Active Site Of Class Research Articles

Bacterial β-carbonic anhydrases.

β-Carbonic anhydrases (β-CA; EC 4.2.1.1) are widespread zinc metalloenzymes which catalyze the interconversion of carbon dioxide and bicarbonate. They have been isolated in many pathogenic and non-pathogenic bacteria where they are involved in multiple roles, often related to their growth and survival. β-CAs are structurally distant from the CAs of other classes. In the active site, located at the interface of a fundamental dimer, the zinc ion is coordinated to two cysteines and one histidine. β-CAs have been divided in two subgroups depending on the nature of the fourth ligand on the zinc ion: class I have a zinc open configuration with a hydroxide ion completing the metal coordination, which is the catalytically active species in the mechanism proposed for the β-CAs similar to the well-known of α-CAs, while in class II an Asp residue substitute the hydroxide. This latter active site configuration has been showed to be typical of an inactive form at pH below 8. An Asp-Arg dyad is thought to play a key role in the pH-induced catalytic switch regulating the opening and closing of the active site in class II β-CAs, by displacing the zinc-bound solvent molecule. An allosteric site well-suited for bicarbonate stabilizes the inactive form. This bicarbonate binding site is composed by a triad of well conserved residues, strictly connected to the coordination state of the zinc ion. Moreover, the escort site is a promiscuous site for a variety of ligands, including bicarbonate, at the dimer interface, which may be the route for bicarbonate to the allosteric site.

Structure-based virtual screening, molecular docking, and molecular dynamics simulation approaches for identification of new potential inhibitors of class a β-lactamase enzymes

Bacteria are smart organisms that create drug resistance by decreasing the effect of antibiotics in different ways, such as secretion of the β-lactamase enzymes. Finding the compounds that can act as the inhibitors of these enzymes is a great help in reducing drug resistance and treat all types of infections. In this study, using molecular docking and molecular dynamics simulation techniques, we introduced two Relebactam substructures as new inhibitors of class A β-lactamase enzymes. Results of molecular docking show that the conformation of these two compounds in the active site of class A β-lactamase enzymes has a good match with Relebactam and their binding affinity to enzymes is equal to or better than Relebactam. Results showed a good tendency for binding and the formation of van der Waals and hydrogen interactions between the desired compounds and the β-lactamase enzymes. The results of the analysis of the molecular dynamics simulation trajectories showed that in the presence of the desired compounds, the second structures of the enzymes did not undergo many changes and in none of the systems, the binding of the compounds to the enzyme did not cause much instability, and in most cases made the structure stable. The hydrogen bonds were stable during the simulation time and in most cases, the new compounds formed more hydrogen bonds and had better binding affinity than Relebactam confirms the docking results. The results of this study can be helpful in designing new beta-lactamase inhibitors and new treatment methods to deal with drug resistance. Communicated by Ramaswamy H. Sarma

The molecular origin of various DNA-repair quantum yield in photolyases.

Photolyases is a blue-light-activated flavoenzyme that use FADH− as the catalytic cofactor to repair UV-induced DNA lesions including cyclobutene pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts (6-4 PP). Different classes of CPD photolyases show diverse genetic sequences but have similar folding structure. Class I CPD photolyases from bacteria have much higher repair quantum yields than class II CPD photolyases from plants. The difference mainly comes from a bifurcation in initial electron transfer: class I CPD photolyases mainly use a tunnelling pathway (electron from the isoalloxazine ring directly tunnels to the CPD substrate), while class II CPD photolyases mainly use a two-step hopping pathway (electron first jumps to the adenine and then jumps to the CPD substrate). In this study, we switched two key residues in the active sites of class I (N341, R342 in EcPL from Escherichia coli) and class II photolyases (G381, F382 in AtPL from Arabidopsis thaliana). Steady-state repair quantum yield measurements show dramatic lower repair quantum yields in EcPL mutants compared to EcPL while a different trend is observed in AtPL and its mutants. To reveal how these residues affect the repair reaction, ultrafast laser spectroscopy was used to determine the reaction rates of seven electron-transfer reactions in 10 elementary steps. We found that the repair quantum yields can be tuned by favoring either electron tunnelling or hopping channel, and thus adjusting the quantum yield of electron injection to the CPD substrate. Photolyases evolved to have high affinity and specificity towards DNA lesion with reasonably repair quantum yield. Solely increasing repair quantum yield by single mutation may disrupt the delicate balance between substrate binding and CPD repair.

