Biomedical subjects

E Hohenester

Publications and source records attributed to E Hohenester.

At least 37 records · Page 2Linked to original sources

PubMed1998

Crystal structure of the angiogenesis inhibitor endostatin at 1.5 A resolution.

A number of extracellular proteins contain cryptic inhibitors of angiogenesis. Endostatin is a 20 kDa C-terminal proteolytic fragment of collagen XVIII that potently inhibits endothelial cell proliferation and angiogenesis. Therapy of experimental cancer with endostatin leads to tumour dormancy and does not induce resistance. We have expressed recombinant mouse endostatin and determined its crystal structure at 1.5 A resolution. The structure reveals a compact fold distantly related to the C-type lectin carbohydrate recognition domain and the hyaluronan-binding Link module. The high affinity of endostatin for heparin is explained by the presence of an extensive basic patch formed by 11 arginine residues. Endostatin may inhibit angiogenesis by binding to the heparan sulphate proteoglycans involved in growth factor signalling.

Amino Acid Sequence↗

PubMed1998

Three-dimensional structure of O-acetylserine sulfhydrylase from Salmonella typhimurium.

The last step in cysteine biosynthesis in enteric bacteria is catalyzed by the pyridoxal 5'-phosphate-dependent enzyme O-acetylserine sulfhydrylase. Here we report the crystal structure at 2.2 A resolution of the A-isozyme of O-acetylserine sulfhydrylase isolated from Salmonella typhimurium. O-acetylserine sulfhydrylase shares the same fold with tryptophan synthase-beta from Salmonella typhimurium but the sequence identity level is below 20%. There are some major structural differences: the loops providing the interface to the alpha-subunit in tryptophan synthase-beta and two surface helices of tryptophan synthase-beta are missing in O-acetylserine sulfhydrylase. The hydrophobic channel for indole transport from the alpha to the beta active site of tryptophan synthase-beta is, not unexpectedly, also absent in O-acetylserine sulfhydrylase. The dimer interface, on the other hand, is more or less conserved in the two enzymes. The active site cleft of O-acetylserine sulfhydrylase is wider and therefore more exposed to the solvent. A possible binding site for the substrate O-acetylserine is discussed.

Binding Sites↗

PubMed1997

Crystal structure of a pair of follistatin-like and EF-hand calcium-binding domains in BM-40.

BM-40 (also known as SPARC or osteonectin) is an anti-adhesive secreted glycoprotein involved in tissue remodelling. Apart from an acidic N-terminal segment, BM-40 consists of a follistatin-like (FS) domain and an EF-hand calcium-binding (EC) domain. Here we report the crystal structure at 3.1 A resolution of the FS-EC domain pair of human BM-40. The two distinct domains interact through a small interface that involves the EF-hand pair of the EC domain. Residues implicated in cell binding, inhibition of cell spreading and disassembly of focal adhesions cluster on one face of BM-40, opposite the binding epitope for collagens and the N-linked carbohydrate. The elongated FS domain is structurally related to serine protease inhibitors of the Kazal family. Notable differences are an insertion into the inhibitory loop in BM-40 and a protruding N-terminal beta-hairpin with striking similarities to epidermal growth factor. This hairpin is likely to act as a rigid spacer in proteins containing tandemly repeated FS domains, such as follistatin and agrin, and forms the heparin-binding site in follistatin.

Agrin↗

PubMed1997

Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP.

Serum amyloid P component (SAP) is a glycoprotein that binds in a calcium-dependent fashion to a variety of ligands including other proteins, glycosaminoglycans and DNA. SAP is universally associated with the amyloid deposits in all forms of amyloidoses including Alzheimer's disease. Small-molecule ligands that displace SAP from amyloid fibrils and thereby expose the fibrils to proteolytic clearance mechanisms hold potential as drugs for the prevention and treatment of amyloidosis. We have carried out a screen for novel SAP ligands and have identified 2'-deoxyadenosine-5'-monophosphate (dAMP) as a ligand. The crystal structure of the SAP-dAMP complex determined at 2.8 A resolution (R = 0.232, R(free) = 0.252) reveals a decamer in which all interactions between SAP pentamers are mediated by the ligand. The stability of the decamer in solution has been demonstrated by gel filtration chromatography. The two calcium ions of SAP are bridged by the dAMP phosphate group and five hydrogen bonds are formed between the protein and the ligand, including specific interactions made by the adenine base. This mode of dAMP binding is not compatible with the nucleotide being part of double-helical DNA. The SAP-dAMP decamer is stabilized mainly by base-stacking of adjacent ligand molecules and possibly by electrostatic interactions involving the dAMP phosphate groups; decamerization buries 1000 A2 (2.6%) of the pentamer solvent-accessible surface. Ligand-induced decamerization of SAP, which utilizes the high cooperativity of a multiple-site interaction, may be a strategy to overcome the problems for drug design associated with the rather modest affinities of SAP for small-molecule ligands.

