Soluble PQQ-Dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus: A Comprehensive Study

The ability to switch on the activity of an enzyme through its spontaneous reconstitution has proven to be a valuable tool in fundamental studies of enzyme structure/reactivity relationships or in the design of artificial signal transduction systems in bioelectronics, synthetic biology, or bioanalytical applications. In particular, those based on the spontaneous reconstitution/activation of the apo-PQQ-dependent soluble glucose dehydrogenase (sGDH) from Acinetobacter calcoaceticus were widely developed. However, the reconstitution mechanism of sGDH with its two cofactors, i.e., pyrroloquinoline quinone (PQQ) and Ca²⁺, remains unknown. The objective here is to elucidate this mechanism by stopped-flow kinetics under single-turnover conditions. The reconstitution of sGDH exhibited biphasic kinetics, characteristic of a square reaction scheme associated with two activation pathways. From a complete kinetic analysis, we were able to fully predict the reconstitution dynamics and also to demonstrate that when PQQ first binds to apo-sGDH, it strongly impedes the access of Ca²⁺ to its enclosed position at the bottom of the enzyme binding site, thereby greatly slowing down the reconstitution rate of sGDH. This slow calcium insertion may purposely be accelerated by providing more flexibility to the Ca²⁺ binding loop through the specific mutation of the calcium-coordinating P248 proline residue, reducing thus the kinetic barrier to calcium ion insertion. The dynamic nature of the reconstitution process is also supported by the observation of a clear loop shift and a reorganization of the hydrogen-bonding network and van der Waals interactions observed in both active sites of the apo and holo forms, a structural change modulation that was revealed from the refined X-ray structure of apo-sGDH (PDB: 5MIN).

The cooperativity effect in the reaction of soluble quinoprotein (PQQ-containing) glucose dehydrogenase is not due to subunit interaction but to substrate-assisted catalysis

Soluble quinoprotein (PQQ-containing) glucose dehydrogenase (sGDH, EC 1.1.99.35) catalyzes the oxidation of β-d-glucose to d-glucono-δ-lactone. Although sGDH has many analytical applications, the relationship between activity and substrate concentration is not well established. Previous steady-state kinetic studies revealed a negative cooperativity effect which has recently been ascribed to subunit interaction. To investigate this conclusion, stopped-flow kinetic experiments were carried out on the reaction in which oxidized enzyme (E_ox ) was reduced with substrates to E_red . The appearance of E_red is observed to be preceded by formation of an intermediate enzyme form, Int, which is mono-exponentially formed from E_ox . However, the rate of conversion of Int into E_red depends hyperbolically on the concentration of substrate (leading to a 35-fold stimulation in the case of glucose). Evidence is provided that substrate not only binds to E_ox but also to Int and E_red as well, and that the binding to Int causes the significant stimulation of Int decay. It is proposed that a proton shuffling step is involved in the decay, which is facilitated by binding of substrate to Int. Substituting the PQQ-activating Ca by a Ba ion lowered all reaction rates but did not change the stimulation factor. In summary, the previous proposal that the cooperativity effect of sGDH is due to interaction between its substrate-loaded subunits is incorrect; it is due to substrate-assisted catalysis of the enzyme.

ENZYMES

EC 1.1.99.35 - soluble quinoprotein glucose dehydrogenase.

Biochemical and structural characterization of quinoprotein aldose sugar dehydrogenase from Thermus thermophilus HJ6: Mutational analysis of Tyr156 in the substrate-binding site

The gene encoding a quinoprotein aldose sugar dehydrogenase (ASD) from Thermus thermophilus HJ6 (Tt_ASD) was cloned and sequenced; it comprised 1059 nucleotides encoding a protein containing 352 amino acids that had a predicted molecular mass of 38.9 kDa. The deduced amino acid sequence showed 42.9% and 33.9% identities to the ASD proteins from Pyrobaculum aerophilum and Escherichia coli, respectively. The biochemical properties of Tt_ASD were characterized. The optimum pH for the oxidation of glucose was 7.0-7.5 and the optimum temperature was 70 °C. The half-life of heat inactivation for the apoenzyme was about 25 min at 85 °C. The enzyme was highly thermostable, and the activity of the pyrroloquinoline quinone-bound holoenzyme was not lost after incubation at 85 °C for 100 min. Tt_ASD could oxidize various sugars, including hexoses, pentoses, disaccharides, and polysaccharides, in addition to alcohols. Structural analysis suggested that Tyr156 would be the substrate-binding residue. Two mutants, Y156A and Y156K, had impaired activities and affinities for all substrates and completely lost their activities for alcohols. This structural and mutational analysis of Tt_ASD demonstrates the crucial role of Tyr156 in determining substrate specificity.

