A radical approach to enzyme catalysis

Proteome profile changes during poly-hydroxybutyrate intracellular mobilization in gram positive Bacillus cereus tsu1

BACKGROUND

Bacillus cereus is a bacterial species which grows efficiently on a wide range of carbon sources and accumulates biopolymer poly-hydroxybutyrate (PHB) up to 80% cell dry weight. PHB is an aliphatic polymer produced and stored intracellularly as a reservoir of carbon and energy, its mobilization is a key biological process for sporulation in Bacillus spp. Previously, B. cereus tsu1 was isolated and cultured on rapeseed cake substrate (RCS), with maximum of PHB accumulation reached within 12 h, and depleted after 48 h. Fore-spore and spore structure were observed after 24 h culture.

RESULTS

Quantitative proteomic analysis of B. cereus tsu1 identified 2952 quantifiable proteins, and 244 significantly changed proteins (SCPs) in the 24 h:12 h pair of samples, and 325 SCPs in the 48 h:12 h pair of samples. Based on gene ontology classification analysis, biological processes enriched only in the 24 h:12 h SCPs include purine nucleotide metabolism, protein folding, metal ion homeostasis, response to stress, carboxylic acid catabolism, and cellular amino acid catabolism. The 48 h:12 h SCPs were enriched into processes including carbohydrate metabolism, protein metabolism, oxidative phosphorylation, and formation of translation ternary structure. A key enzyme for PHB metabolism, poly(R)-hydroxyalkanoic acid synthase (PhaC, KGT44865) accumulated significantly higher in 12 h-culture. Sporulation related proteins SigF and SpoEII were significantly higher in 24 h-samples. Enzymes for nitrate respiration and fermentation accumulated to the highest abundance level in 48 h-culture.

CONCLUSIONS

Changes in proteome of B. cereus tsu1 during PHB intracellular mobilization were characterized in this study. The key enzyme PhaC for PHB synthesis increased significantly after 12 h-culture which supports the highest PHB accumulation at this time point. The protein abundance level of SpoIIE and SigF also increased, correlating with sporulation in 24 h-culture. Enzymes for nitrate respiration and fermentation were significantly induced in 48 h-culture which indicates the depletion of oxygen at this stage and carbon flow towards fermentative growth. Results from this study provide insights into proteome profile changes during PHB accumulation and reuse, which can be applied to achieve a higher PHB yield and to improve bacterial growth performance and stress resistance.

A conformational sampling model for radical catalysis in pyridoxal phosphate- and cobalamin-dependent enzymes

Cobalamin-dependent enzymes enhance the rate of C–Co bond cleavage by up to ∼10¹²-fold to generate cob(II)alamin and a transient adenosyl radical. In the case of the pyridoxal 5′-phosphate (PLP) and cobalamin-dependent enzymes lysine 5,6-aminomutase and ornithine 4,5 aminomutase (OAM), it has been proposed that a large scale domain reorientation of the cobalamin-binding domain is linked to radical catalysis. Here, OAM variants were designed to perturb the interface between the cobalamin-binding domain and the PLP-binding TIM barrel domain. Steady-state and single turnover kinetic studies of these variants, combined with pulsed electron-electron double resonance measurements of spin-labeled OAM were used to provide direct evidence for a dynamic interface between the cobalamin and PLP-binding domains. Our data suggest that following ligand binding-induced cleavage of the Lys⁶²⁹-PLP covalent bond, dynamic motion of the cobalamin-binding domain leads to conformational sampling of the available space. This supports radical catalysis through transient formation of a catalytically competent active state. Crucially, it appears that the formation of the state containing both a substrate/product radical and Co(II) does not restrict cobalamin domain motion. A similar conformational sampling mechanism has been proposed to support rapid electron transfer in a number of dynamic redox systems.

