Non-crystallographic Twofold Axis Research Articles

Structural insights revealed by crystal structure of B38-CAP, an isoenzyme of carboxypeptidase ACE2, the receptor of SARS-CoV-2

The worldwide pandemic of Coronavirus disease 2019 (COVID-19) is triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and further worsened by the emergence of a variety of SARS-CoV-2 variants. Angiotensin-converting enzyme 2 (ACE2), a carboxypeptidase of M32 family, serves as the receptor of SARS-CoV-2 and key regulator of host renin-angiotensin system (RAS), both of which are mainly mediated via the carboxypeptidase domain of ACE2 (sACE2) or its activity. sACE2 is thus promising in the treatment of COVID-19 but unfortunately weakened by its unstrigent substrate preference and complex interplay with host RAS. B38-CAP, an isoenzyme of ACE2, partically compensates these defects but still encounters the problem related to carboxypeptidase activity and specificity. In this study, we firstly determined the crystal structure of B38-CAP at a resolution of 2.44 Å which exists in dimeric form with the non-crystallographic two-fold axis being in coincidence with the crystallographic two-fold axis. Further structural analysis revealed the structural conservatism feature among M32 family, particularly the catalytic core and moreover lead us to hypothesize that conformational flexibility might play an pivotal role in the catalysis of B38-CAP and ACE2. The work provided here presents key features of the M32 family carboxypeptidase and provides structural basis for further development of B38-CAP-based anti-SARS-CoV-2 drugs.

Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase)

The structures of Aspergillus oryzae α-amylase were determined in a tetragonal crystal, having one molecule as asymmetric unit, and a monoclinic crystal with two molecules as asymmetric unit. Both crystal forms were obtained from trace contaminants of an old commercial lipase preparation. Structures were determined and refined to 1.65Å and 1.43Å resolution respectively. The latter crystal has a non-crystallographic (NCS) twofold axis within the asymmetric unit. Glycosylation at Asn197 is evident, and in the tetragonal crystal can be seen to include three, partially disordered sugar residues following the initial N-acetyl glucosamine (NAG). Superposition of the tetragonal crystal model on the α-amylases from Bacillus subtilis (PDB:1BAG), pig pancreas (PDB:3L2L), and barley (PDB:1AMY), show a high degree of coincidence, particularly for the (β/α)8-barrel domains, and especially within the active site. Using this structural agreement between amylases, we extrapolated the binding model of a six residue, limit dextrin found in pig pancreas α-amylase to the A.oryzae enzyme model, which predicts substrate interacting amino acid residues.

The third structural switch in the archaeal translation initiation factor 2 (aIF2) molecule and its possible role in the initiation of GTP hydrolysis and the removal of aIF2 from the ribosome.

The structure of the γ subunit of archaeal translation initiation factor 2 (aIF2) from Sulfolobus solfataricus (SsoIF2γ) was determined in complex with GDPCP (a GTP analog). Crystals were obtained in the absence of magnesium ions in the crystallization solution. They belonged to space group P1, with five molecules in the unit cell. Four of these molecules are related in pairs by a common noncrystallographic twofold symmetry axis, while the fifth has no symmetry equivalent. Analysis of the structure and its comparison with other known aIF2 γ-subunit structures in the GTP-bound state show that (i) the magnesium ion is necessary for the formation and the maintenance of the active form of SsoIF2γ and (ii) in addition to the two previously known structural switches 1 and 2, eukaryotic translation initiation factor 2 (eIF2) and aIF2 molecules have another flexible region (switch 3), the function of which may consist of initiation of the hydrolysis of GTP and the removal of e/aIF2 from the ribosome after codon-anticodon recognition.

Crystal structure of the starch-binding domain of glucoamylase from Aspergillus niger.