Computer Graphics↗

PubMed1997

Limited cleavage of extracellular matrix protein BM-40 by matrix metalloproteinases increases its affinity for collagens.

The 33-kDa matrix protein BM-40 (SPARC, osteonectin) consists of an acidic N-terminal domain I, a central cysteine-rich follistatin-like module, and a C-terminal extracellular calcium-binding (EC) module. Previous studies attributed collagen IV and high affinity calcium binding of BM-40 to its EC module, which was shown by x-ray crystallography to consist of an EF-hand pair surrounded by several alpha-helical and loop segments. This module was now shown by surface plasmon resonance assay to bind with similar affinities to collagens I, III, and V. Cleavage of recombinant BM-40 and its EC module by collagenase-3, gelatinases A and B, matrilysin, and stromelysin-1 showed similar fragment patterns, whereas collagenase-1 was inactive. Some differences were, however, observed in cleavage rates and the preference of certain cleavage sites. Edman degradation of fragments demonstrated only three to four major cleavage sites in the central region of domain I and a single uniform cleavage in helix C of the EC module. Cleavage is accompanied by a 7-20-fold increase in binding activity for collagens I, IV, and V but revealed only small effects on calcium-dependent alpha-helical changes in the EC module. The data were interpreted to indicate that helix C cleavage is mainly responsible for enhancing collagen affinity by exposing the underlying helix A of the EC module. A similar activation may also occur in situ as indicated previously for tissue-derived BM-40.

Amino Acid Sequence↗

PubMed1997

Structural and functional aspects of calcium binding in extracellular matrix proteins.

Ca2+ ions play crucial roles in many matrix-matrix, cell-matrix and cell-cell contacts. Recent X-ray and NMR structure determinations have revealed an intriguing diversity of Ca(2+)-binding sites in extracellular proteins, ranging from the stabilization of isolated domains to intimate involvement in the superstructure of macromolecular assemblies. The central role of Ca2+ in extracellular proteins is illustrated by the molecular characterization of hereditary connective tissue disorders in humans. Point mutations of Ca(2+)-binding residues in fibrillin and cartilage oligomeric matrix protein are responsible for Marfan syndrome and pseudoachondroplasia, respectively. We also discuss the possibility that structure and function of extracellular proteins may be regulated by physiologically relevant Ca2+ gradients.

Amino Acid Sequence↗

PubMed1996

Crystal structures and solution studies of oxime adducts of mitochondrial aspartate aminotransferase.

The interaction of mitochondrial aspartate aminotransferase with hydroxylamine and five derivatives (in which the hydroxyl hydrogen is replaced by the side chain of naturally occurring amino acids) was investigated by X-ray diffraction as well as by kinetic and spectral measurements with the enzyme in solution. The inhibitors react with pyridoxal 5'-phosphate in the enzyme active site, both in solution and in the crystalline state, in a reversible single-step reaction forming spectrally distinct oxime adducts. Dissociation constants determined in solution range from 10(-8) M to 10(-6) M depending on the nature of the side-chain group. The crystal structures of the adducts of mitochondrial aspartate aminotransferase with the monocarboxylic analogue of L-aspartate in the open and closed enzyme conformation were determined at 0.23-nm and 0.25-nm resolution, respectively. This inhibitor binds to both the open and closed crystal forms of the enzyme without disturbing the crystalline order. Small differences in the conformation of the cofactor pyridoxal phosphate were detected between the omega-carboxylate of the inhibitor and Arg292 of the neighbouring subunit is mainly responsible for the attainment of near-coplanarity of the aldimine bond with the pyridine ring in the oxime adducts. Studies with a fluorescent probe aimed to detect shifts in the open/closed conformational equilibrium of the enzyme in oxime complexes showed that the hydroxylamine-derived inhibitors, even those containing a carboxylate group, do not induce the 'domain closure' in solution. This is probably due to the absence of the alpha-carboxylate group in the monocarboxylic hydroxylamine-derived inhibitors, emphasizing that both carboxylates of the substrates L-Asp and L-Glu are essential for stabilizing the closed form of aspartate aminotransferase.