Analysis of β-lactone formation by clinically observed carbapenemases informs on a novel antibiotic resistance mechanism

An important mechanism of resistance to β-lactam antibiotics is via their β-lactamase–catalyzed hydrolysis. Recent work has shown that, in addition to the established hydrolysis products, the reaction of the class D nucleophilic serine β-lactamases (SBLs) with carbapenems also produces β-lactones. We report studies on the factors determining β-lactone formation by class D SBLs. We show that variations in hydrophobic residues at the active site of class D SBLs (i.e. Trp105, Val120, and Leu158, using OXA-48 numbering) impact on the relative levels of β-lactones and hydrolysis products formed. Some variants, i.e. the OXA-48 V120L and OXA-23 V128L variants, catalyze increased β-lactone formation compared with the WT enzymes. The results of kinetic and product studies reveal that variations of residues other than those directly involved in catalysis, including those arising from clinically observed mutations, can alter the reaction outcome of class D SBL catalysis. NMR studies show that some class D SBL variants catalyze formation of β-lactones from all clinically relevant carbapenems regardless of the presence or absence of a 1β-methyl substituent. Analysis of reported crystal structures for carbapenem-derived acyl-enzyme complexes reveals preferred conformations for hydrolysis and β-lactone formation. The observation of increased β-lactone formation by class D SBL variants, including the clinically observed carbapenemase OXA-48 V120L, supports the proposal that class D SBL-catalyzed rearrangement of β-lactams to β-lactones is important as a resistance mechanism.

19 F NMR Monitoring of Reversible Protein Post-Translational Modifications: Class D β-Lactamase Carbamylation and Inhibition.

Bacterial production of β‐lactamases with carbapenemase activity is a global health threat. The active sites of class D carbapenemases such as OXA‐48, which is of major clinical importance, uniquely contain a carbamylated lysine residue which is essential for catalysis. Although there is significant interest in characterizing this post‐translational modification, and it is a promising inhibition target, protein carbamylation is challenging to monitor in solution. We report the use of 19F NMR spectroscopy to monitor the carbamylation state of 19F‐labelled OXA‐48. This method was used to investigate the interactions of OXA‐48 with clinically used serine β‐lactamase inhibitors, including avibactam and vaborbactam. Crystallographic studies on 19F‐labelled OXA‐48 provide a structural rationale for the sensitivity of the 19F label to active site interactions. The overall results demonstrate the use of 19F NMR to monitor reversible covalent post‐translational modifications.

Mimicking Class I b Mn2 -Ribonucleotide Reductase: A MnII2 Complex and Its Reaction with Superoxide.

A fascinating discovery in the chemistry of ribonucleotide reductases (RNRs) has been the identification of a dimanganese (Mn2 ) active site in class I b RNRs that requires superoxide anion (O2.- ), rather than dioxygen (O2 ), to access a high-valent Mn2 oxidant. Complex 1 ([Mn2 (O2 CCH3 )(N-Et-HPTB)](ClO4 )2 , N-Et-HPTB=N,N,N',N'-tetrakis(2-(1-ethylbenzimidazolyl))-2-hydroxy-1,3-diaminopropane) was synthesised in high yield (90 %). 1 was reacted with O2.- at -40 °C resulting in the formation of a metastable species (2). 2 displayed electronic absorption features (λmax =460, 610 nm) typical of a Mn-peroxide species and a 29-line EPR signal typical of a MnII MnIII entity. Mn K-edge X-ray absorption near-edge spectroscopy (XANES) suggested a formal oxidation state change of MnII2 in 1 to MnII MnIII for 2. Electrospray ionisation mass spectrometry (ESI-MS) suggested 2 to be a MnII MnIII -peroxide complex. 2 was capable of oxidizing ferrocene and weak O-H bonds upon activation with proton donors. Our findings provide support for the postulated mechanism of O2.- activation at class I b Mn2 RNRs.