Glucoamylases are widely used commercially to produce glucose syrup from starch. The starch-binding domain (SBD) of glucoamylase from Aspergillus niger is a small globular protein containing a disulfide bond. The structure of A. niger SBD has been determined by NMR, but the conformation surrounding the disulfide bond was unclear. Therefore, X-ray crystal structural analysis was used to attempt to clarify the conformation of this region. The SBD was purified from an Escherichia coli-based expression system and crystallized at 293 K. The initial phase was determined by the molecular-replacement method, and the asymmetric unit of the crystal contained four protomers, two of which were related by a noncrystallographic twofold axis. Finally, the structure was solved at 2.0 Å resolution. The SBD consisted of seven β-strands and eight loops, and the conformation surrounding the disulfide bond was determined from a clear electron-density map. Comparison of X-ray- and NMR-determined structures of the free SBD showed no significant difference in the conformation of each β-strand, but the conformations of the loops containing the disulfide bond and the L5 loop were different. In particular, the difference in the position of the Cα atom of Cys509 between the X-ray- and NMR-determined structures was 13.3 Å. In addition, the B factors of the amino-acid residues surrounding the disulfide bond are higher than those of other residues. Therefore, the conformation surrounding the disulfide bond is suggested to be highly flexible.

Crystal structure of {2-[({2-[(2-amino-ethyl)amino]-ethyl}imino)-meth-yl]-6-hy-droxy-phenolato-κ(4) N,N',N'',O (1)}(nitrato-κO)copper(II) ethanol 0.25-solvate.

In the crystal structure of the title mononuclear CuII complex, [Cu(C11H16N3O2)(NO3)]·0.25C2H5OH, the complex molecules are linked by N—H⋯O and O—H⋯O hydrogen bonds, forming a dimer with an approximate non-crystallographic twofold rotation axis of symmetry. In the monomeric unit, the Cu2+ ion exhibits a distorted square-pyramidal configuration, whereby the anionic [HL]− Schiff base ligand binds in a tetradentate fashion via the O and the three N atoms which all are approximately coplanar. The O atom of a nitrate anion occupies the fifth coordination site, causing the CuII atom to move slightly out of the approximate basal plane toward the bound nitrate group. The structure exhibits disorder of the ethanol solvent mol­ecule.

A novel NAD(P)H-dependent carbonyl reductase specifically expressed in the thyroidectomized chicken fatty liver: catalytic properties and crystal structure.

A gene encoding a functionally unknown protein that is specifically expressed in the thyroidectomized chicken fatty liver and has a predicted amino acid sequence similar to that of NAD(P)H-dependent carbonyl reductase was overexpressed in Escherichia coli; its product was purified and characterized. The expressed enzyme was an NAD(P)H-dependent broad substrate specificity carbonyl reductase and was inhibited by arachidonic acid at 1.5 μm. Enzymological characterization indicated that the enzyme could be classified as a cytosolic-type carbonyl reductase. The enzyme's 3D structure was determined using the molecular replacement method at 1.98 Å resolution in the presence of NADPH and ethylene glycol. The asymmetric unit consisted of two subunits, and a noncrystallographic twofold axis generated the functional dimer. The structures of the subunits, A and B, differed from each other. In subunit A, the active site contained an ethylene glycol molecule absent in subunit B. Consequently, Tyr172 in subunit A rotated by 103.7° in comparison with subunit B, which leads to active site closure in subunit A. In Y172A mutant, the Km value for 9,10-phenanthrenequinone (model substrate) was 12.5 times higher than that for the wild-type enzyme, indicating that Tyr172 plays a key role in substrate binding in this carbonyl reductase. Because the Tyr172-containing active site lid structure (Ile164-Gln174) is not conserved in all known carbonyl reductases, our results provide new insights into substrate binding of carbonyl reductase. The catalytic properties and crystal structure revealed that thyroidectomized chicken fatty liver carbonyl reductase is a novel enzyme.

Three-dimensional structure of the human breast cancer resistance protein (BCRP/ABCG2) in an inward-facing conformation.