Amino Acid Sequence↗

PubMed1996

Extracellular calcium-binding proteins.

Point mutations in Ca2+-binding sites of extracellular matrix proteins have been identified as the cause of human disorders such as Marfansyndrome and pseudoachondroplasia. Although the modes of Ca2+ binding and the effects of point mutations are not yet understood in these two cases, new insight was recently gained by X-ray and NMR structure determinations of several other extracellular proteins; these studies revealed a diversity of functions of Ca2+ ions. Ca2+ may induce a profound conformational change within a single domain, may bridge adjacent domains and thus direct the relative domain orientation and supramolecular structure, or may be involved in carbohydrate and membrane binding.

1-Carboxyglutamic Acid↗

PubMed1996

Structure of a novel extracellular Ca(2+)-binding module in BM-40.

The EF-hand is a highly conserved Ca(2+)-binding motif found in many cytosolic Ca(2+)-modulated proteins. Here we report the crystal structure at 2.0 A resolution of the carboxy-terminal domain of human BM-40 (SPARC, osteonectin), an extracellular matrix protein containing an EF-hand pair. The two EF-hands interact canonically but their detailed structures are unusual. In the first EF-hand a one-residue insertion is accommodated by a cis-peptide bond and by substituting a carboxylate by a peptide carbonyl as a Ca2+ ligand. The second EF-hand is stabilized by a disulphide bond. The EF-hand pair interacts tightly with an amphiphilic amino-terminal helix, reminiscent of target peptide binding by calmodulin. The present structure defines a novel protein module occurring in several other extracellular proteins.

Amino Acid Sequence↗

PubMed1995

The C-terminal portion of BM-40 (SPARC/osteonectin) is an autonomously folding and crystallisable domain that binds calcium and collagen IV.

The extracellular glycoprotein BM-40 consists of three domains, an acidic domain I, a follistatin (FS)-like domain II and a calcium-binding EC domain with an EF-hand related motif. BM-40 and several other related proteins (QR1, SC1/hevin, testican and tsc-36/FRP) are members of a novel modular protein family that share the FS domain followed by an EC domain. We have expressed this pair of FS and EC domains (mutant delta I) and the calcium-binding EC domain alone (mutant delta I, II) of human BM-40 as recombinant proteins in human 293 cells. Circular dichroism demonstrated that both mutants were obtained as folded proteins with a distinct three-dimensional conformation. In addition, mutant delta I, II could be readily crystallized and diffraction patterns with a resolution limit of 2.4 A resolution were obtained. Calcium binding to this fragment was ten times weaker (Kd = 0.8 microM) than for the wild-type protein. Identical reversible increases in alpha-helicity upon calcium binding were observed for the 150-residue long mutant delta I, II and for BM-40 (286 residues). A 26-residue synthetic peptide corresponding to the EF-hand related motif exhibited much weaker calcium binding. The apparent dissociation constant decreased with increasing peptide concentration (from Kd 2.4 mM at 1 microM, to Kd 0.3 mM at 100 microM peptide concentration) and calcium binding was accompanied by dimerization of the peptide. This suggests that for strong calcium binding the EF-hand related motif has to be embedded into a larger protein domain that can form an autonomously folding protein module. The EC domain was also shown by surface plasmon resonance assay to be responsible for calcium-dependent binding to collagen IV with an affinity (Kd = 19 microM) only sixfold lower than that of intact human BM-40.

Amino Acid Sequence↗

PubMed1995

Structural and mechanistic analysis of two refined crystal structures of the pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase.