Mimicking Class I b Mn2‐Ribonucleotide Reductase: A MnII2 Complex and Its Reaction with Superoxide

AbstractA fascinating discovery in the chemistry of ribonucleotide reductases (RNRs) has been the identification of a dimanganese (Mn2) active site in class I b RNRs that requires superoxide anion (O2.−), rather than dioxygen (O2), to access a high‐valent Mn2 oxidant. Complex 1 ([Mn2(O2CCH3)(N‐Et‐HPTB)](ClO4)2, N‐Et‐HPTB=N,N,N′,N′‐tetrakis(2‐(1‐ethylbenzimidazolyl))‐2‐hydroxy‐1,3‐diaminopropane) was synthesised in high yield (90 %). 1 was reacted with O2.− at −40 °C resulting in the formation of a metastable species (2). 2 displayed electronic absorption features (λmax=460, 610 nm) typical of a Mn‐peroxide species and a 29‐line EPR signal typical of a MnIIMnIII entity. Mn K‐edge X‐ray absorption near‐edge spectroscopy (XANES) suggested a formal oxidation state change of MnII2 in 1 to MnIIMnIII for 2. Electrospray ionisation mass spectrometry (ESI‐MS) suggested 2 to be a MnIIMnIII‐peroxide complex. 2 was capable of oxidizing ferrocene and weak O−H bonds upon activation with proton donors. Our findings provide support for the postulated mechanism of O2.− activation at class I b Mn2 RNRs.

Modified Penicillin Molecule with Carbapenem-Like Stereochemistry Specifically Inhibits Class C β-Lactamases.

Bacterial β-lactamases readily inactivate most penicillins and cephalosporins by hydrolyzing and "opening" their signature β-lactam ring. In contrast, carbapenems resist hydrolysis by many serine-based class A, C, and D β-lactamases due to their unique stereochemical features. To improve the resistance profile of penicillins, we synthesized a modified penicillin molecule, MPC-1, by "grafting" carbapenem-like stereochemistry onto the penicillin core. Chemical modifications include the trans conformation of hydrogen atoms at C-5 and C-6 instead of cis, and a 6-α hydroxyethyl moiety to replace the original 6-β aminoacyl group. MPC-1 selectively inhibits class C β-lactamases, such as P99, by forming a nonhydrolyzable acyl adduct, and its inhibitory potency is ∼2 to 5 times higher than that for clinically used β-lactamase inhibitors clavulanate and sulbactam. The crystal structure of MPC-1 forming the acyl adduct with P99 reveals a novel binding mode for MPC-1 that resembles carbapenem bound in the active site of class A β-lactamases. Furthermore, in this novel binding mode, the carboxyl group of MPC-1 blocks the deacylation reaction by occluding the critical catalytic water molecule and renders the acyl adduct nonhydrolyzable. Our results suggest that by incorporating carbapenem-like stereochemistry, the current collection of over 100 penicillins and cephalosporins can be modified into candidate compounds for development of novel β-lactamase inhibitors.

Structural basis for the extended substrate spectrum of AmpC BER and structure-guided discovery of the inhibition activity of citrate against the class C β-lactamases AmpC BER and CMY-10.

AmpC BER is an extended substrate spectrum class C β-lactamase with a two-amino-acid insertion in the R2 loop compared with AmpC EC2. The crystal structures of AmpC BER (S64A mutant) and AmpC EC2 were determined. Structural comparison of the two proteins revealed that the insertion increases the conformational flexibility of the R2 loop. Two citrate molecules originating from the crystallization solution were observed in the active site of the S64A mutant. One citrate molecule makes extensive interactions with active-site residues that are highly conserved among class C β-lactamases, whereas the other one is weakly bound. Based on this structural observation, it is demonstrated that citrate, a primary metabolite that is widely used as a food additive, is a competitive inhibitor of two class C β-lactamases (AmpC BER and CMY-10). Consequently, the data indicate enhancement of the flexibility of the R2 loop as an operative strategy for molecular evolution of extended-spectrum class C β-lactamases, and also suggest that the citrate scaffold is recognized by the active sites of class C β-lactamases.

Conformational Change Observed in the Active Site of Class C β-Lactamase MOX-1 upon Binding to Aztreonam.

We solved the crystal structure of the class C β-lactamase MOX-1 complexed with the inhibitor aztreonam at 1.9Å resolution. The main-chain oxygen of Ser315 interacts with the amide nitrogen of aztreonam. Surprisingly, compared to that in the structure of free MOX-1, this main-chain carboxyl changes its position significantly upon binding to aztreonam. This result indicates that the interaction between MOX-1 and β-lactams can be accompanied by conformational changes in the B3 β-strand main chain.