EPR characterization of ascorbyl and sulfur dioxide anion radicals trapped during the reaction of bovine Cytochrome c Oxidase with molecular oxygen

The reaction intermediates of reduced bovine Cytochrome c Oxidase (CcO) were trapped following its reaction with oxygen at 50 micros-6 ms by innovative freeze-quenching methods and studied by EPR. When the enzyme was reduced with either ascorbate or dithionite, distinct radicals were generated; X-band (9 GHz) and D-band (130 GHz) CW-EPR measurements support the assignments of these radicals to ascorbyl and sulfur dioxide anion radical (SO2(-.)), respectively. The X-band spectra show a linewidth of 12 G for the ascorbyl radical and 11 G for the SO2(-.) radical and an isotropic g-value of 2.005 for both species. The D-band spectra reveal clear distinctions in the g-tensors and powder patterns of the two species. The ascorbyl radical spectrum displays approximate axial symmetry with g-values of g(x)=2.0068, g(y)=2.0066, and g(z)=2.0023. The SO2(-.) radical has rhombic symmetry with g-values of g(x)=2.0089, g(y)=2.0052, and g(z)=2.0017. When the contributions from the ascorbyl and SO2(-.) radicals were removed, no protein-based radical on CcO could be identified in the EPR spectra.

Insights into the mechanisms of adenosylcobalamin (coenzyme B12)-dependent enzymes from rapid chemical quench experiments

Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that use free radicals to catalyse unusual and chemically difficult rearrangements involving 1,2-migrations of hydrogen atoms. A key mechanistic feature of these enzymes is the transfer of the migrating hydrogen atom between substrate, coenzyme and product. The present review summarizes recent experiments from my laboratory that have used rapid chemical quench techniques to identify intermediates in the reaction and probe the mechanism of hydrogen transfer through a variety of pre-steady-state kinetic isotope effect measurements.

Trends in ground-state entropies for transition metal based hydrogen atom transfer reactions

Reported herein are thermochemical studies of hydrogen atom transfer (HAT) reactions involving transition metal H-atom donors M(II)LH and oxyl radicals. [Fe(II)(H(2)bip)(3)](2+), [Fe(II)(H(2)bim)(3)](2+), [Co(II)(H(2)bim)(3)](2+), and Ru(II)(acac)(2)(py-imH) [H(2)bip = 2,2'-bi-1,4,5,6-tetrahydropyrimidine, H(2)bim = 2,2'-bi-imidazoline, acac = 2,4-pentandionato, py-imH = 2-(2'-pyridyl)imidazole)] each react with TEMPO (2,2,6,6-tetramethyl-1-piperidinoxyl) or (t)Bu(3)PhO(*) (2,4,6-tri-tert-butylphenoxyl) to give the deprotonated, oxidized metal complex M(III)L and TEMPOH or (t)Bu(3)PhOH. Solution equilibrium measurements for the reaction of [Co(II)(H(2)bim)(3)](2+) with TEMPO show a large, negative ground-state entropy for hydrogen atom transfer, -41 +/- 2 cal mol(-1) K(-1). This is even more negative than the DeltaS(o)(HAT) = -30 +/- 2 cal mol(-1) K(-1) for the two iron complexes and the DeltaS(o)(HAT) for Ru(II)(acac)(2)(py-imH) + TEMPO, 4.9 +/- 1.1 cal mol(-1) K(-1), as reported earlier. Calorimetric measurements quantitatively confirm the enthalpy of reaction for [Fe(II)(H(2)bip)(3)](2+) + TEMPO, thus also confirming DeltaS(o)(HAT). Calorimetry on TEMPOH + (t)Bu(3)PhO(*) gives DeltaH(o)(HAT) = -11.2 +/- 0.5 kcal mol(-1) which matches the enthalpy predicted from the difference in literature solution BDEs. A brief evaluation of the literature thermochemistry of TEMPOH and (t)Bu(3)PhOH supports the common assumption that DeltaS(o)(HAT) approximately 0 for HAT reactions of organic and small gas-phase molecules. However, this assumption does not hold for transition metal based HAT reactions. The trend in magnitude of |DeltaS(o)(HAT)| for reactions with TEMPO, Ru(II)(acac)(2)(py-imH) << [Fe(II)(H(2)bip)(3)](2+) = [Fe(II)(H(2)bim)(3)](2+) < [Co(II)(H(2)bim)(3)](2+), is surprisingly well predicted by the trends for electron transfer half-reaction entropies, DeltaS(o)(ET), in aprotic solvents. This is because both DeltaS(o)(ET) and DeltaS(o)(HAT) have substantial contributions from vibrational entropy, which varies significantly with the metal center involved. The close connection between DeltaS(o)(HAT) and DeltaS(o)(ET) provides an important link between these two fields and provides a starting point from which to predict which HAT systems will have important ground-state entropy effects.