Engineering PQQ-glucose dehydrogenase into an allosteric electrochemical Ca2+ sensor

Electrochemical biosensors convert biological events to an electrical current.

Effect of substrate inhibition and cooperativity on the electrochemical responses of glucose dehydrogenase. Kinetic characterization of wild and mutant types

Thanks to its insensitivity to dioxygen and to its good catalytic reactivity, and in spite of its poor substrate selectivity, quinoprotein glucose dehydrogenase (PQQ-GDH) plays a prominent role among the redox enzymes that can be used for analytical purposes, such as glucose detection, enzyme-based bioaffinity assays, and the design of biofuel cells. A detailed kinetic analysis of the electrochemical catalytic responses, leading to an unambiguous characterization of each individual steps, seems a priori intractable in view of the interference, on top of the usual ping-pong mechanism, of substrate inhibition and of cooperativity effects between the two identical subunits of the enzyme. Based on simplifications suggested by extended knowledge previously acquired by standard homogeneous kinetics, it is shown that analysis of the catalytic responses obtained by means of electrochemical nondestructive techniques, such as cyclic voltammetry, with ferrocene methanol as a mediator, does allow a full characterization of all individual steps of the catalytic reaction, including substrate inhibition and cooperativity and, thus, allows to decipher the reason that makes the enzyme more efficient when the neighboring subunit is filled with a glucose molecule. As a first practical illustration of this electrochemical approach, comparison of the native enzyme responses with those of a mutant (in which the asparagine amino acid in position 428 has been replaced by a cysteine residue) allowed identification of the elementary steps that makes the mutant type more efficient than the wild type when cooperativity between the two subunits takes place, which is observed at large mediator and substrate concentrations. A route is thus opened to structure-reactivity relationships and therefore to mutagenesis strategies aiming at better performances in terms of catalytic responses and/or substrate selectivity.

Designing a highly active soluble PQQ-glucose dehydrogenase for efficient glucose biosensors and biofuel cells

We report for the first time a soluble PQQ-glucose dehydrogenase that is twice more active than the wild type for glucose oxidation and was obtained by combining site directed mutagenesis, modelling and steady-state kinetics. The observed enhancement is attributed to a better interaction between the cofactor and the enzyme leading to a better electron transfer. Electrochemical experiments also demonstrate the superiority of the new mutant for glucose oxidation and make it a promising enzyme for the development of high-performance glucose biosensors and biofuel cells.

Structure and activity assay of nanozymes prepared by the coimmobilization of practically useful enzymes and hydrophilic block copolymers on gold nanoparticles

Enzyme/polymer/gold nanoparticle hybrids, called "nanozymes", were prepared and structurally analyzed by dynamic light scattering (DLS), ultraviolet-visible spectroscopy, and zeta-potential and transmission electron microscopy (TEM) measurements, which showed that the nanozyme particles were mainly composed of a single gold nanoparticle, on whose surface the enzyme and polymer were coimmobilized. This kind of structure resulted in the high dispersion stability of the nanozyme under various conditions, accompanied by improved thermal stability of the enzyme.

Soluble Aldose Sugar Dehydrogenase from Escherichia coli

A water-soluble aldose sugar dehydrogenase (Asd) has been purified for the first time from Escherichia coli. The enzyme is able to act upon a broad range of aldose sugars, encompassing hexoses, pentoses, disaccharides, and trisaccharides, and is able to oxidize glucose to gluconolactone with subsequent hydrolysis to gluconic acid. The enzyme shows the ability to bind pyrroloquinoline quinone (PQQ) in the presence of Ca2+ in a manner that is proportional to its catalytic activity. The x-ray structure has been determined in the apo-form and as the PQQ-bound active holoenzyme. The beta-propeller fold of this protein is conserved between E. coli Asd and Acinetobacter calcoaceticus soluble glucose dehydrogenase (sGdh), with major structural differences lying in loop and surface-exposed regions. Many of the residues involved in binding the cofactor are conserved between the two enzymes, but significant differences exist in residues likely to contact substrates. PQQ is bound in a large cleft in the protein surface and is uniquely solvent-accessible compared with other PQQ enzymes. The exposed and charged nature of the active site and the activity profile of this enzyme indicate possible factors that underlie a low affinity for glucose but generic broad substrate specificity for aldose sugars. These structural and catalytic properties of the enzymes have led us to propose that E. coli Asd provides a prototype structure for a new subgroup of PQQ-dependent soluble dehydrogenases that is distinct from the A. calcoaceticus sGdh subgroup.

