Structures of wild-type and P28L/Y173F tryptophan synthase alpha-subunits from Escherichia coli

The alpha-subunit of tryptophan synthase (alphaTS) catalyzes the cleavage of indole-3-glycerol phosphate to glyceraldehyde-3-phosphate and indole, which is used to yield the amino acid tryptophan in tryptophan biosynthesis. Here, we report the first crystal structures of wild-type and double-mutant P28L/Y173F alpha-subunit of tryptophan synthase from Escherichia coli at 2.8 and 1.8A resolution, respectively. The structure of wild-type alphaTS from E. coli was similar to that of the alpha(2)beta(2) complex structure from Salmonella typhimurium. As compared with both structures, the conformational changes are mostly in the interface of alpha- and beta-subunits, and the substrate binding region. Two sulfate ions and two glycerol molecules per asymmetric unit bind with the residues in the active sites of the wild-type structure. Contrarily, double-mutant P28L/Y173F structure is highly closed at the window for the substrate binding by the conformational changes. The P28L substitution induces the exposure of hydrophobic amino acids and decreases the secondary structure that causes the aggregation. The Y173F suppresses to transfer a signal from the alpha-subunit core to the alpha-subunit surface involved in interactions with the beta-subunit and increases structural stability.     

Three-dimensional structures of idiotypically related Fabs with intermediate and high affinity for fluorescein

Multi-disciplinary studies of fluorescein-protein conjugates have led to the generation of a family of antibodies with common idiotypes and affinities for fluorescein ranging over five orders of magnitude. The high affinity 4-4-20 prototype traps the ligand in a highly complementary binding slot, which is lined by multiple aromatic side-chains. An antibody (9-40) of intermediate affinity belongs to the same idiotypic family as 4-4-20 and shares substantial amino acid identities within the VL and VH domains. To establish the structural basis for the affinity differences, we solved the crystal structure of the 9-40 Fab-fluorescein complex at a resolution of 2.3A. Similar to 4-4-20, 9-40 binds fluorescein in a tight aromatic slot with its xanthenonyl ring system accommodated by end-on insertion. However, the combined effects of the amino acid substitutions have resulted in reorganization of the binding site, with the HCDR3 loops showing the greatest differences in conformations. Access to the binding site of 9-40 is substantially more open, leaving the fluorescein's phenylcarboxylate moiety partially exposed to solvent. In addition to the usage of a different D (diversity) mini-gene encoding the HCDR3 loop, the decrease in fluorescein affinity in the 9-40 antibody family appears to be correlated with the substitution of histidine (9-40) for arginine (4-4-20) in position 34 of the antibody light chains.     

Ferromagnetic interactions in copper(II) and nickel(II) coordination polymers containing nitronyl nitroxide radical and terephthalate

Two new complexes [Cu(NITmPy)₂(tp)] 1 and [Ni(NITmPy)₂(tp)(H₂O)₂] 2 (NITmPy=2-(3^′-pyridyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide and tp=terephthalato dianion) were synthesized and structurally and magnetically characterized. The structure of 1 is a neutral infinite chain where Cu(NITmPy)₂ units are linked by terephthalate ligands. In complex 2, the 1-D chains of Ni(NITmPy)₂ (H₂O)₂ units connected by tp develop into 2-D network via hydrogen bond interactions. The magnetic properties of 1 and 2 have been investigated in the temperature range 2-300 K. Both complexes exhibit ferromagnetic coupling and antiferromagnetic interactions dominate at low temperature. The magnetic behavior is discussed based on their structures.     

Synthesis, solid-state characterization and antimicrobial activities of three different polymorphs of a copper(II) complex with 4-isopropyltropolone (hinokitiol)