Large ground-state entropy changes for hydrogen atom transfer reactions of iron complexes

Reported herein are the hydrogen atom transfer (HAT) reactions of two closely related dicationic iron tris(alpha-diimine) complexes. FeII(H2bip) (iron(II) tris[2,2'-bi-1,4,5,6-tetrahydropyrimidine]diperchlorate) and FeII(H2bim) (iron(II) tris[2,2'-bi-2-imidazoline]diperchlorate) both transfer H* to TEMPO (2,2,6,6-tetramethyl-1-piperidinoxyl) to yield the hydroxylamine, TEMPO-H, and the respective deprotonated iron(III) species, FeIII(Hbip) or FeIII(Hbim). The ground-state thermodynamic parameters in MeCN were determined for both systems using both static and kinetic measurements. For FeII(H2bip) + TEMPO, DeltaG degrees = -0.3 +/- 0.2 kcal mol-1, DeltaH degrees = -9.4 +/- 0.6 kcal mol-1, and DeltaS degrees = -30 +/- 2 cal mol-1 K-1. For FeII(H2bim) + TEMPO, DeltaG degrees = 5.0 +/- 0.2 kcal mol-1, DeltaH degrees = -4.1 +/- 0.9 kcal mol-1, and DeltaS degrees = -30 +/- 3 cal mol-1 K-1. The large entropy changes for these reactions, |TDeltaS degrees | = 9 kcal mol-1 at 298 K, are exceptions to the traditional assumption that DeltaS degrees approximately 0 for simple HAT reactions. Various studies indicate that hydrogen bonding, solvent effects, ion pairing, and iron spin equilibria do not make major contributions to the observed DeltaS degrees HAT. Instead, this effect arises primarily from changes in vibrational entropy upon oxidation of the iron center. Measurement of the electron-transfer half-reaction entropy, |DeltaS degrees Fe(H2bim)/ET| = 29 +/- 3 cal mol-1 K-1, is consistent with a vibrational origin. This conclusion is supported by UHF/6-31G* calculations on the simplified reaction [FeII(H2N=CHCH=NH2)2(H2bim)]2+...ONH2 left arrow over right arrow [FeII(H2N=CHCH=NH2)2(Hbim)]2+...HONH2. The discovery that DeltaS degrees HAT can deviate significantly from zero has important implications on the study of HAT and proton-coupled electron-transfer (PCET) reactions. For instance, these results indicate that free energies, rather than enthalpies, should be used to estimate the driving force for HAT when transition-metal centers are involved.

Comparative model of EutB from coenzyme B12-dependent ethanolamine ammonia-lyase reveals a beta8alpha8, TIM-barrel fold and radical catalytic site structural features

The structure of the EutB protein from Salmonella typhimurium, which contains the active site of the coenzyme B12 (adenosylcobalamin)-dependent enzyme, ethanolamine ammonia-lyase, has been predicted by using structural proteomics techniques of comparative modelling. The 453-residue EutB protein displays no significant sequence identity with proteins of known structure. Therefore, secondary structure prediction and fold recognition algorithms were used to identify templates. Multiple three-dimensional template matching (threading) servers identified predominantly beta8alpha8, TIM-barrel proteins, and in particular, the large subunits of diol dehydratase (PDB: 1eex:A, 1dio:A) and glycerol dehydratase (PDB: 1mmf:A), as templates. Consistent with this identification, the dehydratases are, like ethanolamine ammonia-lyase, Class II coenzyme B12-dependent enzymes. Model building was performed by using MODELLER. Models were evaluated by using different programs, including PROCHECK and VERIFY3D. The results identify a beta8alpha8, TIM-barrel fold for EutB. The beta8alpha8, TIM-barrel fold is consistent with a central role of the alpha/beta-barrel structures in radical catalysis conducted by the coenzyme B12- and S-adenosylmethionine-dependent (radical SAM) enzyme superfamilies. The EutB model and multiple sequence alignment among ethanolamine ammonia-lyase, diol dehydratase, and glycerol dehydratase from different species reveal the following protein structural features: (1) a "cap" loop segment that closes the N-terminal region of the barrel, (2) a common cobalamin cofactor binding topography at the C-terminal region of the barrel, and (3) a beta-barrel-internal guanidinium group from EutB R160 that overlaps the position of the active-site potassium ion found in the dehydratases. R160 is proposed to have a role in substrate binding and radical catalysis.

