J.M. Guss

X-ray crystal structure analysis of plastocyanin at 2.7 Å resolution

The three-dimensional structure of plastocyanin, a ‘blue’ or ‘Type 1’ copper-protein, has been determined at a resolution of 2.7 Å. The copper atom has a highly distorted tetrahedral coordination geometry. It is coordinated by a cysteine thiol group, a methionine thioether group, and two histidine imidazole groups.

Hyaluronic acid: molecular conformations and interactions in two sodium salts.

Abstract A detailed structure for the tetragonal form ( a = b = 0.989 nm, c , fibre axis, = 3.394 nm) of sodium hyaluronate has been obtained by analysing X-ray fibre diffraction data using new molecular modelling techniques. Two polysaccharide chains pass through each unit cell, one at the corner and one at the centre. The chains are anti-parallel to one another. Each chain is a left-handed, 4-fold helix of disaccharide units. There are intramolecular hydrogen bonds stabilising each glycosidic linkage. Octahedrally co-ordinated sodium ions link, by O … Na + … O bridges, neighbouring polysaccharide chains that are further linked by hydrogen bonds. No double-helix model (as originally proposed for this structure) has been found to be free of unacceptable non-bonded contacts or to fit the diffraction intensities as closely. The tetragonal form, which is stable at zero relative humidity, contains no detectable water molecules. At higher relative humidities a related orthorhombic form is observed in which only the a dimension of the lattice is different ( a = 1.153 nm, b = 0.989 nm, c = 3.386 nm). In this form the hyaluronate helix is 2-fold with tetrasaccharide units conformationally similar to the 4-fold helix of the tetragonal form. The Na + … O binding and hydrogen bonds lost on expansion of the tetragonal lattice are all replaced in the orthorhombic structure by bridges through water molecules, four of which associated with each tetrasaccharide.

Hyaluronic Acid: A Novel, Double Helical Molecule

Films prepared from a deformable gel (or putty) of hyaluronic acid show high crystallinity and orientation in their x-ray diffraction patterns. We have derived a probable structure for the molecules in these films. This is a double helix in which two identical, left-handed strands are antiparallel to one another. Each strand has four disaccharide residues per pitch length. Although the putty is prepared at pH 2.5, at which dilute solutions of hyaluronic have exaggerated rheological properties, the double helical form can also exist at physiological pH and therefore may be a biologically important form.

Crystal structure of plastocyanin from a green alga, Enteromorpha prolifera☆

The crystal structure of the Cu-containing protein plastocyanin (Mr 10,500) from the green alga Enteromorpha prolifera has been solved by molecular replacement. The structure was refined by constrained-restrained and restrained reciprocal space least-squares techniques. The refined model includes 111 solvent sites. There is evidence for alternate conformers at eight residues. The residual is 0.12 for a data set comprising 74% of all observations accessible at 1.85 A resolution. The beta-sandwich structure of the algal plastocyanin is effectively the same as that of poplar leaf (Populus nigra var. italica) plastocyanin determined at 1.6 A resolution. The sequence homology between the two proteins is 56%. Differences between the contacts in the hydrophobic core create some significant (0.5 to 1.2 A) movements of the polypeptide backbone, resulting in small differences between the orientations and separations of corresponding beta-strands. These differences are most pronounced at the end of the molecule remote from the Cu site. The largest structural differences occur in the single non-beta strand, which includes the sole turn of helix in the molecule: two of the residues in a prominent kink of the poplar plastocyanin backbone are missing from the algal plastocyanin sequence, and there is a significant change in the position of the helical segment in relation to the beta-sandwich. Several other small but significant structural differences can be correlated with intermolecular contacts in the crystals. An intramolecular carboxyl-carboxylate hydrogen bond in the algal plastocyanin may be associated with an unusually high pKa. The dimensions of the Cu site in the two plastocyanins are, within the limits of precision, identical.

Structure and inhibition of human diamine oxidase

Humans have three functioning genes that encode copper-containing amine oxidases. The product of the AOC1 gene is a so-called diamine oxidase (hDAO), named for its substrate preference for diamines, particularly histamine. hDAO has been cloned and expressed in insect cells and the structure of the native enzyme determined by X-ray crystallography to a resolution of 1.8 A. The homodimeric structure has the archetypal amine oxidase fold. Two active sites, one in each subunit, are characterized by the presence of a copper ion and a topaquinone residue formed by the post-translational modification of a tyrosine. Although hDAO shares 37.9% sequence identity with another human copper amine oxidase, semicarbazide sensitive amine oxidase or vascular adhesion protein-1, its substrate binding pocket and entry channel are distinctly different in accord with the different substrate specificities. The structures of two inhibitor complexes of hDAO, berenil and pentamidine, have been refined to resolutions of 2.1 and 2.2 A, respectively. They bind noncovalently in the active-site channel. The inhibitor binding suggests that an aspartic acid residue, conserved in all diamine oxidases but absent from other amine oxidases, is responsible for the diamine specificity by interacting with the second amino group of preferred diamine substrates.