Crystallization of quinoprotein glucose dehydrogenase variants and homologues by microseeding

The soluble quinoprotein glucose dehydrogenase oxidizes glucose, maltose and a variety of other monosaccharides and disaccharides to the corresponding lactones. An efficient microseeding protocol is reported to produce crystals of three variants that display reduced activity towards maltose. Similar cross-seeding protocols to grow crystals of homologues from Escherichia coli and Streptomyces coelicolor are described.

The PQQ story

About twenty years ago, the cofactor pyrroloquinoline quinone, PQQ, was discovered. Here the author gives his personal view on the reasons why this cofactor was so lately discovered and how the steps in its identification were made. The discovery not only led to subsequent studies on the physiological significance of PQQ but also initiated investigations on other enzymes where the presence of PQQ was expected, resulting in the discovery of three other quinone cofactors, TPQ, TTQ, and LTQ, which differ from PQQ as they are part of the protein chain of the enzyme to which they belong. Enzymes using quinone cofactors, the so-called quinoproteins, copper-quinoproteins, and quinohemoproteins, are mainly involved in the direct oxidation of alcohols, sugars, and amines. Some of the PQQ-containing ones participate in incomplete bacterial oxidation processes like the conversion of ethanol into vinegar and of D-glucose into (5-keto)gluconic acid. Soluble glucose dehydrogenase is the sensor in diagnostic test strips used for glucose determination in blood samples of diabetic patients. Quinohemoprotein alcohol dehydrogenases have an enantiospecificity suited for the kinetic resolution of racemic alcohols to their enantiomerically pure form, certain enantiomers being interesting candidates as building block for synthesis of high-value-added chemicals. Making up for balance after twenty years of quinoprotein research, the following conclusions can be drawn: since quinoproteins do not catalyze unique reactions, we know now that there are more enzymes which catalyze one and the same reaction than we did before, but do not understand the reason for this (compare e.g. NAD/NADP-dependent glucose dehydrogenases, flavoprotein glucose oxidase/dehydrogenase, and soluble/membrane-bound, PQQ-containing glucose dehydrogenases, enzymes all catalyzing the oxidation of beta-D-glucose to delta-gluconolactone but being quite different from each other); however, taking a pragmatic point of view, the foregoing can also be regarded as a positive development since as illustrated by the examples given above, the enlargement of the catalytic arsenal with quinoprotein enzymes provides in more possibilities for enzyme applications; the hopes that PQQ could be a new vitamin have diminished strongly after it has become clear that its occurrence is restricted to bacteria; the impact factor is broader than just the development of the field of quinoproteins, since together with that of enzymes containing a one-electron oxidized amino acid residue as cofactor, it has emphasized that cofactors not only derive from nucleotides (e.g. FAD, NAD) but also from amino acids. Finally, strong indications exist to assume that this is not the end of the story since other quinone cofactors seem awaiting their discovery.

Determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase

Molecular dynamics (MD) simulations have been carried out to study the enzymatic mechanisms of quinoproteins, methanol dehydrogenase (MDH), and soluble glucose dehydrogenase (sGDH). The mechanisms of reduction of the orthoquinone cofactor (PQQ) of MDH and sGDH involve concerted base-catalyzed proton abstraction from the hydroxyl moiety of methanol or from the 1-hydroxyl of glucose, and hydride equivalent transfer from the substrate to the quinone carbonyl carbon C5 of PQQ. The products of methanol and glucose oxidation are formaldehyde and glucolactone, respectively. The immediate product of PQQ reduction, PQQH- [-HC5(O-)-C4(=O)-] and PQQH [-HC5(OH)-C4(=O)-] converts to the hydroquinone PQQH2 [-C5(OH)=C4(OH)-]. The main focus is on MD structures of MDH * PQQ * methanol, MDH * PQQH-, MDH * PQQH, sGDH * PQQ * glucose, sGDH * PQQH- (glucolactone, and sGDH * PQQH. The reaction PQQ-->PQQH- occurs with Glu 171-CO2- and His 144-Im as the base species in MDH and sGDH, respectively. The general-base-catalyzed hydroxyl proton abstraction from substrate concerted with hydride transfer to the C5 of PQQ is assisted by hydrogen-bonding to the C5=O by Wat1 and Arg 324 in MDH and by Wat89 and Arg 228 in sGDH. Asp 297-COOH would act as a proton donor for the reaction PQQH(-)-->PQQH, if formed by transfer of the proton from Glu 171-COOH to Asp 297-CO2- in MDH. For PQQH-->PQQH2, migration of H5 to the C4 oxygen may be assisted by a weak base like water (either by crystal water Wat97 or bulk solvent, hydrogen-bonded to Glu 171-CO2- in MDH and by Wat89 in sGDH).