There exist at least three different polymorphs in the copper(II) complex [Cu(hino)₂] with a hinokitiol ligand (Hhino; 4-isopropyltropolone¹). In addition to deep-green plate crystals 1a and deep-green rod crystals 1b, whose crystal structures have been recently reported, novel green needle crystals 1c of [Cu(hino)₂] were found, the crystal structure of which was here determined by single-crystal X-ray analysis. Since only one crystal structure has been reported for the copper(II) complex [Cu(trop)₂] with a tropolone ligand (Htrop), the polymorphism found in the crystals of [Cu(hino)₂] would be due to the presence of the isopropyl group on the tropolone ring. The synthetic conditions giving the three polymorphs in good yields were found and the crystals were characterized with elemental analysis, FT-IR, TG/DTA and X-ray powder diffraction (XPD) measurements, as well as solution molecular weight measurements for 1a. The solid-state magnetic behaviors or the temperature-dependent magnetic susceptibilities were measured with Superconductivity Quantum Interference Devices (SQUID): 1a showed a weak ferromagnetic interaction, 1b showed a paramagnetic nature with S=1/2, while 1c showed a weak antiferromagnetic interaction. The antimicrobial activities for selected bacteria, yeasts and molds were also measured in the water-suspension system: 1a and 1b showed no activity, while 1c showed modest activities, and these activities were compared with those of the neutral Hino and the anionic hino⁻ ligands.     

Synthesis, structure, and formation mechanism of the halogen-bridged tricobalt clusters, [Co3Cp3(μ3-CPh)2(μ-X)] (X=Cl, Br, and I)

Reactions of a benzylidyne-capped tricobalt cluster, [Co₃Cp₃(μ₃-CPh)₂] (1), with halogens (X₂ = Cl₂, Br₂, and I₂) in CH₂Cl₂ afforded halogen-adducts of 1. The structure of four isolated salts [Co₃Cp₃(μ₃-CPh)₂(μ-Cl)]PF₆ · MeCN (2PF₆ · MeCN), [Co₃Cp₃(μ₃-CPh)₂(μ-Br)]SbF₆ (3SbF₆), [Co₃Cp₃(μ₃-CPh)₂(μ-I)]SbF₆ · CH₂Cl₂ (4SbF₆ · CH₂Cl₂), and [Co₃Cp₃(μ₃-CPh)₂(μ-I)]I₃ (4I₃) determined by X-ray diffraction can be regarded formally as halide-adducts of 1²⁺. The halogen atom in each structure lies in the Co₃ plane. The halogen-bridged Co-Co edge was elongated (in 2PF₆ · MeCN = 2.6072(4), in 3SbF₆ = 2.6106(7), in 4SbF₆ · CH₂Cl₂ = 2.622(2), and in 4I₃=2.6718(9) Å), and the Co-Co distances that had no halogen-bridge remained unchanged from the Co-Co distance of 1 (2.382(8) Å), (in 2PF₆=2.4037(8) and 2.3948(7), in 3SbF₆=2.3888(6) and 2.4017(7), in 4SbF₆ · CH₂Cl₂ = 2.393(2) and 2.388(1), and in 4I₃ = 2.397(1) and 2.3868(9) Å). The UV-Vis absorption spectra of 2⁺, 3⁺, and 4⁺ had characteristic absorption peaks at 796, 819, and 844 nm, respectively. Cyclic voltammograms of 2PF₆ in CH₂Cl₂ with 0.1 M ⁿBu₄NPF₆ as the supporting electrolyte showed a chemically reversible oxidation (at a potential of 0.75 V versus Fc/Fc⁺), and an irreversible reduction wave at −0.57 V. The irreversible reduction resulted in the recovery of 1. The redox properties of 3⁺ and 4⁺ are very similar to that of 2⁺. Cyclic voltammetry of 1 in 0.1 M ⁿBu₄NCl/MeCN indicates that the formation of 2⁺ is a multi-step reaction. Initially, 1 is oxidized to 1⁺, and then, 1⁺ is coordinated by Cl⁻ followed by immediate oxidation to 2⁺.     