Perturbing the general base residue Glu166 in the active site of class A β-lactamase leads to enhanced carbapenem binding and acylation.

Most class A β-lactamases cannot hydrolyze carbapenem antibiotics effectively. The molecular mechanism of this catalytic inefficiency has been attributed to the unique stereochemistry of carbapenems, including their 6-α-hydroxyethyl side chain and the transition between two tautomeric states when bound at the active site. Previous studies have shown that the 6-α-hydroxyethyl side chain of carbapenems can interfere with catalysis by forming hydrogen bonds with the deacylation water molecule to reduce its nucleophilicity. Here our studies of a class A noncarbapenemase PenP demonstrate that substituting the general base residue Glu166 with Ser or other residues leads to a significant enhancement of the acylation kinetics by ∼100-500 times toward carbapenems like meropenem. The structures of PenP and Glu166Ser both in apo form and in complex with meropenem reveal that Glu166 is critical for the formation of a hydrogen bonding network within the active site that locks Asn170 in an orientation to impose steric clash with the 6-α-hydroxyethyl side chain of meropenem. The Glu166Ser substitution weakens this network and enables Asn170 to adopt an alternative conformation to avoid steric clash and accommodate faster acylation kinetics. Furthermore, the weakened hydrogen bonding network caused by the Glu166Ser substitution allows the 6-α-hydroxyethyl moiety to adopt a catalytically favorable orientation as seen in class A carbapenemases. In summary, our data identify a previously unreported role of the universally conserved general base residue Glu166 in impeding the proper binding of carbapenems by restricting their 6-α-hydroxyethyl group.

Class D β-Lactamases: A Reappraisal after Five Decades

Despite 70 years of clinical use, β-lactam antibiotics still remain at the forefront of antimicrobial chemotherapy. The major challenge to these life-saving therapeutics is the presence of bacterial enzymes (i.e., β-lactamases) that can hydrolyze the β-lactam bond and inactivate the antibiotic. These enzymes can be grouped into four classes (A-D). Among the most genetically diverse are the class D β-lactamases. In this class are β-lactamases that can inactivate the entire spectrum of β-lactam antibiotics (penicillins, cephalosporins, and carbapenems). Class D β-lactamases are mostly found in Gram-negative bacteria such as Pseudomonas aeruginosa , Escherichia coli , Proteus mirabilis , and Acinetobacter baumannii . The active-sites of class D β-lactamases contain an unusual N-carboxylated lysine post-translational modification. A strongly hydrophobic active-site helps create the conditions that allow the lysine to combine with CO2, and the resulting carbamate is stabilized by a number of hydrogen bonds. The carboxy-lysine plays a symmetric role in the reaction, serving as a general base to activate the serine nucleophile in the acylation reaction, and the deacylating water in the second step. There are more than 250 class D β-lactamases described, and the full set of variants shows remarkable diversity with regard to substrate binding and turnover. Narrow-spectrum variants are most effective against the earliest generation penicillins and cephalosporins such as ampicillin and cephalothin. Extended-spectrum variants (also known as extended-spectrum β-lactamases, ESBLs) pose a more dangerous clinical threat as they possess a small number of substitutions that allow them to bind and hydrolyze later generation cephalosporins that contain bulkier side-chain constituents (e.g., cefotaxime, ceftazidime, and cefepime). Mutations that permit this versatility seem to cluster in the area surrounding an active-site tryptophan resulting in a widened active-site to accommodate the oxyimino side-chains of these cephalosporins. More concerning are the class D β-lactamases that hydrolyze clinically important carbapenem β-lactam drugs (e.g., imipenem). Whereas carbapenems irreversibly acylate and inhibit narrow-spectrum β-lactamases, class D carbapenemases are able to recruit and activate a deacylating water. The rotational orientation of the C6 hydroxyethyl group found on all carbapenem antibiotics likely plays a role in whether the deacylating water is effective or not. Inhibition of class D β-lactamases is a current challenge. Commercially available inhibitors that are active against other classes of β-lactamases are ineffective against class D enzymes. On the horizon are several compounds, consisting of both β-lactam derivatives and non-β-lactams, that have the potential of providing novel leads to design new mechanism-based inactivators that are effective against the class D enzymes. Several act synergistically when given in combination with a β-lactam antibiotic, and others show a unique mechanism of inhibition that is distinct from the traditional β-lactamase inhibitors. These studies will bolster structure-based inhibitor design efforts to facilitate the optimization and development of these compounds as class D inactivators.