Two refined structures, differing in alkali metal ion content, of the bifunctional, pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase (DGD) are presented in detail. The enzyme is an alpha 4 tetramer, built up as a dimer of dimers, with a subunit molecular mass of 46.5 kDa. The fold of DGD is similar to those of aspartate aminotransferase, omega-amino acid aminotransferase and tyrosine phenol-lyase. The structure has two binding sites for alkali metal ions. DGD with potassium in site 1 (near the active site) and sodium in site 2 (at the surface of the molecule) has been refined against 2.6A resolution data (R-factor = 17.6%), and DGD with sodium at both sites has been refined against 2.1 A resolution data (R-factor = 17.8%). The proximity of site 1 to the active site accounts for the dependence of enzyme activity on potassium ions, and the observed active site structural changes caused by ion exchange at this site explain the inhibition of activity by sodium. DGD catalyzes both the decarboxylation of dialkylglycine species and the transamination of L-amino acids in its normal catalytic cycle. The active site structure of DGD is moderately homologous to that of aspartate aminotransferase, which catalyzes only transamination; both the differences and similarities provide mechanistic guidelines for the DGD-catalyzed reactions. Models of the L-isovaline and L-alanine external aldimine intermediates suggest mechanisms by which the decarboxylation and transamination reactions could be accomplished within the single active site. Decarboxylation is proposed to be at least partially catalyzed by stereoelectronic activation of the C alpha-carboxylate bond achieved by orienting this bond perpendicular to the plane of the pyridinium ring in the dialkylglycine external aldimine intermediate. Transamination is proposed to be catalyzed by a similar effect on the C alpha-H bond of the L-amino acid external aldimine intermediate, combined with general base catalysis provided by Lys272, in analogy to the mechanism of aspartate aminotransferase.

Amino Acid Sequence↗

PubMed1994

An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase.

The pyridoxal 5'-phosphate-dependent enzyme dialkylglycine decarboxylase (DGD) is activated by K+ and Rb+ ions, whereas Li+ and Na+ ions are inhibitory. A binding site for alkali metal ions close to the active site (site 1) was discovered in the crystal structure of DGD, and an exchange of K+ for Na+ at this site was shown to affect the conformation of two active site residues [Toney, M. D., Hohenester, E., Cowan, S. W., & Jansonius, J. N. (1993) Science 261, 756-759]. We have investigated the effects of alkali metal ions on DGD activity and have determined the crystal structures at 2.8 A resolution of DGD with Li+ and Rb+ bound at site 1. Due to the weak scattering of the Li+ ion, its position had to be modeled using information from small molecule structures. A comparison of the DGD structures with Li+, Na+, K+, and Rb+ bound at site 1 reveals a striking correlation between active site structure and enzymatic activity. The small, inhibitory ions Li+ and Na+ are accommodated by replacing two protein-derived ligands of the larger, activating ions K+ and Rb+ by a single water molecule. This actuates a two-state structural switch between active and inactive enzyme that involves a concerted reorientation of the active site residues Ser80 and Tyr301 and a small change in the quaternary structure of the DGD tetramer. An important role of the essential K+ ion in both cofactor binding and the organization of a catalytically competent active site structure is proposed. In the structure of DGD with Rb+ bound at site 1, a second Rb+ ion has partially replaced the structural Na+ ion at metal binding site 2 on the surface of the DGD molecule, without significantly altering the protein structure. In contrast to Na+, the Rb+ ion is bound with unfavorable geometry, and it is proposed that the rigid site 2 structure results in a pronounced selectivity for Na+ ions.

Binding Sites↗

PubMed1994

Crystallization and preliminary X-ray analysis of recombinant 1-aminocyclopropane-1-carboxylate synthase from apple. A key enzyme in the biosynthesis of the plant hormone ethylene.

Crystals of recombinant 1-aminocyclopropane-1-carboxylate synthase from apple have been obtained with polyethylene glycol as precipitant using a combination of vapour diffusion and macroseeding techniques. The crystals are of space group P2(1), with unit-cell constants a = 53.7 A, b = 69.3 A, c = 123.7 A and beta = 89.9 degrees. The asymmetric unit content is a 1-aminocyclopropane-1-carboxylate synthase dimer with a molecular mass of 94 kDa. Diffraction extends to 2.2 A resolution.