Mechanism of Glucose Oxidation by Quinoprotein Soluble Glucose Dehydrogenase: Insights from Molecular Dynamics Studies

We have generated 3 ns molecular dynamic (MD) simulations, in aqueous solution, of the bacterial soluble glucose dehydrogenase enzyme.PQQ.glucose complex and intermediates formed in PQQ reduction. In the MD structure of enzyme.PQQ.glucose complex the imidazole of His144 is hydrogen bonded to the hydroxyl hydrogen of H[bond]OC1(H) of glucose. The tightly hydrogen-bonded triad Asp163-His144-glucose (2.70 and 2.91 A) is involved in proton abstraction from glucose concerted with the hydride transfer from the C1[bond]H of glucose to the >C5[double bond]O quinone carbon of PQQ. The reaction is assisted by Arg228 hydrogen bonding to the carbonyl oxygen of >C5[double bond]O. The rearrangement of [bond](H)C5(O-)[bond]C4([double bond]O)[bond] of II to [bond]C5(OH)[double bond]C4(OH)[bond] of PQQH(2) hydroquinone is assisted by general acid protonatation of the >C4[double bond]O oxygen by protonated His144 and hydrogen bonds of Arg228 to the oxyanion O5. The continuous hydrogen bonding of the amide side chain of Asn229 to >C4[double bond]O4 oxygen and that of the O5 oxygen of the cofactor to Wat89 is observed throughout the entire reaction.

Cofactor diversity in biological oxidations: implications and applications

Until recently, it was generally believed that enzymatic oxidation and reduction requires the participation of either a nicotinamide (NAD(P)+) or a flavin (FAD, FMN), in agreement with the existence of NAD(P)/H-dependent dehydrogenases/reductases and flavoprotein dehydrogenases/reductases/oxidases. However, during the past 20 years, the unraveling of the enzymology of the oxidation and reduction of C1-compounds by bacteria has led to the discovery of many new redox cofactors, some of them discussed here as they have a wider physiological significance than just enabling enzymatic C1-conversions to occur. A good example is the quinone cofactors, encompassing PQQ (2,7,9-tricarboxy-1H-pyrrolo[2,3-f]-quinoline-4,5-dione), TTQ (tryptophyl tryptophanquinone), TPQ (topaquinone), LTQ (lysyl topaquinone), and several others whose structures have still to be elucidated. Another example is mycothiol (1-O-(2'-[N-acetyl-L-cysteinyl]amido-2'-deoxy-alpha-D-glucopyranosyl)-D-myo-inosoitol), the counterpart of glutathione, once thought to be a universal coenzyme. Because these novel cofactors assist in reactions that can also be catalyzed by already known enzyme "classic cofactor" combinations, and first indications suggest that the chemistry of the reactions is not unique, one may wonder about the evolutionary background for this cofactor diversity. However, as will be illustrated by examples, from a practical point of view the diversity is beneficial, as it has increased the arsenal of enzymes suitable for application.

