Crystal structure of the human tRNA microhelix isoacceptor G9990 at 1.18 Å resolution

The tRNA^Gly/Glycyl-tRNA synthetase system belongs to the so called ‘class II’ in which tRNA identity elements consist of relative few and simple motifs, as compared to ‘class I’ where the tRNA determinants are more complicated and spread over different parts of the tRNA, mostly including the anticodon. The determinants from ‘class II’ although, are located in the aminoacyl stem and sometimes include the discriminator base. There exist predominant structure differences for the Glycyl-tRNA-synthetases and for the tRNA^Gly identity elements comparing eucaryotic/archaebacterial and eubacterial systems.We focus on comparative X-ray structure analysis of tRNA^Gly acceptor stem microhelices from different organisms. Here, we report the X-ray structure of the human tRNA^Gly microhelix isoacceptor G9990 at 1.18 Å resolution. Superposition experiments to another human tRNA^Gly microhelix and a detailed comparison of the RNA hydration patterns show a great number of water molecules with identical positions in both RNAs. This is the first structure comparison of hydration layers from two isoacceptor tRNA microhelices with a naturally occurring base pair exchange.     

The 1.2 Å crystal structure of an E. coli tRNA acceptor stem microhelix reveals two magnesium binding sites

tRNA identity elements assure the correct aminoacylation of tRNAs by the cognate aminoacyl-tRNA synthetases. tRNA^Ser belongs to the so-called class II system, in which the identity elements are rather simple and are mostly located in the acceptor stem region, in contrast to ‘class I’, where tRNA determinants are more complex and are located within different regions of the tRNA.The structure of an Escherichia coli tRNA^Ser acceptor stem microhelix was solved by high resolution X-ray structure analysis. The RNA crystallizes in the space group C2, with one molecule per asymmetric unit and with the cell constants a = 35.79, b = 39.13, c = 31.37 Å, and β = 111.1°. A defined hydration pattern of 97 water molecules surrounds the tRNA^Ser acceptor stem microhelix. Additionally, two magnesium binding sites were detected in the tRNA^Ser aminoacyl stem.     

The crystal structure of a Thermus thermophilus tRNA acceptor stem microhelix at 1.6 Å resolution

tRNAs are aminoacylated with the correct amino acid by the cognate aminoacyl-tRNA synthetase. The tRNA/synthetase systems can be divided into two classes: class I and class II. Within class I, the tRNA identity elements that enable the specificity consist of complex sequence and structure motifs, whereas in class II the identity elements are assured by few and simple determinants, which are mostly located in the tRNA acceptor stem.The tRNA^Gly/glycyl-tRNA-synthetase (GlyRS) system is a special case regarding evolutionary aspects. There exist two different types of GlyRS, namely an archaebacterial/human type and an eubacterial type, reflecting the evolutionary divergence within this system. We previously reported the crystal structures of an Escherichia coli and of a human tRNA^Gly acceptor stem microhelix. Here we present the crystal structure of a thermophilic tRNA^Gly aminoacyl stem from Thermus thermophilus at 1.6 Å resolution and provide insight into the RNA geometry and hydration.     

Crystal structure of a human tRNA(Gly) microhelix at 1.2A resolution

The tRNA^Gly/glycyl-tRNA synthetase (GlyRS) system belongs to the so-called ‘class II aminoacyl-tRNA synthetase system’ in which tRNA identity elements are assured by rather few and simple determinants mostly located in the tRNA acceptor stem. Regarding evolutionary aspects, the tRNA^Gly/GlyRS system is a special case. There exist two different types of GlyRS, namely an archaebacterial/human type and a eubacterial type reflecting an evolutionary divergence within this system.Here we report the crystal structure of a human tRNA^Gly acceptor stem microhelix at 1.2 Å resolution. The local geometric parameters of the microhelix and the water network surrounding the RNA are presented. The structure complements the previously published Escherichia coli tRNA^Gly aminoacyl stem structure.     