Synthesis and Protein Degradation Capacity of Photoactivated Enediynes

[structure: see text] The viability of proteins as targets of thermally and photoactivated enediynes has been confirmed at the molecular level. Model studies using a labeled substrate confirmed the efficacy of atom transfer from diyl radicals produced from enediynes to form captodatively stabilized carbon centered aminoacyl radicals, which then undergo either fragmentation or dimerization. To exploit this finding, a family of enediynes was developed using an intramolecular coupling strategy. Derivatives were prepared and used to target specific proteins, showing good correlation between affinity and photoinduced protein degrading activity. The findings have potential applications in the design of artificial chemical proteases and add to our understanding of the mechanism of action of the clinically important enediyne antitumor antibiotics.

S-adenosylmethionine radical enzymes

The role of S-adenosylmethionine (SAM) as a precursor to organic radicals, generated by one-electron reduction of SAM and subsequent fission to form 5'-deoxyadenosyl radical and methionine, has been known for some time. Only recently, however, has it become apparent how widespread such enzymes are, and what a wide range of chemical reactions they catalyze. In the last few years several new SAM radical enzymes have been identified. Spectroscopic and kinetic investigations have begun to uncover the mechanism by which an iron sulfur cluster unique to these enzymes reduces SAM to generate adenosyl radical. Most recently, the first X-ray structures of SAM radical enzymes, coproporphyrinogen-III oxidase, and biotin synthase have been solved, providing a structural framework within which to interpret mechanistic studies.

The radical chemistry of galactose oxidase

Galactose oxidase is a free radical metalloenzyme containing a novel metalloradical complex, comprised of a protein radical coordinated to a copper ion in the active site. The unusually stable protein radical is formed from the redox-active side chain of a cross-linked tyrosine residue (Tyr-Cys). Biochemical studies on galactose oxidase have revealed a new class of oxidation mechanisms based on this free radical coupled-copper catalytic motif, defining an emerging family of enzymes, the radical-copper oxidases. Isotope kinetics and substrate reaction profiling have provided insight into the elementary steps of substrate oxidation in these enzymes, complementing structural studies on their active site. Galactose oxidase is remarkable in the extent to which free radicals are involved in all aspects of the enzyme function: serving as a key feature of the active site structure, defining the characteristic reactivity of the complex, and directing the biogenesis of the Tyr-Cys cofactor during protein maturation.

Galactose oxidase

The free radical-coupled copper catalytic motif has emerged as the unifying feature of a new family of enzymes, the radical copper oxidases. Their highly evolved active sites include a novel amino acid modification, the Tyr-Cys dimer, that forms spontaneously through self-processing of the protein during its maturation. The active site is remarkable in the extent to which metal ligands participate in the catalytic process. Rather than simply coordinating the metal ion, the ligands perform essential redox and proton-transfer functions in the chemistry of the active site, directed by their interactions with the copper center in the protein. The wide phylogenetic distribution and range of functions represented within the family hint of a fundamental role for these enzymes in the biology of oxygen. The roles for these enzymes are further expanding through a variety of biotechnological applications.

Protein degradation with photoactivated enediyne-amino acid conjugates

A series of photoactivated enediynes was prepared, and successfully employed for the selective degradation of target proteins.

Adenosylcobalamin-dependent isomerases: new insights into structure and mechanism

Adenosylcobalamin-dependent isomerases catalyze a variety of chemically difficult 1,2-rearrangements that proceed through a mechanism involving free radical intermediates. These radicals are initially generated by homolysis of the cobalt-carbon bond of the coenzyme. Recently, the crystal structures of several of these enzymes have been solved, revealing two modes of coenzyme binding and highlighting the role of the protein in controlling the rearrangement of reactive substrate radical intermediates. Complementary data from kinetic, spectroscopic and theoretical studies have produced insights into the mechanism by which substrate radicals are generated at the active site, and the pathways by which they rearrange.