ABCG2 is an efflux drug transporter that plays an important role in drug resistance and drug disposition. In this study, the first three-dimensional structure of human full-length ABCG2 analysed by electron crystallography from two-dimensional crystals in the absence of nucleotides and transported substrates is reported at 2 nm resolution. In this state, ABCG2 forms a symmetric homodimer with a noncrystallographic twofold axis perpendicular to the two-dimensional crystal plane, as confirmed by subtomogram averaging. This configuration suggests an inward-facing configuration similar to murine ABCB1, with the nucleotide-binding domains (NBDs) widely separated from each other. In the three-dimensional map, densities representing the long cytoplasmic extensions from the transmembrane domains that connect the NBDs are clearly visible. The structural data have allowed the atomic model of ABCG2 to be refined, in which the two arms of the V-shaped ABCG2 homodimeric complex are in a more closed and narrower conformation. The structural data and the refined model of ABCG2 are compatible with the biochemical analysis of the previously published mutagenesis studies, providing novel insight into the structure and function of the transporter.

High-resolution crystal structures of alternate forms of the human CD44 hyaluronan-binding domain reveal a site for protein interaction.

Two new crystal structures of the extracellular hyaluronan-binding domain of human CD44 are described at high resolution. A hexagonal crystal form at 1.60 Å resolution and a monoclinic form at 1.08 Å resolution both have two molecules in the asymmetric unit arranged about a similar noncrystallographic twofold axis of symmetry. These structures are compared with those previously reported at 2.20 Å resolution to show that the fold is quite resistant to structural deformation in different crystal environments. Unexpectedly, a short peptide is found in the monoclinic crystals at a site remote from the known hyaluronan-binding groove. The peptide with a valine at the carboxy-terminus must have co-purified from the bacterial expression host and binds on the opposite side of the domain from the known hyaluronan-binding groove. This opportunistic binding may identify a site of interaction used as CD44 assembles with other proteins to accomplish effective signaling regarding changes to the extracellular environment.

A low-temperature modification of hexa-tert-butyldisilane and a new polymorph of 1,1,2,2-tetra-tert-butyl-1,2-diphenyldisilane.

Crystals of hexa-tert-butyldisilane, C24H54Si2, undergo a reversible phase transition at 179 (2) K. The space group changes from Ibca (high temperature) to Pbca (low temperature), but the lattice constants a, b and c do not change significantly during the phase transition. The crystallographic twofold axis of the molecule in the high-temperature phase is replaced by a noncrystallographic twofold axis in the low-temperature phase. The angle between the two axes is 2.36 (4)°. The centre of the molecule undergoes a translation of 0.123 (1) Å during the phase transition, but the conformation angles of the molecule remain unchanged. Between the two tri-tert-butylsilyl subunits there are six short repulsive intramolecular C-H···H-C contacts, with H···H distances between 2.02 and 2.04 Å, resulting in a significant lengthening of the Si-Si and Si-C bonds. The Si-Si bond length is 2.6863 (5) Å and the Si-C bond lengths are between 1.9860 (14) and 1.9933 (14) Å. Torsion angles about the Si-Si and Si-C bonds deviate by approximately 15° from the values expected for staggered conformations due to intramolecular steric H···H repulsions. A new polymorph is reported for the crystal structure of 1,1,2,2-tetra-tert-butyl-1,2-diphenyldisilane, C28H46Si2. It has two independent molecules with rather similar conformations. The Si-Si bond lengths are 2.4869 (8) and 2.4944 (8) Å. The C-Si-Si-C torsion angles deviate by between -3.4 (1) and -18.5 (1)° from the values expected for a staggered conformation. These deviations result from steric interactions. Four Si-C(t-Bu) bonds are almost staggered, while the other four Si-C(t-Bu) bonds are intermediate between a staggered and an eclipsed conformation. The latter Si-C(t-Bu) bonds are about 0.019 (2) Å longer than the staggered Si-C(t-Bu) bonds.

Crystallization and preliminary X-ray crystallographic analysis of the small subunit of the heterodimeric laccase POXA3b from Pleurotus ostreatus.