Crystal structure of an Escherichia coli tRNA(Gly) microhelix at 2.0 A resolution

tRNA identity elements determine the correct aminoacylation by the cognate aminoacyl-tRNA synthetase. In class II aminoacyl tRNA synthetase systems, tRNA specificity is assured by rather few and simple recognition elements, mostly located in the acceptor stem of the tRNA. Here we present the crystal structure of an Escherichia coli tRNA(Gly) aminoacyl stem microhelix at 2.0 A resolution. The tRNA(Gly) microhelix crystallizes in the space group P3(2)21 with the cell constants a=b=35.35 A, c=130.82 A, gamma=120 degrees . The helical parameters, solvent molecules and a potential magnesium binding site are discussed.     

Superposition of two tRNA acceptor stem crystal structures: Comparison of structure, ligands and hydration

We solved the X-ray structures of two Escherichia coli tRNA^Ser acceptor stem microhelices. As both tRNAs are aminoacylated by the same seryl-tRNA-synthetase, we performed a comparative structure analysis of both duplexes to investigate the helical conformation, the hydration patterns and magnesium binding sites. It is well accepted, that the hydration of RNA plays an important role in RNA-protein interactions and that the extensive solvent content of the minor groove has a special function in RNA. The detailed comparison of both tRNA^Ser microhelices provides insights into the structural arrangement of the isoacceptor tRNA aminoacyl stems with respect to the surrounding water molecules and may eventually help us to understand their biological function at atomic resolution.     

Comparative X-ray structure analysis of human and Escherichia coli tRNA(Gly) acceptor stem microhelices

tRNA identity elements assure the correct aminoacylation of tRNAs by the aminoacyl-tRNA synthetases with the cognate amino acid. The tRNA^Gly/glycyl-tRNA sythetase system is member of the so-called ‘class II system’ in which the tRNA determinants consist of rather simple elements. These are mostly located in the tRNA acceptor stem and in the glycine case additionally the discriminator base at position 73 is required. Within the glycine-tRNA synthetases, the archaebacterial/human and the eubacterial sytems differ with respect to their protein structures and the required tRNA identity elements, suggesting a unique evolutionary divergence.In this study, we present a comparison between the crystal structures of the eubacterial Escherichia coli and the human tRNA^Gly acceptor stem microhelices and their surrounding hydration patterns.     

Crystal structure at 1.5 Å resolution of the PsbV2 cytochrome from the cyanobacterium Thermosynechococcus elongatus

PsbV2 is a c-type cytochrome present in a very low abundance in the thermophilic cyanobacterium Thermosynechococcus elongatus. We purified this cytochrome and solved its crystal structure at a resolution of 1.5 Å. The protein existed as a dimer in the crystal, and has an overall structure similar to other c-type cytochromes like Cytc₆ and Cytc₅₅₀, for example. However, the 5th and 6th heme iron axial ligands were found to be His51 and Cys101, respectively, in contrast to the more common bis-His or His/Met ligands found in most cytochromes. Although a few other c-type cytochromes were suggested to have this axial coordination, this is the first crystal structure reported for a c-type heme with this unusual His/Cys axial coordination. Previous spectroscopic characterizations of PsbV2 are discussed in relation to its structural properties.     

The 1.59 Å resolution structure of the minor pseudopilin EpsH of Vibrio cholerae reveals a long flexible loop