Romidepsin (Istodax, NSC 630176, FR901228, FK228, depsipeptide): a natural product recently approved for cutaneous T-cell lymphoma

Romidepsin (Istodax), a selective inhibitor of histone deacetylases (HDACs), was approved for the treatment of cutaneous T-cell lymphoma in November 2009 by the US Food and Drug Administration. This unique natural product was discovered from cultures of Chromobacterium violaceum, a Gram-negative bacterium isolated from a Japanese soil sample. This bicyclic compound acts as a prodrug, its disulfide bridge being reduced by glutathione on uptake into the cell, allowing the free thiol groups to interact with Zn ions in the active site of class I and II HDAC enzymes. Due to the synthetic complexity of the compound, as well as the low yield from the producing organism, analogs are sought to create synthetically accessible alternatives. As a T-cell lymphoma drug, romidepsin offers a valuable new treatment for diseases with few effective therapies.

Structural and Biochemical Evidence That a TEM-1 β-Lactamase N170G Active Site Mutant Acts via Substrate-assisted Catalysis

TEM-1 beta-lactamase is the most common plasmid-encoded beta-lactamase in Gram-negative bacteria and is a model class A enzyme. The active site of class A beta-lactamases share several conserved residues including Ser(70), Glu(166), and Asn(170) that coordinate a hydrolytic water involved in deacylation. Unlike Ser(70) and Glu(166), the functional significance of residue Asn(170) is not well understood even though it forms hydrogen bonds with both Glu(166) and the hydrolytic water. The goal of this study was to examine the importance of Asn(170) for catalysis and substrate specificity of beta-lactam antibiotic hydrolysis. The codon for position 170 was randomized to create a library containing all 20 possible amino acids. The random library was introduced into Escherichia coli, and functional clones were selected on agar plates containing ampicillin. DNA sequencing of the functional clones revealed that only asparagine (wild type) and glycine at this position are consistent with wild-type function. The determination of kinetic parameters for several substrates revealed that the N170G mutant is very efficient at hydrolyzing substrates that contain a primary amine in the antibiotic R-group that would be close to the Asn(170) side chain in the acyl-intermediate. In addition, the x-ray structure of the N170G enzyme indicated that the position of an active site water important for deacylation is altered compared with the wild-type enzyme. Taken together, the results suggest the N170G TEM-1 enzyme hydrolyzes ampicillin efficiently because of substrate-assisted catalysis where the primary amine of the ampicillin R-group positions the hydrolytic water and allows for efficient deacylation.

Analysis of the plasticity of location of the Arg244 positive charge within the active site of the TEM-1 beta-lactamase.

A large number of beta-lactamases have emerged that are capable of conferring bacterial resistance to beta-lactam antibiotics. Comparison of the structural and functional features of this family has refined understanding of the catalytic properties of these enzymes. An arginine residue present at position 244 in TEM-1 beta-lactamase interacts with the carboxyl group common to penicillin and cephalosporin antibiotics and thereby stabilizes both the substrate and transition state complexes. A comparison of class A beta-lactamase sequences reveals that arginine at position 244 is not conserved, although a positive charge at this structural location is conserved and is provided by an arginine at positions 220 or 276 for those enzymes lacking arginine at position 244. The plasticity of the location of positive charge in the beta-lactamase active site was experimentally investigated by relocating the arginine at position 244 in TEM-1 beta-lactamase to positions 220, 272, and 276 by site-directed mutagenesis. Kinetic analysis of the engineered beta-lactamases revealed that removal of arginine 244 by alanine mutation reduced catalytic efficiency against all substrates tested and restoration of an arginine at positions 272 or 276 partially suppresses the catalytic defect of the Arg244Ala substitution. These results suggest an evolutionary mechanism for the observed divergence of the position of positive charge in the active site of class A beta-lactamases.