Laccases are multicopper oxidases of great biotechnological potential. While laccases are generally monomeric glycoproteins, the white-rot fungus Pleurotus ostreatus produces two closely related heterodimeric isoenzymes composed of a large subunit, homologous to the other fungal laccases, and a small subunit. The sequence of the small subunit does not show significant homology to any other protein or domain of known function and consequently its function is unknown. The highest similarity to proteins of known structure is to a putative enoyl-CoA hydratase/isomerase from Acinetobacter baumannii, which shows an identity of 27.8%. Diffraction-quality crystals of the small subunit of the heterodimeric laccase POXA3b (sPOXA3b) from P. ostreatus were obtained using the sitting-drop vapour-diffusion method at 294 K from a solution consisting of 1.8 M sodium formate, 0.1 M Tris-HCl pH 8.5. The crystals belonged to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = 126.6, c = 53.9 Å. The asymmetric unit contains two molecules related by a noncrystallographic twofold axis. A complete data set extending to a maximum resolution of 2.5 Å was collected at 100 K using a wavelength of 1.140 Å.

Expression, purification, crystallization and X-ray crystallographic studies of different redox states of the active site of thioredoxin 1 from the whiteleg shrimp Litopenaeus vannamei.

Thioredoxin (Trx) is a 12 kDa cellular redox protein that belongs to a family of small redox proteins which undergo reversible oxidation to produce a cystine disulfide bond through the transfer of reducing equivalents from the catalytic site cysteine residues (Cys32 and Cys35) to a disulfide substrate. In this study, crystals of thioredoxin 1 from the Pacific whiteleg shrimp Litopenaeus vannamei (LvTrx) were successfully obtained. One data set was collected from each of four crystals at 100 K and the three-dimensional structures of the catalytic cysteines in different redox states were determined: reduced and oxidized forms at 2.00 Å resolution using data collected at a synchrotron-radiation source and two partially reduced structures at 1.54 and 1.88 Å resolution using data collected using an in-house source. All of the crystals belonged to space group P3212, with unit-cell parameters a = 57.5 (4), b = 57.5 (4), c = 118.1 (8) Å. The asymmetric unit contains two subunits of LvTrx, with a Matthews coefficient (VM) of 2.31 Å(3) Da(-1) and a solvent content of 46%. Initial phases were determined by molecular replacement using the crystallographic model of Trx from Drosophila melanogaster as a template. In the present work, LvTrx was overexpressed in Escherichia coli, purified and crystallized. Structural analysis of the different redox states at the Trx active site highlights its reactivity and corroborates the existence of a dimer in the crystal. In the crystallographic structures the dimer is stabilized by several interactions, including a disulfide bridge between Cys73 of each LvTrx monomer, a hydrogen bond between the side chain of Asp60 of each monomer and several hydrophobic interactions, with a noncrystallographic twofold axis.

The structural characterization of bacterioferritin, BfrA, from Mycobacterium tuberculosis

Tuberculosis is a deadly disease caused by Mycobacterium tuberculosis. Like most bacterial pathogens, iron acquisition, regulation, and storage are critical for its survival. Due to the poor solubility of iron under physiological conditions, both eukaryotes and prokaryotes possess ferritins, large protein complexes that store iron and keep it bioavailable. Mtb encodes for two ferritin homologs: a heme-containing bacterioferritin (Mtb-BfrA) and a non-heme eukaryotic-like ferritin (Mtb-BfrB). A conserved feature of bacterioferritins is the presence of a heme group at the interface between two subunits of each dimer that is related by a non-crystallographic two-fold axis. The structure of a selenomethionine derivative of Mtb-BfrA was previously reported (PDB ID: 2WTL); however, a proposed heme degradation product was modeled into the heme-binding site, as electron density for intact heme was not observed. Here, the purification and structure determination of recombinant Mtb-BfrA is reported. As-isolated Mtb-BfrA from Escherichia coli is not fully heme loaded. However, the absorption spectrum features suggest binding of intact heme. In an attempt to fully complement Mtb-BfrA with heme, two different methodologies are described. Electronic spectroscopy and structure determination were used to confirm varying amounts of intact bis-methionine coordinated heme to Mtb-BfrA. We also report that increased heme incorporation only slightly increases Mtb-BfrA ferroxidase activity. Finally, the cognate partner of Mtb-BfrA is proposed to be a putative encoded gene which is located approximately 300 bps upstream of Mycobacterium tuberculosisbfrA, homologous to the cognate partner of Pseudomonas aeruginosa bacterioferritin, a 7 kDa ferrodoxin Bfd.