The type II secretion complex exports folded proteins from the periplasm to the extracellular milieu. It is used by the pathogenic bacterium Vibrio cholerae to export several proteins, including its major virulence factor, cholera toxin. The pseudopilus is an essential component of the type II secretion system and likely acts as a piston to push the folded proteins across the outer membrane through the secretin pore. The pseudopilus is composed of the major pseudopilin, EpsG, and four minor pseudopilins, EpsH, EpsI, EpsJ and EpsK. We determined the x-ray crystal structure of the head domain of EpsH at 1.59 Å resolution using molecular replacement with the previously reported EpsH structure, 2qv8, as the template. Three additional N-terminal amino acids present in our construct prevent an artifactual conformation of residues 160–166, present in one of the two monomers of the 2qv8 structure. Additional crystal contacts stabilize a long flexible loop comprised of residues 104–135 that is more disordered in the 2qv8 structure but is partially observed in our structure in very different positions for the two EpsH monomers in the asymmetric unit. In one of the conformations the loop is highly extended. Modeling suggests the highly charged loop is capable of contacting EpsG and possibly secreted protein substrates, suggesting a role in specificity of pseudopilus assembly or secretion function.     

Crystal structures of 26 kDa Clonorchis sinensis glutathione S-transferase reveal zinc binding and putative metal binding

The crystal structures of CsGST in two different space groups revealed that Asp26 and His79 coordinate a zinc ion. In one space group, His46 of an adjacent molecule participates in the coordination within 2.0 Å. In the other space group, Asp26, His79 and a water molecule coordinate a zinc ion. The CsGST–D26H structure showed that four histidine residues – His26 and His79 from one molecule and the same residues from a symmetry-related neighboring molecule – coordinate a zinc ion. The coordinated zinc ions are located between two molecules and mediate molecular contacts within the crystal.     

Ultrahigh (0.93 Å) resolution structure of manganese peroxidase from Phanerochaete chrysosporium: Implications for the catalytic mechanism

Manganese peroxidase (MnP) is an extracellular heme enzyme produced by the lignin-degrading white-rot fungus Phanerochaete chrysosporium. MnP catalyzes the peroxide-dependent oxidation of Mn^II to Mn^III. The Mn^III is released from the enzyme in complex with oxalate, enabling the oxalate-Mn^III complex to serve as a diffusible redox mediator capable of oxidizing lignin, especially under the mediation of unsaturated fatty acids. One heme propionate and the side chains of Glu35, Glu39 and Asp179 have been identified as Mn^II ligands in our previous crystal structures of native MnP. In our current work, new 0.93 Å and 1.05 Å crystal structures of MnP with and without bound Mn^II, respectively, have been solved. This represents only the sixth structure of a protein of this size at 0.93 Å resolution. In addition, this is the first structure of a heme peroxidase from a eukaryotic organism at sub-Ångstrom resolution. These new structures reveal an ordering/disordering of the C-terminal loop, which is likely required for Mn binding and release. In addition, the catalytic Arg42 residue at the active site, normally thought to function only in the peroxide activation process, also undergoes ordering/disordering that is coupled to a transient H-bond with the Mn ligand, Glu39. Finally, these high-resolution structures also reveal the exact H atoms in several parts of the structure that are relevant to the catalytic mechanism.     

Similarities between a predicted secondary structure for the M1 RNA ribozyme and the tRNA binding center of 16 S rRNA from E. coli

We propose a new model for the secondary structure of the M1 RNA component of E. coli RNase P which is based on significant sequence homologies with parts of the E. coli 16 S rRNA. A large domain of the new model resembles closely the secondary structure of the tRNA binding center of 16 S rRNA. We suggest that this domain of M1 RNA when functioning as a ribozyme binds the mature part of the precursor tRNA.     

Zinc complexes of 6-methyl-2-pyridinecarboxylic acid. Crystal structure of [Zn(MeC5H3NCOO)2(H2O)] · H2O