Synthesis and structural studies of heteroleptic complexes of ytterbium(III) involving aryloxy- or alkoxy- and cyclopentadienyl ligands

Treatment of tris-cyclopentadienyl-ytterbium in thf with one equivalent of 2,6-di(tert-butyl)phenol, N,N-dimethyl-2-aminoethanol or N,N-diethyl-2-aminoethanol resulted in substitution of one cyclopentadienyl ligand and formation of [YbCp₂(O-C₆H₃^tBu-2,6)(thf)] (1), [{YbCp₂(μ-OCH₂CH₂NMe₂)}₂] (2) or [{YbCp₂(μ-OCH₂CH₂NEt₂)}₂] · (thf)₂ (3), respectively. All compounds were characterised by spectroscopic and X-ray crystallographic techniques, the latter two also being studied by variable temperature ¹H NMR spectroscopy. Compound (1) is mononuclear with the Yb centre bound by two η⁵-cyclopentadienyl ligands one O-bound thf and an O-bound phenoxy ligand. Compounds (2) and (3) are centrosymmetric dimers with the Yb centre bound by two η⁵-cyclopentadienyl ligands, while the bidentate ligands chelate the metal centre and also bridge to the adjacent Yb through the alkoxy oxygen atom. Variable temperature ¹H NMR studies on compounds (2) and (3) show a solution-state equilibrium between the dimeric solid-state structure and one with the nitrogen atoms non-bound to Yb.     

Synthesis and structural characterization of five-, six-, and seven-coordinate mononuclear manganese(II) complexes with N-tridentate ligands

A series of four mononuclear manganese (II) complexes with the N-tridentate neutral ligands 2,2^′:6,2^′′-terpyridine (terpy) and N,N-bis(2-pyridylmethyl)ethylamine (bpea) have been synthesized and crystallographically characterized. The complexes have five- to seven-coordinate manganese(II) ions depending on the additional ligands used. The [Mn(bpea)(Br)₂] complex (1) has a five-coordinated manganese atom with a bipyramidal trigonal geometry, while [Mn(terpy)₂](I)₂ (2) is hexa-coordinated with a distorted octahedral geometry. Otherwise, the reactions of Mn(NO₃)₂ · 4H₂O with terpy or bpea afforded novel seven-coordinate complexes [Mn(terpy)(NO₃)₂(H₂O)] (3) and [Mn(bpea)(NO₃)₂] (4), respectively. 3 has a coordination polyhedron best described as a distorted pentagonal bipyramid geometry with one nitrate acting as a bidentate chelating ligand and the other nitrate as a monodentate one. 4 possesses a highly distorted polyhedron geometry with two bidentate chelating nitrate ligands. These complexes represent unusual examples of structurally characterized complexes with a coordination number seven for the Mn(II) ion and join a small family of nitrate complexes.     

Oxidations of sulfur rich heterocycles - new S-oxides of the parent 1,2,4-trithiolane and its tetramethyl derivative: synthesis and structural investigations

Whereas oxidation of 1,2,4-trithiolane (1) with 1 molar equiv. of m-chloroperbenzoic acid (mCPBA) yielded 1,2,4-trithiolane 4-oxide (3) and a small amount of 1,2,4-trithiolane 1-oxide (2), the reaction with 2.5 molar equiv. of mCPBA afforded exclusively 1,2,4-trithiolane 1,4-dioxide (trans-7). The oxidation of 3,3,5,5-tetramethyl-1,2,4-trithiolane (4) with peroxyacetic acid (1 molar equiv. H₂O₂/AcOH) gave a mixture of regioisomeric 3,3,5,5-tetramethyl-1,2,4-trithiolane 4-oxide (6) as a major product and only traces of 1-oxide 5. Using 2.5 molar equiv. of peroxyacetic acid in reaction with 4 a mixture of both stereoisomers of 3,3,5,5-tetramethyl-1,2,4-trithiolane 1,4-dioxides cis-8 and trans-8 was isolated. Furthermore, 4 was oxidized to 3,3,5,5-tetramethyl-1,2,4-trithiolane 1,1,4,4-tetraoxide (9) using 6 molar equiv. of peroxyacetic acid. The molecular structures of 3, trans-7, trans-8 and 9 were unambiguously established by X-ray structure analysis. Compounds 1-4, trans-7, trans-8 and 9 were investigated by Raman spectroscopy. Ab initio calculations were used to obtain the optimized geometries and the vibrational wavenumbers of the title compounds. The vibrational assignment was accomplished by using the calculated harmonic wavenumbers and their Raman intensities. The calculated values of both structural parameters and the vibrational modes fitted in with experimental data. The spectroscopic changes observed in the spectra were correlated with the structural parameters in order to gain information about the influence of the oxidation on the molecule structure. The experimental data indicated, that in comparison with starting 1,2,4-trithiolanes 1 and 4 their oxidized derivatives showed remarkable shortening of the S-S bonds.     