Crystal structure of tandem ACT domain‐containing protein ACTP from Galdieria sulphuraria

The ACT domain is a structurally conserved small molecule binding domain which is mostly involved in amino acid and purine metabolism. Here, we report the crystal structure of a tandem ACT domain-containing protein (ACTP) from Galdieria sulphuraria. The two ACTP monomers in the asymmetric unit form a dimer with a non-crystallographic twofold axis in a domain-swapped manner, showing a horseshoe-like structure with a central crevice. This structure contributes to expand our knowledge on the structural diversity of ACT domain-containing proteins.

1,3-Bis[2-hydroxy-2-(6-methoxy-2,2-dimethyl-3a,5,6,6a-tetrahydro-2H-furo[2,3-d][1,3]dioxol-5-yl)ethyl]-2,3-dihydro-1H-1,3-benzodiazol-2-one

In the title benzimidazolone, C27H38N2O11, which has N-bound glycosidic units, all five-membered O-heterocyclic rings adopt envelope conformations [for the outer rings, the C atom with the dimethyl groups represents the flap atom]. The two glycosidic units are related by a non-crystallographic twofold rotation axis that passes through the carbonyl portion. In the mol­ecular structure, the hy­droxy groups are hydrogen-bond donors to the carbonyl O atom. Weak inter­molecular C—H⋯O hydrogen bonding is present in the crystal structure.

2-{[2-(2-Hydroxy-3-methoxybenzylidene)hydrazin-1-ylidene]methyl}-6-methoxyphenol

The title compound, C16H16N2O4, was obtained from the reaction of hydrazine hydrate and o-vanilin in absolute ethanol. The mol­ecule is almost planar (except for the methyl H atoms), with a mean deviation from the plane of 0.0259 Å. The mol­ecular structure also exhibits an approximate non-crystallographic twofold axis. Intra­molecular O—H⋯N hydrogen bonds occur. In the crystal, inter­molecular C—H⋯O hydrogen bonds generate mol­ecular zigzag sheets. The sheets stack through C—H⋯π inter­actions, leading to a three-dimensional-network.

A novel mechanism of sulfur transfer catalyzed by O-acetylhomoserine sulfhydrylase in the methionine-biosynthetic pathway of Wolinella succinogenes.

O-Acetylhomoserine sulfhydrylase (OAHS) is a pyridoxal 5'-phosphate (PLP) dependent sulfide-utilizing enzyme in the L-cysteine and L-methionine biosynthetic pathways of various enteric bacteria and fungi. OAHS catalyzes the conversion ofO-acetylhomoserine to homocysteine using sulfide in a process known as direct sulfhydrylation. However, the source of the sulfur has not been identified and no structures of OAHS have been reported in the literature. Here, the crystal structure of Wolinella succinogenes OAHS (MetY) determined at 2.2 Å resolution is reported. MetY crystallized in space group C2 with two monomers in the asymmetric unit. Size-exclusion chromatography, dynamic light scattering and crystal packing indicate that the biological unit is a tetramer insolution. This is further supported by the crystal structure, inwhich a tetramer is formed using a combination of noncrystallographic and crystallographic twofold axes. A search for structurally homologous proteins revealed that MetY has the same fold as cystathionine γ-lyase and methionine γ-lyase. The active sites of these enzymes, which are also PLP-dependent, share a high degree of structural similarity, suggesting that MetY belongs to the γ-elimination subclass of the Cys/Met metabolism PLP-dependent family of enzymes. The structure of MetY, together with biochemical data, provides insight into the mechanism of sulfur transfer to a small molecule via a protein thiocarboxylate intermediate.