Review Article Coenzyme-B(12)-Dependent Glutamate Mutase

Adenosylcobalamin (coenzyme B12)-dependent glutamate mutase catalyzes a most unusual carbon skeleton rearrangement involving the isomerization of l-glutamate to L-threo-methylaspartate, a reaction that is without precedent in organic chemistry. This reaction proceeds through a mechanism involving free radical intermediates that are initiated by homolysis of the cobalt-carbon bond of the coenzyme. The enzyme serves as a paradigm for adenosylcobalamin-dependent catalysis and, more generally, provides insights into how enzymes generate and control reactive free radical species. This review describes how recent studies on the mechanism and structure of glutamate mutase have contributed to our understanding of adenosylcobalamin-mediated catalysis. Copyright 2000 Academic Press.

Understanding enediyne-protein interactions: diyl atom transfer results in generation of aminoacyl radicals

[formula: see text] The origin of the protein modulating capacity of enediynes has been probed. A series of synthetic enediyne-derived diyls participated in atom transfer chemistry with a labeled amino acid. Subsequent experiments suggest that diyl radicals may modulate protein architecture via formation of captodatively stabilized radicals.

Adenosylcobalamin-dependent ribonucleoside triphosphate reductase from Lactobacillus leichmannii. Rapid, improved purification involving dGTP-based affinity chromatography plus biophysical characterization studies demonstrating enhanced, "crystallographic level" purity

Ribonucleoside triphosphate reductase (RTPR, EC 1.17.4.2) from Lactobacillus leichmannii is a 5'-deoxyadenosylcobalamin-dependent (AdoCbl; Coenzyme B12) enzyme. RTPR is also a prototypical adenosylcobalamin-dependent ribonucleotide reductase, one that, as its name indicates, converts ribonucleoside triphosphates (NTP) to deoxyribonucleoside triphosphates (dNTP). Upon substrate binding to RTPR, AdoCbl's cobalt-carbon bond is cleaved to generate cob(II)alamin, 5'-deoxyadenosine, and the cysteine (C408) derived thiyl radical. Five key cysteines (Cys 119, 408, 419, 731, and 736), from among the ten total cysteines, are involved in RTPR's catalytic mechanism. A critical examination of the RTPR isolation and purification literature suggested that the purification protocol currently used results in RTPR which contains 2040% microheterogeneity, along with minor contamination by other proteins. In addition, no report of crystalline RTPR has ever appeared. The literature indicates that irreversible cysteine oxidation (e.g., to -SO2H or -SO3H) is one highly plausible reason for the microheterogeneity of RTPR. The literature also indicates that improvement in the level of enzyme purity is the most effective next step in coaxing enzymes to crystallize that have previously failed to do so. A shortened, improved purification of RTPR has been developed, one involving a shorter purification time, a lower pH, a higher concentration of the more effective reductant DTT (all designed to help protect the cysteines from oxidation), and a final step utilizing our recently reported, improved dGTP-based affinity chromatography resin. The resultant RTPR is approximately 20-30% higher in both specific activity and in its ability to undergo single turnovers, and is homogeneous by mass spectrometry and dynamic light scattering. Additionally, the revised purification procedure eliminates > 30 proteins present in 2-3% amounts along with damaged RTPR that does not bind properly (i.e. tightly) to the dGTP-affinity resin. Finally, dGTP-based affinity chromatography purified RTPR has yielded the first reported, albeit small, single crystals of RTPR.

The reaction of the substrate analog 2-ketoglutarate with adenosylcobalamin-dependent glutamate mutase

Glutamate mutase is one of several adenosylcobalamin-dependent enzymes that catalyze unusual rearrangements that proceed through a mechanism involving free radical intermediates. The enzyme exhibits remarkable specificity, and so far no molecules other than L-glutamate and L-threo-3-methylaspartate have been found to be substrates. Here we describe the reaction of glutamate mutase with the substrate analog, 2-ketoglutarate. Binding of 2-ketoglutarate (or its hydrate) to the holoenzyme elicits a change in the UV-visible spectrum consistent with the formation of cob(II)alamin on the enzyme. 2-ketoglutarate undergoes rapid exchange of tritium between the 5'-position of the coenzyme and C-4 of 2-ketoglutarate, consistent with the formation of a 2-ketoglutaryl radical analogous to that formed with glutamate. Under aerobic conditions this leads to the slow inactivation of the enzyme, presumably through reaction of free radical species with oxygen. Despite the formation of a substrate-like radical, no rearrangement of 2-ketoglutarate to 3-methyloxalacetate could be detected. The results indicate that formation of the C-4 radical of 2-ketoglutarate is a facile process but that it does not undergo further reactions, suggesting that this may be a useful substrate analog with which to investigate the mechanism of coenzyme homolysis.