Reaction of Zn(AcO)₂ · 2H₂O with 6-methyl-2-pyridinecarboxylic acid (L) yielded a new compound [Zn(MeC₅H₃NCOO)₂(H₂O)] · H₂O. This complex was characterised by elemental analyses, conductivity measurements, infrared, ¹H and ¹³C{¹H} NMR spectroscopies and single-crystal X-ray diffraction. The crystal structure consists of discrete molecules involving a pentacoordinated Zn atom with a geometry intermediate between a trigonal bipyramid and a square pyramid and with the two N_py atoms occupying the apical sites. Treatment of the complex [Zn(MeC₅H₃NCOO)₂(H₂O)] · H₂O with 2,2^′-bipyridine (bpy) produced [Zn(MeC₅H₃NCOO)₂(bpy)]. The metallic atom in this complex displays a distorted octahedral geometry and is coordinated to two ligands (L) via the pyridine nitrogen and the carbonyl oxygen atoms and to one 2,2^′-bypyridine (bpy).     

Syntheses, spectroscopic and structural characterization of some (solvated) binuclear adducts of the form Ag(oxyanion):dpem(:S) (1:1(:x))2 (oxyanion = ClO4, F3CCO2, F3CSO3; dpem = Ph2E(CH2)EPh2 (E = P, As))

Syntheses, spectroscopic (IR, NMR and ESI MS) and single crystal X-ray structural characterizations are reported for a wide variety of adducts of Ag(oxyanion):dpem(:S) (1:1(:n))₂ (oxyanion = ClO₄, F₃CCO₂ (tfa) F₃CSO₃ (tfs); dpem = Ph₂E(CH₂)EPh₂) stoichiometry among which the basic Ag(Ph₂E(CH₂)EPh₂)₂Ag core is diversely perturbed by interactions with anions and solvent molecules. ESI MS and ³¹P NMR spectroscopy indicated that dinuclear species also exist in solution.     

A structural investigation of complex I and I + III2 supercomplex from Zea mays at 11-13 Å resolution: Assignment of the carbonic anhydrase domain and evidence for structural heterogeneity within complex I

The projection structures of complex I and the I + III₂ supercomplex from the C₄ plant Zea mays were determined by electron microscopy and single particle image analysis to a resolution of up to 11 Å. Maize complex I has a typical L-shape. Additionally, it has a large hydrophilic extra-domain attached to the centre of the membrane arm on its matrix-exposed side, which previously was described for Arabidopsis and which was reported to include carbonic anhydrase subunits. A comparison with the X-ray structure of homotrimeric γ-carbonic anhydrase from the archaebacterium Methanosarcina thermophila indicates that this domain is also composed of a trimer. Mass spectrometry analyses allowed to identify two different carbonic anhydrase isoforms, suggesting that the γ-carbonic anhydrase domain of maize complex I most likely is a heterotrimer. Statistical analysis indicates that the maize complex I structure is heterogeneous: a less-abundant “type II” particle has a 15 Å shorter membrane arm and an additional small protrusion on the intermembrane-side of the membrane arm if compared to the more abundant “type I” particle. The I + III₂ supercomplex was found to be a rigid structure which did not break down into subcomplexes at the interface between the hydrophilic and the hydrophobic arms of complex I. The complex I moiety of the supercomplex appears to be only of “type I”. This would mean that the “type II” particles are not involved in the supercomplex formation and, hence, could have a different physiological role.     

Square-planar copper(II) complexes with tetradentate amido-carboxylate ligands. Crystal structure of Na2[Cu(obap)]2 · 2H2O. Strain analysis and spectral assignments of complexes

Novel N-N-N-O-type of tetradentate ligands H₃obap (H₃obap = oxamido-N-aminopropyl-N′-benzoic acid) and H₃maeb (H₃maeb = malamido-N-aminoethyl-N′-benzoic acid) and the corresponding square-planar copper(II) complexes have been prepared and characterized. The obap³⁻ and maeb³⁻ ligands coordinate to the copper(II) ion via four ligating atoms (three deprotonated atoms: one carboxylate oxygen and two deprotonated amide nitrogens; one amine nitrogen) with in-plane square chelation. A four coordinate, square-planar geometry has been established crystallographically for the binuclear Na₂[Cu(obap)]₂ · 2H₂O complex. Structural data correlating the square-planar geometry of the [Cu(obap)]⁻ unit and an extensive strain analysis are discussed in relation to the information obtained for similar complexes. The infrared and electronic absorption spectra of the complexes are discussed in comparison to the related complexes of known geometries. Antibacterial activity of ligands and copper(II) complexes towards common Gram-negative and Gram-positive bacteria are reported as well.     