Lysine Nζ-Decarboxylation Switch and Activation of the β-Lactam Sensor Domain of BlaR1 Protein of Methicillin-resistant Staphylococcus aureus

The integral membrane protein BlaR1 of methicillin-resistant Staphylococcus aureus senses the presence of β-lactam antibiotics in the milieu and transduces the information to the cytoplasm, where the biochemical events that unleash induction of antibiotic resistance mechanisms take place. We report herein by two-dimensional and three-dimensional NMR experiments of the sensor domain of BlaR1 in solution and by determination of an x-ray structure for the apo protein that Lys-392 of the antibiotic-binding site is posttranslationally modified by N(ζ)-carboxylation. Additional crystallographic and NMR data reveal that on acylation of Ser-389 by antibiotics, Lys-392 experiences N(ζ)-decarboxylation. This unique process, termed the lysine N(ζ)-decarboxylation switch, arrests the sensor domain in the activated ("on") state, necessary for signal transduction and all the subsequent biochemical processes. We present structural information on how this receptor activation process takes place, imparting longevity to the antibiotic-receptor complex that is needed for the induction of the antibiotic-resistant phenotype in methicillin-resistant S. aureus.

Bis[(1-methyl-1H-tetrazol-5-yl)sulfanyl]ethane

The title compound, C6H10N8S2, was prepared by the nucleophilic substitution reaction of 5-mercapto-1-methyl­tetra­zole and dichloro­ethane. In the crystal, the mol­ecule possesses an approximate non-crystallographic twofold symmetry axis. The crystal packing is stabilized by weak inter­molecular C—H⋯N and π–π inter­actions [centroid–centroid distances = 3.448 (6), 3.5085 (5) and 3.4591 (2) Å]. The two five-membered rings form a dihedral angle of 1.9 (2)°.

Bis[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methane

The mol­ecule of the title compound, C5H8N8S2, lies on a twofold rotation axis that relates on 1-methyl­tetra­zolyl group to the other; the five-membered rings are twisted by 53.1 (1)°.

Bis(tetraethylammonium) bis(dimethylformamide)tetrakis(μ-N,2-dioxidobenzene-1-carboximidato)pentacopper(II)

The title compound, (C8H20N)2[Cu5(C7H4NO3)4(C3H7NO)2], abbreviated as (TEA)2[CuII(12-MCCuII N(shi)-4](DMF)2 [where TEA is tetra­ethyl­ammonium, shi3− is salicyl­hydroximate (or N,2-dioxidobenzene-1-carboximidate) and DMF is N,N-dimethyl­formamide], contains five CuII ions. Four of the CuII ions are members of a metallacrown ring (MC), while the fifth CuII is bound in a central cavity. Two of the ring CuII ions are five-coordinate with distorted square-pyramidal geometry. The coordination sphere is composed of two shi3− ligands and one DMF mol­ecule. The other two ring CuII ions and the central CuII ion are four-coordinate with square-planar geometry. The coordination spheres of these ions are only composed of shi3− ligands. The charge of the [CuII(12-MCCuII N(shi)-4]2− unit is balanced by two uncoordinated TEA+ countercations. The structure shows severe static disorder with the metallacrown, the tetra­ethyl­ammonium cations and the DMF solvent mol­ecule all disordered over each of two mutually exclusive sites, with occupancy rates for the major moieties of 0.6215 (6) for the metallacrown, 0.759 (3) for the tetra­ethyl­ammonium ion and 0.537 (6) for the DMF mol­ecules. The metallacrown unit is located on a crystallographic inversion center and disordered about a non-crystallographic twofold axis. The DMF mol­ecule and the tetra­ethyl­ammonium ion are disordered about a non-crystallographic twofold axis and pseudo-inversion center, respectively.