Structure of N-acetyl-beta-D-glucosaminidase (GcnA) from the Endocarditis Pathogen Streptococcus gordonii and its Complex with the Mechanism-based Inhibitor NAG-thiazoline

The crystal structure of GcnA, an N-acetyl-beta-D-glucosaminidase from Streptococcus gordonii, was solved by multiple wavelength anomalous dispersion phasing using crystals of selenomethionine-substituted protein. GcnA is a homodimer with subunits each comprised of three domains. The structure of the C-terminal alpha-helical domain has not been observed previously and forms a large dimerisation interface. The fold of the N-terminal domain is observed in all structurally related glycosidases although its function is unknown. The central domain has a canonical (beta/alpha)(8) TIM-barrel fold which harbours the active site. The primary sequence and structure of this central domain identifies the enzyme as a family 20 glycosidase. Key residues implicated in catalysis have different conformations in two different crystal forms, which probably represent active and inactive conformations of the enzyme. The catalytic mechanism for this class of glycoside hydrolase, where the substrate rather than the enzyme provides the cleavage-inducing nucleophile, has been confirmed by the structure of GcnA complexed with a putative reaction intermediate analogue, N-acetyl-beta-D-glucosamine-thiazoline. The catalytic mechanism is discussed in light of these and other family 20 structures.

Mucopolysaccharides: Comparison of Chondroitin Sulfate Conformations with Those of Related Polyanions

X-ray diffraction shows that chondroitin 6-sulfate, and some further rulfated derivatives, can occur in two ordered structures in stretched films. Both structures contain single helices with similar projected disaccharide lengths (9.6 and 9.8 angstroms) but with very different turn angles between successive disaccharides (120 and 45 degrees). In contrast, coaxial double helices of hyaluronates and t-carrageenates have shorter projected disaccharide lengths (8.5 and 8.9 angstroms).

Dermatan sulfate and chondroitin 6-sulfate conformations

Abstract X-ray diffraction patterns show that dermatan sulfate in oriented, crystalline films occurs as two or three or eight-fold helices. The two-fold helix has a greater axial rise per disaccharide residue [ h = 9.6 A ] than the corresponding chondroitin 6-sulfate helix [ h = 9.3 A ] . Three-fold dermatan sulfate and chondroitin 6-sulfate helices both have h = 9.5 A . Consequently the α-L-iduronate residues in dermatan sulfate helices have the C1 chair conformation like β-D-glucuronate in chondroitin 6-sulfate. Since the eight-fold dermatan sulfate helix has h = 9.3 A rather less than the eight-fold chondroitin 6-sulfate helix [ h = 9.8 A ] the possibility of α-L-iduronate 1C chairs cannot be ruled out for it. Computer methods have been used to produce molecular models. In these the polysaccharide chains are almost linear. Each backbone conformation can accommodate a variety of arrangements of charged side groups.

Crystal and molecular structure of the dimer of variable domains of the Bence-Jones protein ROY

Abstract The crystal and molecular structure of the dimer of variable domains of the Bence-Jones protein ROY has been determined by Patterson function search procedures, using the known structure of the protein REI. The structure has been partially refined at 3.0 A resolution to a crystallographic R -factor value of 0.33. One of the 18 residues differentiating ROY from REI is the substitution of Tyr96 for Leu96, a substitution which makes the combining site of the ROY dimer larger. Substantial movement of Tyr49 suggests that point substitutions in the hypervariable segments may affect the conformation of neighbouring residues in the antigen-combining site, possibly producing differences in specificity larger than might otherwise be expected.

Metal-substituted derivatives of the rubredoxin from Clostridium pasteurianum.

Five different metal-substituted forms of Clostridium pasteurianum rubredoxin have been prepared and crystallized. The single Fe atom present in the Fe(S-Cys)(4) site of the native form of the protein was exchanged in turn for Co, Ni, Ga, Cd and Hg. All five forms of rubredoxin crystallized in space group R3 and were isomorphous with the native protein. The Co-, Ni- and Ga-substituted proteins exhibited metal sites with geometries similar to that of the Fe form (effective D(2d) local symmetry), as did the Cd and Hg proteins, but with a significant expansion of the metal-sulfur bond lengths. A knowledge of these structures contributes to a molecular understanding of the function of this simple iron-sulfur electron-transport protein.