Enhanced functional and structural domain assignments using remote similarity detection procedures for proteins encoded in the genome of<Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> H37Rv

The sequencing of theMycobacterium tuberculosis (MTB) H37Rv genome has facilitated deeper insights into the biology of MTB, yet the functions of many MTB proteins are unknown. We have used sensitive profile-based search procedures to assign functional and structural domains to infer functions of gene products encoded in MTB. These domain assignments have been made using a compendium of sequence and structural domain families. Functions are predicted for 78% of the encoded gene products. For 69% of these, functions can be inferred by domain assignments. The functions for the rest are deduced from their homology to proteins of known function. Superfamily relationships between families of unknown and known structures have increased structural information by ∼ 11%. Remote similarity detection methods have enabled domain assignments for 1325 ‘hypothetical proteins’. The most populated families in MTB are involved in lipid metabolism, entry and survival of the bacillus in host. Interestingly, for 353 proteins, which we refer to as MTB-specific, no homologues have been identified. Numerous, previously unannotated, hypothetical proteins have been assigned domains and some of these could perhaps be the possible chemotherapeutic targets. MTB-specific proteins might include factors responsible for virulence. Importantly, these assignments could be valuable for experimental endeavors. The detailed results are publicly available at http://hodgkin.mbu.iisc.ernet.in/∼dots. An erratum to this article is available at .     

Oligosaccharide preferences of beta1,4-galactosyltransferase-I: crystal structures of Met340His mutant of human beta1,4-galactosyltransferase-I with a pentasaccharide and trisaccharides of the N-glycan moiety

beta-1,4-Galactosyltransferase-I (beta4Gal-T1) transfers galactose from UDP-galactose to N-acetylglucosamine (GlcNAc) residues of the branched N-linked oligosaccharide chains of glycoproteins. In an N-linked biantennary oligosaccharide chain, one antenna is attached to the 3-hydroxyl-(1,3-arm), and the other to the 6-hydroxyl-(1,6-arm) group of mannose, which is beta-1,4-linked to an N-linked chitobiose, attached to the aspargine residue of a protein. For a better understanding of the branch specificity of beta4Gal-T1 towards the GlcNAc residues of N-glycans, we have carried out kinetic and crystallographic studies with the wild-type human beta4Gal-T1 (h-beta4Gal-T1) and the mutant Met340His-beta4Gal-T1 (h-M340H-beta4Gal-T1) in complex with a GlcNAc-containing pentasaccharide and several GlcNAc-containing trisaccharides present in N-glycans. The oligosaccharides used were: pentasaccharide GlcNAcbeta1,2-Manalpha1,6 (GlcNAcbeta1,2-Manalpha1,3)Man; the 1,6-arm trisaccharide, GlcNAcbeta1,2-Manalpha1,6-Manbeta-OR (1,2-1,6-arm); the 1,3-arm trisaccharides, GlcNAcbeta1,2-Manalpha1,3-Manbeta-OR (1,2-1,3-arm) and GlcNAcbeta1,4-Manalpha1,3-Manbeta-OR (1,4-1,3-arm); and the trisaccharide GlcNAcbeta1,4-GlcNAcbeta1,4-GlcNAc (chitotriose). With the wild-type h-beta4Gal-T1, the K(m) of 1,2-1,6-arm is approximately tenfold lower than for 1,2-1,3-arm and 1,4-1,3-arm, and 22-fold lower than for chitotriose. Crystal structures of h-M340H-beta4Gal-T1 in complex with the pentasaccharide and various trisaccharides at 1.9-2.0A resolution showed that beta4Gal-T1 is in a closed conformation with the oligosaccharide bound to the enzyme, and the 1,2-1,6-arm trisaccharide makes the maximum number of interactions with the enzyme, which is in concurrence with the lowest K(m) for the trisaccharide. Present studies suggest that beta4Gal-T1 interacts preferentially with the 1,2-1,6-arm trisaccharide rather than with the 1,2-1,3-arm or 1,4-1,3-arm of a bi- or tri-antennary oligosaccharide chain of N-glycan.