The crystal structure of uncomplexed-hydrated cyclooctaamylose

Cyclooctaamylose crystallizes from aqueous solution with space-group symmetry P2₁ and lattice parameters: $\text{a}\text{= 20.253(8),}\text{b}\text{= 10.494(5),}\text{c}\text{= 16.892(6)}$ A and β = 105.32(1)^o, Z = 2; the apparent formular per asymmetric unit is C₄₈H₈₀O₄₀·17H₂O. The macrocycle is in an open conformation but displays significant deviations from ideal eight fold molecular symmetry. Of the 19 water molecules thus far located, four of which have occupancy factors of one half, 12 may be characterized as being in the torus of the cycloamylose.     

The crystal structure of Afc-containing peptides

A systematic structural analysis of Afc (9-amino-fluorene-9-carboxylic acid) containing peptides is here reported. The crystal structures of four fully protected tripeptides containing the Afc residue in position 2: Z-X(1)-Afc(2)-Y(3)-OMe (peptide a: X = Y = Gly; peptide b: X = Aib, C(alpha, alpha)-dimethylglycine, Y = Gly; peptide c: X = Gly, Y = Aib; peptide d: X = Y = Aib) have been solved by x-ray crystallography. All the results suggest that the Afc residue has a high propensity to assume an extended conformation. In fact, the Afc residue adopts an extended conformation in three peptides examined in this paper (peptides a-c). In contrast, Afc was found in a folded conformation, in the 3(10)-helical region, only in the peptide d, in which it is both preceded and followed by the strong helix promoting Aib.     

The crystal structure of UUCG tetraloop

All large structured RNAs contain hairpin motifs made of a stem closed by several looped nucleotides. The most frequent loop motif is the UUCG one. This motif belongs to the tetraloop family and has the peculiarity of being highly thermodynamically stable. Here, we report the first crystal structure of two UUCG tetraloops embedded in a larger RNA-protein complex solved at 2.8 A resolution. The two loops present in the asymmetric unit are in a different crystal packing environment but, nevertheless, have an identical conformation. The observed structure is globally close to that obtained in solution by nuclear magnetic resonance. However, subtle differences point to a more detailed picture of the role played by 2'-hydroxyl groups in stabilising this tetraloop.     

漆酶结构的研究进展

漆酶是一种含铜的多酚氧化酶,具有特异的氧化还原电位,能够催化氧化酚类和芳胺类化合物,同时伴随4个电子的传递,最终将O2还原成水。本文就近年来漆酶的结构及其特性的研究进展做扼要综述。     

The crystal structure of cholesteryl 17-bromoheptadecanoate

Crystals of cholesteryl-17-bromoheptadecanoate (C₄₄H₇₇BrO₂) are monoclinic (P2₁) with a = 7.663(2), b = 10.311(5), c = 55.96(2) A and β = 103.10(3°). These are two molecules in the asymmetric unit which have different conformations of the cholesterol side chain and about the ester bond. The molecules pack with regions of only steroid skeleta alternating with regions of hydrocarbon chains. Due to the packing requirements of the skeleta the carbon chains are forced into a hybrid type packing which contains features of the earlier known O⊥ and T∥ subcells. The subcell (HS1) is orthorhombic with a_s = 10.3, b_s = 7.5 and c_s = 2.54A. The molecular packing is such that the ω-bromine atoms do not continue the trans-carbon chains but adopt a gauche conformation.     

The crystal structure of diazomethyl beta-D-galactopyranosyl ketone

The title compound (C8H12N2O6) crystallizes in the orthorhombic space group P2(1)2(1)2(1) (Z = 4), with a = 4.871(1), b = 11.136(2), c = 18.301(2) A. The structure was solved by the multi-solution technique and refined by full-matrix least-squares to a final R-index of 0.042. The compound adopts the 4C1(D) conformation. Bond lengths in the diazoacetyl group are consistent with the presence of a zwitterion.     

The crystal structure of a Dcp-containing peptide

We have investigated the conformational preferences of a newly synthesized C(alpha,alpha) symmetrically disubstituted glycine, namely alpha,alpha-dicyclopropylglycine (Dcp). We report here the crystal structure of a fully protected dipeptide containing Dcp, namely Z-Dcp(1)-Dcp(2)-OCH(3). Both Dcp residues are in a folded conformation. The overall peptide structural organization corresponds to an alpha-pleated sheet conformation, similar to that observed in linear peptides made up of alternating D- and L-residues and in Z-Aib-Aib-OCH(3) (Aib: alpha,alpha-dimethylglycine). These preliminary data suggest that the Dcp could represent an alternative as molecular tool to stabilize folded conformations.     