Exact Location of the Region Responsible for the Extended Substrate Spectrum in Class C β-Lactamases

In a recently published article (9), Wachino et al. reported that a single amino acid substitution (I292S) responsible for the expansion of the hydrolyzing activity against several extended-spectrum cephalosporins (ceftazidime or cefepime) is near the H-10 helix region of CMY-19. However, other reports (2, 7, 8) have concluded that the region responsible for the extended substrate spectrum in class C β-lactamases is in (not near) the H-10 helix. Wachino and colleagues designated the amino acid sequence from 279 to 287 as the H-10 helix (Fig. ​(Fig.1),1), which may be based on the crystal structure of AmpC K-12 (PDB code 2BLS), although they did not state the fact. However, one previous report described residues 279 to 294 as the H-10 helix, according to the crystal structure of GC1 (3). Our recent report (5) showed that the sequence from 289 to 294 was the H-10 (α10) helix (Fig. ​(Fig.1),1), based on superposed crystal structures among CMY-10 (5), P99, and GC1 β-lactamases. There are different positions of the H-10 helix that is related to the extended substrate spectrum in class C β-lactamases. Therefore, we propose that the exact region responsible for the extended substrate spectrum is the R2 loop (residues 289 to 307) (Fig. ​(Fig.1)1) described in our recent report (5). There are three important reasons why the exact region is the R2 loop in the R2 active site, referring to the region that accommodates the R2 side chain at C3 of the β-lactam nucleus in extended-spectrum cephalosporins. FIG. 1. A sequence alignment of amino acid residues near the H-9 (α9) and H-10 helix (α10) of class C β-lactamases with extended substrate spectrum. Alignment among CMY-10, P99, and GC1 β-lactamases whose structures are available ... First, the R2 loop includes all regions responsible for the extended substrate spectrum in all reported class C extended-spectrum β-lactamases except HKY28 (4): (i) six-amino-acid deletion (residues 289 to 294) of CHE (2); (ii) the single amino acid substitution (L296H) of AmpC KL (7); (iii) four-amino-acid deletion (residues 293 to 296) of HD (8); (iv) three-amino-acid deletion (residues 303 to 305) of CMY-10 (5); (v) the single amino acid substitution (I292S) of CMY-19 (9); and (vi) the L293P substitution of Ear2 (1). Second, mutations in the R2 loop can change the architecture of the active site in class C extended-spectrum β-lactamases, thereby affecting their hydrolyzing activity. Owing to the deletion in CMY-10, for example, the R2 loop in the R2 active site displays noticeable structural alterations: the shortened path of the connection R2 loop between α10 and β11 (Fig. ​(Fig.1)1) induces a ∼2.5-A shift of α9 and α10 relative to the adjacent helix α11 in CMY-10, compared with both P99 and GC1 β-lactamases, opening the gap between α9-α10 and α11 (5). Therefore, the bulky R2 side chain of extended-spectrum cephalosporins could fit snugly into the significantly widened R2 active site in this way (6). Third, CMY-19 showed 97% sequence identity to CMY-10. But the sequence identity between CMY-19 and AmpC K-12 was 40%. Therefore, it is reasonable for the region responsible for the extended substrate spectrum in CMY-19 to be designated based on the crystal structure of CMY-10 (not AmpC K-12).

Biochemical Characterization of VlmL, a Seryl-tRNA Synthetase Encoded by the Valanimycin Biosynthetic Gene Cluster

Previous studies have shown that the valanimycin producer Streptomyces viridifaciens contains two genes encoding proteins that are similar to seryl-tRNA synthetases (SerRSs). One of these proteins (SvsR) is presumed to function in protein biosynthesis, because it exhibits a high degree of similarity to the single SerRS of Streptomyces coelicolor. The second protein (VlmL), which exhibits a low similarity to the S. coelicolor SerRS, is hypothesized to play a role in valanimycin biosynthesis, because the vlmL gene resides within the valanimycin biosynthetic gene cluster. To investigate the role of VlmL in valanimycin biosynthesis, VlmL and SvsR have been overproduced in soluble form in Escherichia coli, and the biochemical properties of both proteins have been analyzed and compared. Both proteins were found to catalyze a serine-dependent exchange of 32P-labeled pyrophosphate into ATP and to aminoacylate total E. coli tRNA with L-serine. Kinetic parameters for the two enzymes show that SvsR is catalytically more efficient than VlmL. The results of these experiments suggest that the role of VlmL in valanimycin biosynthesis is to produce seryl-tRNA, which is then utilized for a subsequent step in the biosynthetic pathway. Orthologs of VlmL were identified in two other actinomycetes species that also contain orthologs of the S. coelicolor SerRS. The significance of these findings is herein discussed.