Syntheses, electrolytic behaviour and antifungal activities of Zn(II) complexes of isomers of 3,10-C-meso-3,5,7,7,10,12,14,14-octamethyl-1,4,8,11-tetraazacyclotetradecane (L). Crystal and molecular structure of [ZnLB(NO3)]NO3 (LB = a,e,a,e-L)

The isomeric cyclam ligands Me₈[14]anes, designated by L_A, L_B and L_C, produce, on reaction with zinc(II)nitrate, zinc(II)sulphate or zinc(II)chloride corresponding complexes, i.e. dinitrato/mononitrato-nitrate complexes [ZnL(NO₃)₂]/[ZnL(NO₃)](NO₃) (L = L_A, L_B or L_C, where the indices A, B and C refer to differing orientations of the four methyl groups on secondary carbons of Me₈[14]ane)_, the diaqua-sulphates [ZnL(H₂O)₂]SO₄ (L = L_A, L_B or L_C), and the diaqua dichloride and dichlorido complexes [ZnL(H₂O)₂]Cl₂ (L = L_A or L_C) or [ZnL_BCl₂], respectively. The complexes have been characterised on the basis of elemental analyses, IR, UV-Vis, ¹H and ¹³C NMR spectroscopies, magnetic and conductance data. The structure of [ZnL_B(NO₃)](NO₃) has been determined by X-ray crystallography. The zinc centre is coordinated to a N₄O donor set in a square-pyramidal geometry. The complexes show differing electrolytic behaviour in different solvents. In chloroform, the complexes are non-electrolytes, indicating that both anions are coordinated to Zn²⁺. Antifungal activity of the ligands and complexes against the phytopathogenic fungi Alternaria alternata and Colletotrichum corcolei have been investigated, and positive results were noted.     

Towards absolute asymmetric synthesis. Synthesis and crystal structure of stereochemically labile MCl2 (M = Co, Ni, Cu, Zn) complexes with diamine ligands

In search for new conglomerates, seven stereochemically labile complexes between MCl₂ (M = Co, Cu, Ni, Zn) and bidentate ligands, the commercially available N,N,N′-trimethylethane-1,2-diamine (trimeda) and the somewhat bulkier N-isopropyl-N,N′,N′-trimethylethane-1,2-diamine (itmeda), have been synthesized and characterized using single crystal X-ray diffraction. The trimeda and itmeda ligands exhibit chirogenic nitrogen centers and may form chiral metal complexes that are candidates for total spontaneous resolution. Copper(II) chloride forms the dimeric meso complexes [{CuCl₂(trimeda)}₂] (1) and [{CuCl₂(itmeda)}₂] (2), while [CoCl₂(trimeda)₂] (3) and [NiCl₂(trimeda)₂] (4) exhibit six-coordinate but chiral (R,R)- and (S,S)-complexes. Three examples of the chiral target complex, comprising four-coordinate stereochemically labile monomers, was successfully prepared, viz. [NiCl₂(itmeda)] (5), [ZnCl₂(itmeda)] (6), and [CoCl₂(itmeda)] (7).In all seven complexes, the λ-conformation of the five-membered trimeda-metal chelate ring corresponds to the (S)-configuration at nitrogen, and vice versa. Supramolecular interactions in 3 and 4 form hydrogen-bonded heterochiral ribbons. However, crystals of 5-7 display homochiral interactions resulting in polar phases. Weak CH-Cl interactions in 5 and 6 form homochiral layers. In 7, interactions form homochiral helices along the a-axis.