The structure of a centrosymmetric protein crystal

Crystals of racemic rubredoxin, prepared by independent chemical synthesis of the two enantiomers, have been grown and characterized. The unit cell contains two molecules, one of each enantiomer. Examination of the intensity distribution in the diffraction pattern revealed that the crystals are centrosymmetric. This was confirmed by solution of thestructure to 2 Å resolution via molecular replacement methods. The electron density maps are of very high quality due to the fact that the phaseof each reflection must be exactly 0° or exactly 180°. These results demonstrate the feasibility of using synthetic racemic proteins to yield centrosymmetric protein crystals with electron density maps that have very low phase error and model bias. © 1993 Wiley-Liss, Inc.     

The crystal structure of cholesteryl dihydrogen phosphate

Crystals of cholesteryl dihydrogen phosphate grown from 1,4-dioxane solution are monoclinic, space group C2 with $\text{a = 24.40, b = 6.27, c = 40.86}\text{A}\text{?}\text{and}\text{β = 102.7°}$. The asymmetric unit contains two molecules of cholesteryl phosphate CP and one dioxane molecule of the solvent. The CP molecules pack tail to tail in a bilayer structure. Within the layer they are arranged in double rows with their phosphate groups linked to ribbons by hydrogen bonds. Laterally the double strands of phosphate groups are separated by rows of dioxane molecules. The dioxane serves as hydrogen bond acceptor and as a spacer molecule that compensates the differences in cross-sectional area of the cholesteryl residue (38.4 Ų and the phosphate group (24 Ų). In the cholesterol matrix the CP molecules joined to double rows have packing contact with the smooth side of their skeleta and interdigitate with their annular methyl groups with those of molecules of the adjacent double rows. The branched cholesteryl side chains facing the bilayer center are loosely packed and show considerable disorder and/or thermal motion.     

The 2.0 A crystal structure of cephalosporin acylase

BACKGROUND: Semisynthetic cephalosporins are primarily synthesized from 7-aminocephalosporanic acid (7-ACA), which is usually obtained by chemical deacylation of cephalosporin C (CPC). The chemical production of 7-ACA includes, however, several expensive steps and requires thorough treatment of chemical wastes. Therefore, an enzymatic conversion of CPC to 7-ACA by cephalosporin acylase is of great interest. The biggest obstacle preventing this in industrial production is that cephalosporin acylase uses glutaryl-7ACA as a primary substrate and has low substrate specificity for CPC. RESULTS: We have solved the first crystal structure of a cephalosporin acylase from Pseudomonas diminuta at 2.0 A resolution. The overall structure looks like a bowl with two "knobs" consisting of helix- and strand-rich regions, respectively. The active site is mostly formed by the distinctive structural motif of the N-terminal (Ntn) hydrolase superfamily. Superposition of the 61 residue active-site pocket onto that of penicillin G acylase shows an rmsd in Calpha positions of 1.38 A. This indicates structural similarity in the active site between these two enzymes, but their overall structures are elsewhere quite different. CONCLUSION: The substrate binding pocket of the P. diminuta cephalosporin acylase provides detailed insight into the ten key residues responsible for the specificity of the cephalosporin C side chain in four classes of cephalosporin acylases, and it thereby forms a basis for the design of an enzyme with an improved conversion rate of CPC to 7-ACA. The structure also provides structural evidence that four of the five different classes of cephalosporin acylases can be grouped into one family of the Ntn hydrolase superfamily.     

The crystal structure of lithium L-ascorbate dihydrate.

The crystal structure of lithium L-ascorbate dihydrate is triclinic, Pl; with a = 5.964(9), b = 5.299(9), c = 7.760(15) A; alpha = 100.82(9), beta = 109.78(9), gamma = 92.02(9) degrees. The plant fragment of the ascorbate anion is a part of the five-membered ring [C-1,C-2,C-3(O-3),C-4], and O-4 deviates by 0.053(2) A from this plane. Deprotonated O-3 is an acceptor of three hydrogen bonds, but does not interact with Li+. The coordination number of the Li+ is 5 and it is bonded to two water molecules and three hydroxyl oxygen atoms of two ascorbate anions: O-2 and the gauche O-5, 6 of the side chain.     

The crystal structure of yeast thiamin pyrophosphokinase.

BACKGROUND: Thiamin pyrophosphokinase (TPK) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. TPK has no sequence homologs in the PDB and functions by an unknown mechanism. The TPK structure has been determined as a significant step toward elucidating its catalytic action. RESULTS: The crystal structure of Saccharomyces cerevisiae TPK complexed with thiamin has been determined at 1.8 A resolution. TPK is a homodimer, and each subunit consists of two domains. One domain resembles a Rossman fold with four alpha helices on each side of a 6 strand parallel beta sheet. The other domain has one 4 strand and one 6 strand antiparallel beta sheet, which form a flattened sandwich structure containing a jelly-roll topology. The active site is located in a cleft at the dimer interface and is formed from residues from domains of both subunits. The TPK dimer contains two compound active sites at the subunit interface. CONCLUSIONS: The structure of TPK with one substrate bound identifies the location of the thiamin binding site and probable catalytic residues. The structure also suggests a likely binding site for ATP. These findings are further supported by TPK sequence homologies. Although possessing no significant sequence homology with other pyrophospokinases, thiamin pyrophosphokinase may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.     