Pyrroloquinoline quinone (PQQ) and quinoprotein enzymes

This review summarises the characteristics, identification, and measurement of pyrroloquinoline quinone, the prosthetic group of bacterial quinoprotein dehydrogenases whose structures, mechanisms, and electron transport functions are described in detail. Type I alcohol dehydrogenase includes the "classic" methanol dehydrogenase; its x-ray structure and mechanism are discussed in detail. It is likely that its mechanism involves a direct hydride transfer rather than a mechanism involving a covalent adduct. The x-ray structure of a closely related ethanol dehydrogenase is also described. The type II alcohol dehydrogenase is a soluble quinohaemoprotein, having a C-terminal extension containing haem C, which provides an excellent opportunity for the study of intraprotein electron transfer processes. The type III alcohol dehydrogenase is similar but it has two additional subunits (one of which is a multihaem cytochrome c) bound in an unusual way to the periplasmic membrane. One type of glucose dehydrogenase is a soluble quinoprotein whose role in energy transduction is uncertain. Its x-ray structure (in the presence and absence of substrate) is described together with the detailed mechanism, which also involves a direct hydride transfer. The more widely distributed glucose dehydrogenases are integral membrane proteins, bound to the membrane by transmembrane helices at the N-terminus.

Ca(2+) stabilizes the semiquinone radical of pyrroloquinoline quinone

Spectroelectrochemical studies were performed on the interaction between Ca(2+) and pyrroloquinoline quinone (PQQ) in soluble glucose dehydrogenase (sGDH) and in the free state by applying a mediated continuous-flow column electrolytic spectroelectrochemical technique. The enzyme forms used were holo-sGDH (the holo-form of sGDH from Acinetobacter calcoaceticus) and an incompletely reconstituted form of this, holo-X, in which the PQQ-activating Ca(2+) is lacking. The spectroelectrochemical and ESR data clearly demonstrated the generation of the semiquinone radical of PQQ in holo-sGDH and in the free state in the presence of Ca(2+). In contrast, in the absence of Ca(2+) no semiquinone was observed, either for PQQ in the free state (at pH 7.0) or in the enzyme (holo-X). Incorporation of Ca(2+) into the active site of holo-X, yielding holo-sGDH, caused not only stabilization of the semiquinone form of PQQ but also a negative shift (of 26.5 mV) of the two-electron redox potential, indicating that the effect of Ca(2+) is stronger on the oxidized than on the reduced PQQ. Combining these data with the observations on the kinetic and chemical mechanisms, it was concluded that the strong stimulating effect of Ca(2+) on the activity of sGDH can be attributed to facilitation of certain kinetic steps, and not to improvement of the thermodynamics of substrate oxidation. The consequences of this conclusion are discussed for the oxidative as well as for the reductive part of the reaction of sGDH.

Structural requirements of pyrroloquinoline quinone dependent enzymatic reactions

On the basis of crystal structures of the pyrroloquinoline quinone (PQQ) dependent enzymes methanol dehydrogenase (MDH) and soluble glucose dehydrogenase (s-GDH), different catalytic mechanisms have been proposed. However, several lines of biochemical and kinetic evidence are strikingly similar for both enzymes. To resolve this discrepancy, we have compared the structures of these enzymes in complex with their natural substrates in an attempt to bring them in line with a single reaction mechanism. In both proteins, PQQ is located in the center of the molecule near the axis of pseudo-symmetry. In spite of the absence of significant sequence homology, the overall binding of PQQ in the respective active sites is similar. Hydrogen bonding interactions are made with polar protein side chains in the plane of the cofactor, whereas hydrophobic stacking interactions are important below and above PQQ. One Arg side chain and one calcium ion are ligated to the ortho-quinone group of PQQ in an identical fashion in either active site, in agreement with their proposed catalytic function of polarizing the PQQ C5-O5 bond. The substrates are bound in a similar position above PQQ and within hydrogen bond distance of the putative general bases Asp297 (MDH) and His144 (s-GDH). On the basis of these similarities, we propose that MDH and s-GDH react with their substrates through an identical mechanism, comprising general base-catalyzed hydride transfer from the substrate to PQQ and subsequent tautomerization of the PQQ intermediate to reduced PQQ.

Construction and characterization of mutant water-soluble PQQ glucose dehydrogenases with altered K(m) values--site-directed mutagenesis studies on the putative active site

Based on a PCR mutant enzyme of water-soluble glucose dehydrogenase-harboring pyrroloquinoline quinone as the prosthetic group, PQQGDH-B, a site-directed mutagenesis study was carried out. The substitution of Glu277 residue with Gly resulted in a decrease in the K(m) value for glucose and altered the substrate specificity profile, compared with the wild-type enzyme. Mutational analyses on the neighboring amino acid residues of Glu277 were also carried out and constructed Asp275Glu, Asp276Glu, Ile278Phe, and Asn279His. Considering that Asp275Glu, Asp276Glu and also Glu277Gly showed drastic decreases in EDTA tolerance, this region may construct a PQQGDH-B putative active site, such as a binding site for Ca(2+), which is responsible for the binding PQQ. A series of Glu277 variants, Glu277 substituted by Ala, Val, Asp, Asn, His, Gln, or to Lys, was constructed and they all showed decreased K(m) values and altered substrate specificity profiles. Among them, Glu277Lys showed similar thermal stability with the wild-type enzyme, but its catalytic efficiency increased significantly, compared with the wild-type enzyme. The potential applications of Glu277Lys in analytical use are also discussed.