Construction and analysis of a semi-quantitative energy profile for the reaction catalyzed by the radical enzyme galactose oxidase

Galactose oxidase (GOase) is a mononuclear type 2 copper enzyme which oxidizes primary alcohols to aldehydes using molecular oxygen (RCH2OH + O2 = RCHO + H2O2). An unusual crosslink between tyrosine 272 and cysteine 228 provides a modified tyrosine radical site which acts as a ligand for the active site copper and is believed to act as a one-electron redox center. The single active site copper is believed to act as a second one-electron redox center. The use of the tyrosine one-electron redox center and the copper one-electron redox center allows removal of two electrons from alcohol substrate for subsequent transfer to molecular oxygen. Previously, we and others have proposed a detailed step-by-step radical mechanism for the reaction catalyzed by galactose oxidase. The catalytic cycle can be divided into two half reactions. The first half reaction entails transfer of two electrons and two protons from the alcohol substrate to the enzyme to form aldehyde product and two-electron-reduced enzyme (one electron at the tyrosine center and one at the copper center). The second half reaction entails transfer of two electrons and two protons from the two-electron-reduced enzyme to O2 to form H2O2 product and regenerate fully oxidized catalytically active enzyme ready for another catalytic cycle. In this paper, we describe the construction of a semi-quantitative energy profile for this radical mechanism. Several significant points emerge from this analysis. One point is the prediction that galactose oxidase should have an unusually low redox potential for copper, to our knowledge lower than any other redox active copper protein. Another point is that the distorted or entatic copper site causes the unusually low redox potential. A final point is that crosslinking of tyrosine 272 and cysteine 228 alters the redox properties of the tyrosine center to enhance catalysis compared to what would be expected for a normal tyrosine.

Heme protein radicals: formation, fate, and biological consequences

The oxidation of myoglobin by H2O2 yields ferrylmyoglobin, which contains two oxidizing equivalents: the oxoferryl complex and an amino acid radical. This study examines the electron paramagnetic resonance (EPR) properties of the resulting amino acid radicals and their inherent kinetic features at [H2O2]/[protein] ratios close to physiological conditions (i.e., < or = 1). The EPR spectrum obtained with continuous flow at room temperature consisted of a composite of three signals: a low intensity signal and two high intensity signals. The former had a g-value of 2.014, contributed 10-15% to the overall spectrum and was ascribed to a peroxyl radical. Of the two high intensity signals, one consisted of a six-line spectrum (g = 2.0048) that contributed approximately 17-19% to the overall signal; hyperfine splitting constants to ring protons permitted to identify this signal as a tyrosyl radical. The other high intensity signal (with similar g-value and underlying that of the tyrosyl radical) was ascribed to an aromatic amino acid upon comparison with the EPR characteristics for radicals in aromatic amino acid-containing peptides. Analysis of these data in connection with amino acid analysis and the EPR spectra obtained under similar conditions with another hemoprotein, hemoglobin, allowed to suggest a mechanism for the formation of the protein radicals in myoglobin. The aromatic amino acid radical was observed to be relatively long lived in close proximity to the heme iron. Hence, it is likely that this is the first site of protein radical; reduction of the oxoferryl complex by Tyr (FeIV=O + Tyr-OH + H+ --> FeIII + H2O + Tyr-O.)--and alternatively by other amino acids--leads to the subsequent formation of other amino acid radicals within an electron-transfer process throughout the protein. This view suggests that the protein radical(s) is highly delocalized within the globin moiety in a dynamic process encompassing electron tunneling through the backbone chain or H-bonds and leading to the formation of secondary radicals.