Discrimination of Cognate and Noncognate Substrates at the Active Site of Class I Lysyl-tRNA Synthetase

The aminoacyl-tRNA synthetases are divided into two unrelated structural classes, with lysyl-tRNA synthetase (LysRS) being the only enzyme represented in both classes. On the basis of the structure of l-lysine complexed with Pyrococcus horikoshii class I LysRS (LysRS1) and homology to glutamyl-tRNA synthetase (GluRS), residues implicated in amino acid recognition and noncognate substrate discrimination were systematically replaced in Borrelia burgdorferi LysRS1. The catalytic efficiency of steady-state aminoacylation (k(cat)/K(M)) with lysine by LysRS1 variants fell by 1-4 orders of magnitude compared to that of the wild type. Disruption of putative hydrogen bonding interactions through replacement of G29, T31, and Y269 caused up to 1500-fold reductions in k(cat)/K(M), similar to changes previously observed for comparable variants of class II LysRS (LysRS2). Replacements of W220 and H242, both of which are implicated in hydrophobic interactions with the side chain of lysine, resulted in more dramatic changes with up to 40000-fold reductions in k(cat)/K(M) observed. This indicates that the more compact LysRS1 active site employs both electrostatic and hydrophobic interactions during lysine discrimination, explaining the ability of LysRS1 to discriminate against noncognate substrates accepted by LysRS2. Several of the LysRS1 variants were found to be more specific than the wild type with respect to noncognate amino acid recognition but less efficient in cognate aminoacylation. This indicates that LysRS1 compromises between efficient catalysis and substrate discrimination, in contrast to LysRS2 which is considerably more effective in catalysis but is less specific than its class I counterpart.

Kinetic effects of a single-amino acid mutation in a highly variable loop (residues 114–120) of class IV ADH

Class IV alcohol dehydrogenase shows a deletion at position 117 with respect to class I enzymes, which typically have a Gly residue. In class I structures, Gly117 is part of a loop (residues 114–120) that is highly variable within the alcohol dehydrogenase family. A mutant human class IV enzyme was engineered in which a Gly residue was inserted at position 117 (G117ins). Its kinetic properties, regarding ethanol and primary aliphatic alcohols, secondary alcohols and pH profiles, were determined and compared with the results obtained in previous studies in which the size of the 114–120 loop was modified. For the enzymes considered, a smaller loop was associated with a lower catalytic efficiency towards short-chain alcohols (ethanol and propanol) and secondary alcohols, as well as with a higher K m for ethanol at pH 7.5 than at pH 10.0. The effect can be rationalized in terms of a more open, solvent-accessible active site in class IV alcohol dehydrogenase, which disfavors productive binding of ethanol and short-chain alcohols, specially at physiological pH.

Mutation of Arg273 to Leu Alters the Specificity of the Yeast N-Glycan Processing Class I α1,2-Mannosidase

Class I alpha1,2-mannosidases (glycosyl hydrolase family 47) involved in the processing of N-glycans during glycoprotein maturation have different specificities. Enzymes in the endoplasmic reticulum of yeast and mammalian cells remove a single mannose from Man(9)GlcNAc(2) to form Man(8)GlcNAc(2) isomer B (lacking the alpha1, 2-mannose residue of the middle alpha1, 3-arm), whereas other alpha1,2-mannosidases, including Golgi alpha1,2-mannosidases IA and IB, can convert Man(9)GlcNAc(2) to Man(5)GlcNAc(2). In the present work, it is demonstrated that with a single mutation in its catalytic domain (Arg(273) --> Leu) the yeast endoplasmic reticulum alpha1,2-mannosidase acquires the ability to transform Man(9)GlcNAc to Man(5)GlcNAc. High resolution proton nuclear magnetic resonance analysis of the products shows that the order of removal of mannose from Man(9)GlcNAc is different from that of other alpha1, 2-mannosidases that remove four mannose from Man(9)GlcNAc. These results demonstrate that Arg(273) is in part responsible for the specificity of the endoplasmic reticulum alpha1,2-mannosidase and that small differences in non-conserved amino acids interacting with the oligosaccharide substrate in the active site of class I alpha1, 2-mannosidases are responsible for the different specificities of these enzymes.