Crystallization↗

PubMed1994

Crystallization and preliminary X-ray diffraction studies of recombinant human ornithine aminotransferase.

Human liver ornithine aminotransferase was expressed in Escherichia coli and purified by ammonium sulfate fractionation and anion exchange column chromatography. The purified recombinant enzyme is fully active and crystallized readily over a wide range of polyethylene glycol concentrations. The crystals belong to the trigonal space group P3(1)21 (or its enantiomorph P3(2)21) with unit cell parameters a = b = 116.3 A, and c = 190.0 A, alpha = beta = 90 degrees, gamma = 120 degrees. There are three monomers per asymmetric unit. Self-rotation function studies revealed both 2-fold and 3-fold non-crystallographic symmetry, with the local 3-fold axis being tilted 15 degrees from the c axis and perpendicular to a crystallographic dyad. A complete native data set to 2.3 A resolution was collected using synchrotron radiation.

Cloning, Molecular↗

PubMed1994

Crystalline mitochondrial aspartate aminotransferase exists in only two conformations.

The subunits of the alpha 2-dimeric enzyme aspartate aminotransferase are composed of two distinct domains, one large and one small. The active sites are situated close to both the intersubunit and the interdomain interface. Binding of substrate analogues to the active site induces a large conformational change in the enzyme, whereby the small domain rotates by 13 degrees relative to the large domain and completely buries the ligand. We have determined the crystal structures of chicken mitochondrial aspartate aminotransferase (mAATase) in two new crystal forms. A comparison of the structures of mAATase in five crystal forms, including both the unliganded and the liganded enzyme, shows that mAATase exists in either one of two unique conformations, with only minimal adaptations to the crystal lattice. This suggests that both the open, unliganded and closed, liganded structure of mAATase are, to a large extent, stabilized by intramolecular interactions, and are consequently representative of functional states of the protein in solution. A 2-fold-symmetric packing interaction between small domains occurring identically in three crystal forms of mAATase is described.

Animals↗

PubMed1993

Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites.

The structure of the bifunctional, pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase was determined to 2.1-angstrom resolution. Model building suggests that a single cleavage site catalyzes both decarboxylation and transamination by maximizing stereoelectronic advantages and providing electrostatic and general base catalysis. The enzyme contains two binding sites for alkali metal ions. One is located near the active site and accounts for the dependence of activity on potassium ions. The other is located at the carboxyl terminus of an alpha helix. These sites help show how proteins can specifically bind alkali metals and how these ions can exert functional effects.

Amination↗

PubMed1991

Crystallization and preliminary X-ray diffraction studies of the spinach-chloroplast thioredoxin f.

Thioredoxins are low-molecular-mass proteins that function as hydrogen carriers in DNA synthesis and in the transformation of sulfur metabolites. They also act as regulatory proteins in the light-dependent enzyme activation during photosynthesis. F-type thioredoxin from spinach chloroplasts, a monomeric protein of 113 amino acid residues, has been found to specifically activate fructose-1,6-bisphosphatase and other key enzymes of CO2 assimilation. It has been crystallized in the monoclinic system, space group P2(1) with a = 30.6 A, b = 63.1 A, c = 31.6 A and beta = 110.7 degrees. The crystals are suitable for X-ray diffraction studies.

Chloroplast Thioredoxins↗

PubMed1987

Measurement of prostaglandins, thromboxanes and hydroxy fatty acids by stable isotope dilution gas chromatography/mass spectrometry.

A method for measurement of PGF2 alpha, PGE1, PGE2, 6-keto-PGF1 alpha, TXB2, 2,3-dinor-TXB2 as well as 5-, 8-, 9-, 11-, 12-, 15-HETE and HHT, utilizing negative ion chemical ionization GC/MS is presented. A highly efficient separation and purification procedure prior to the derivatization sequence allows quantification of the arachidonic acid metabolites described in two GC/MS runs. The detection limit was in the femtomole range. Application of the method to the quantitative profiling of arachidonic acid metabolites in various tissues and incubation media is demonstrated.

Gas Chromatography-Mass Spectrometry↗