The crystal structure of prokaryotic phospholipase A2

In this study, the x-ray crystal structures of the calcium-free and calcium-bound forms of phospholipase A(2) (PLA(2)), produced extracellularly by Streptomyces violaceoruber, were determined by using the multiple isomorphous replacement and molecular replacement methods, respectively. The former and latter structures were refined to an R-factor of 18.8% at a 1.4-A resolution and an R-factor of 15.0% at a 1.6-A resolution, respectively. The overall structure of the prokaryotic PLA(2) exhibits a novel folding topology that demonstrates that it is completely distinct from those of eukaryotic PLA(2)s, which have been already determined by x-ray and NMR analyses. Furthermore, the coordination geometry of the calcium(II) ion apparently deviated from that of eukaryotic PLA(2)s. Regardless of the evolutionary divergence, the catalytic mechanism including the calcium(II) ion on secreted PLA(2) seems to be conserved between prokaryotic and eukaryotic cells. Demonstrating that the overall structure determined by x-ray analysis is almost the same as that determined by NMR analysis is useful to discuss the catalytic mechanism at the molecular level of the bacterial PLA(2).     

The first crystal structure of a phospholipase D

BACKGROUND: The phospholipase D (PLD) superfamily includes enzymes that are involved in phospholipid metabolism, nucleases, toxins and virus envelope proteins of unknown function. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. PLD also catalyses a transphosphatidylation reaction in the presence of phosphatidylcholine and a short-chained primary or secondary alcohol. RESULTS: The first crystal structure of a 54 kDa PLD has been determined to 1.9 A resolution using the multiwavelength anomalous dispersion (MAD) method on a single WO(4) ion and refined to 1.4 A resolution. PLD from the bacterial source Streptomyces sp. strain PMF consists of a single polypeptide chain that is folded into two domains. An active site is located at the interface between these domains. The presented structure supports the proposed superfamily relationship with the published structure of the 16 kDa endonuclease from Salmonella typhimurium. CONCLUSIONS: The structure of PLD provides insight into the structure and mode of action of not only bacterial, plant and mammalian PLDs, but also of a variety of enzymes as diverse as cardiolipin synthases, phosphatidylserine synthases, toxins, endonucleases, as well as poxvirus envelope proteins having a so far unknown function. The common features of these enzymes are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.     

The crystal structure of Pichia pastoris lysyl oxidase

Pichia pastoris lysyl oxidase (PPLO) is unique among the structurally characterized copper amine oxidases in being able to oxidize the side chain of lysine residues in polypeptides. Remarkably, the yeast PPLO is nearly as effective in oxidizing a mammalian tropoelastin substrate as is a true mammalian lysyl oxidase isolated from bovine aorta. Thus, PPLO is functionally related to the copper-containing lysyl oxidases despite the lack of any significant sequence similarity with these enzymes. The structure of PPLO has been determined at 1.65 A resolution. PPLO is a homodimer in which each subunit contains a Type II copper atom and a topaquinone cofactor (TPQ) formed by the posttranslational modification of a tyrosine residue. While PPLO has tertiary and quaternary topologies similar to those found in other quinone-containing copper amine oxidases, its active site is substantially more exposed and accessible. The structural elements that are responsible for the accessibility of the active site are identified and discussed.     

The X-ray crystal structure of full-length human plasminogen

Plasminogen is the proenzyme precursor of the primary fibrinolytic protease plasmin. Circulating plasminogen, which comprises a Pan-apple (PAp) domain, five kringle domains (KR1-5), and a serine protease (SP) domain, adopts a closed, activation-resistant conformation. The kringle domains mediate interactions with fibrin clots and cell-surface receptors. These interactions trigger plasminogen to adopt an open form that can be cleaved and converted to plasmin by tissue-type and urokinase-type plasminogen activators. Here, the structure of closed plasminogen reveals that the PAp and SP domains, together with chloride ions, maintain the closed conformation through interactions with the kringle array. Differences in glycosylation alter the position of KR3, although in all structures the loop cleaved by plasminogen activators is inaccessible. The ligand-binding site of KR1 is exposed and likely governs proenzyme recruitment to targets. Furthermore, analysis of our structure suggests that KR5 peeling away from the PAp domain may initiate plasminogen conformational change.