Adenosylcobalamin-dependent glutamate mutase: properties of a fusion protein in which the cobalamin-binding subunit is linked to the catalytic subunit

Adenosylcobalamin-dependent glutamate mutase (EC 5.4.99.1) from Clostridium tetanomorphum comprises two protein components, MutE and MutS. The formation of the holoenzyme is a kinetically complex process that involves the co-operative association of MutS, MutE and adenosylcobalamin. The MutS portion of the cobalamin-binding site is conserved within a group of adenosylcobalamin-dependent enzymes that catalyse similar isomerizations. However, in contrast with glutamate mutase, in these other enzymes the cobalamin-binding region represented by MutS is present as a C-terminal domain. We have investigated the effect on the structural and kinetic properties of glutamate mutase of linking MutS to the C-terminus of MutE. Kinetic analysis of this protein, MutES, showed, unexpectedly, that enzyme activity was still co-operatively dependent on protein concentration. The Km for L-glutamate was unchanged from the wild type, whereas Vmax was decreased to approx. one-thirtieth and the Km for coenzyme increased approx. 10-fold. Investigation of the quaternary structure of MutES by equilibrium ultra-centrifugation indicated that the protein existed in equilibrium between monomeric and dimeric forms. Thus linking MutE and MutS together seems to substantially weaken the contacts that are responsible for the dimerization of MutE. The two domains of the MutES monomer seem unable to communicate, so that active enzyme is formed by the intermolecular association of two MutES subunits in a co-operative manner.

Carboxymethylation of MutS-cysteine-15 specifically inactivates adenosylcobalamin-dependent glutamate mutase. Examination of the role of this residue in coenzyme-binding and catalysis

The sensitivity of adenosylcobalamin (AdoCbl)-dependent glutamate mutase toward thiol-directed reagents has been investigated. Iodoacetate specifically alkylates one cysteine residue, Cys-15, in MutS with concomitant irreversible loss of enzyme activity. Cys-15 lies between the conserved residues Asp-14 and His-16, that are believed to coordinate cobalt to form a Co-His-Asp hydrogen-bonded "triad" when AdoCbl is bound by the enzyme. Although inactive, carboxymethylated MutS still bound AdoCbl with only a 5-fold increase in apparent Kd. To determine whether Cys-15 plays an essential role in catalysis, it was mutated to serine and to alanine. These mutants were active, but both exhibited decreased Vmax and increased apparent Km and Kd for AdoCbl. To mimic the effect of carboxymethylation, Cys15 was mutated to aspartate and, as an isosteric control, to asparagine. Neither of these mutants was active: MutS-C15N bound AdoCbl approximately 10-fold weaker than wild type, whereas MutS-C15N bound AdoCbl over 100 times less strongly than wild type. The results demonstrate both coenzyme-binding and catalysis to be very sensitive to mutations at position 15 that could potentially perturb the Co-His-Asp hydrogen-bonding network.

Homology modeling of human methylmalonyl-CoA mutase: a structural basis for point mutations causing methylmalonic aciduria

Point mutations in the human gene encoding coenzyme B12 (adenosylcobalamin)-dependent methylmalonyl-CoA mutase give rise to an inherited disorder of propionic acid metabolism termed mut methylmalonic aciduria. Almost all such mutations alter amino acids in the homodimeric human enzyme that are identical to residues in the catalytic alpha-subunit of the heterodimeric methylmalonyl-CoA mutase from the bacterium Propionibacterium shermanii, to which the mature human enzyme shows an overall 65% sequence identity. To explore how specific mutations might cause the observed clinical phenotype, 12 known mutations were mapped onto a three-dimensional homology model of the subunit of the human enzyme, generated using the program MODELLER on the basis of the recently published 2.0 A X-ray crystal structure of the P. shermanii methylmalonyl-CoA mutase. Eight mutations are found in the C-terminal B12-binding domain, of which 4 (G623R, G626C, G630E, G703R) are in direct contact with the corrin and are clustered around the histidine ligand (H627) provided by the protein to coordinate the cobalt atom of the B12 cofactor. Introduction of a side chain, particularly one that is charged, at any of these positions is expected to disrupt the flavodoxin-like fold and severely impair its binding of B12. Mutation at either of two other highly conserved glycine residues in this domain (G648D, G717V) also disrupts critical elements in the fold as would the introduction of an additional positive charge in the mutation H678R. Mutation of an arginine in a solvent-exposed loop to a hydrophobic residue (R694W) is also pathogenic. The remaining mutations have been mapped to the N-terminal region of the mutase, two of which introduce a buried, uncompensated charge, either near the subunit interface (A377E), or near the narrow channel through which acyl-CoA esters gain access to the active site (W105R). The extreme N-terminus of methylmalonyl-CoA mutase is predicted to make extensive contacts with the other subunit, and a mutant in this region (R93H) may prevent the correct assembly of the dimer.