Active-site structure of the soluble quinoprotein glucose dehydrogenase complexed with methylhydrazine: a covalent cofactor-inhibitor complex

Soluble glucose dehydrogenase (s-GDH) from the bacterium Acinetobacter calcoaceticus is a classical quinoprotein. It requires the cofactor pyrroloquinoline quinone (PQQ) to catalyze the oxidation of glucose to gluconolactone. The precise catalytic role of PQQ in s-GDH and several other PQQ-dependent enzymes has remained controversial because of the absence of comprehensive structural data. We have determined the crystal structure of a ternary complex of s-GDH with PQQ and methylhydrazine, a competitive inhibitor of the enzyme. This complex, refined at 1.5-A resolution to an R factor of 16.7%, affords a detailed view of a cofactor-binding site of s-GDH. Moreover, it presents the first direct observation of covalent PQQ adduct in the active-site of a PQQ-dependent enzyme, thereby confirming previous evidence that the C5 carbonyl group of the cofactor is the most reactive moiety of PQQ.

The 1.7 A crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal conserved sequence repeat

The crystal structure of a dimeric apo form of the soluble quinoprotein glucose dehydrogenase (s-GDH) from Acinetobacter calcoaceticus has been solved by multiple isomorphous replacement followed by density modification, and was subsequently refined at 1. 72 A resolution to a final crystallographic R-factor of 16.5% and free R-factor of 20.8% [corrected]. The s-GDH monomer has a beta-propeller fold consisting of six four-stranded anti-parallel beta-sheets aligned around a pseudo 6-fold symmetry axis. The enzyme binds three calcium ions per monomer, two of which are located in the dimer interface. The third is bound in the putative active site, where it may bind and functionalize the pyrroloquinoline quinone (PQQ) cofactor. A data base search unexpectedly showed that four uncharacterized protein sequences are homologous to s-GDH with many residues in the putative active site absolutely conserved. This indicates that these homologs may have a similar structure and that they may catalyze similar PQQ-dependent reactions.A structure-based sequence alignment of the six four-stranded beta-sheets in s-GDH's beta-propeller fold shows an internally conserved sequence repeat that gives rise to two distinct conserved structural motifs. The first structural motif is found at the corner of the short beta-turn between the inner two beta-strands of the beta-sheets, where an Asp side-chain points back into the beta-sheet to form a hydrogen-bond with the OH/NH of a Tyr/Trp side-chain in the same beta-sheet. The second motif involves an Arg/Lys side-chain in the C beta-strand of one beta-sheet, which forms a bidentate salt-bridge with an Asp/Glu in the CD loop of the next beta-sheet. These intra and inter-beta-sheet hydrogen-bonds are likely to contribute to the stability of the s-GDH beta-propeller fold.

Mobilization of chromatin-bound Mcm proteins by micrococcal nuclease

Mcm (minichromosome maintenance) proteins are important components of the eukaryotic replication initiation apparatus. We investigate the binding of human Mcm proteins to HeLa cell chromatin using micrococcal nuclease as a tool. In previous work we prepared chromatin under low ionic strength conditions. The use of a low salt buffer was necessary to prevent the dissociation of Mcm proteins. Here we use chromatin prepared at more physiological salt concentrations (100 mM NaCl) following the procedure of Fujita et al. (J. Biol. Chem. 272, 10928-10935; 1997) who had shown that ATP stabilizes the interaction of Mcm proteins with chromatin. We show here that micrococcal nuclease released Mcm proteins early during the digestion process suggesting that Mcm proteins reside on chromatin sites which are more open to nuclease attack than bulk chromatin. Released Mcm proteins sedimented through glycerol gradients as a multiprotein complex comprising several of the six known human Mcm proteins.