Biomedical subjects

Y Lindqvist

Publications and source records attributed to Y Lindqvist.

At least 73 records · Page 4Linked to original sources

PubMed1994

Crystal structure of scytalone dehydratase--a disease determinant of the rice pathogen, Magnaporthe grisea.

BACKGROUND: Rice blast is caused by the pathogenic fungus,-Magnaporthe grisea. Non-pathogenic mutants have been identified that lack enzymes in the biosynthetic pathway of dihydroxynapthalene-derived melanin. These enzymes are therefore prime targets for fungicides designed to control rice blast disease. One of the enzymes identified by genetic analysis as a disease determinant is scytalone dehydratase. RESULTS: The three-dimensional structure of scytalone dehydratase in complex with a competitive inhibitor has been determined at 2.9 A resolution. A novel fold, a cone-shaped alpha + beta barrel, is adopted by the monomer in this trimeric protein, burying the hydrophobic active site in its interior. The interactions of the inhibitor with the protein side chains have been identified. The similarity of the inhibitor to the substrate and the side chains involved in binding afford some insights into possible catalytic mechanisms. CONCLUSIONS: These results provide a first look into the structure and catalytic residues of a non-metal dehydratase, a large class of hitherto structurally uncharacterized enzymes. It is envisaged that a detailed structural description of scytalone dehydratase will assist in the design of new inhibitors for controlling rice blast disease.

Ascomycota↗

PubMed1994

Crystal structure of the FAD-containing fragment of corn nitrate reductase at 2.5 A resolution: relationship to other flavoprotein reductases.

BACKGROUND: In the biological assimilation of nitrate in plants and microorganisms, nitrate is reduced to ammonium by transfer of eight electrons in a two-step process. The first step of the pathway, the reduction of nitrate to nitrite, is catalyzed by nitrate reductase, a multi-redox cofactor enzyme which belongs to the class of flavoprotein pyridine nucleotide cytochrome reductases. The enzyme can be divided into three functional fragments that bind the cofactors molybdopterin, heme-iron and flavin adenine dinucleotide (FAD)/nicotinamide adenine dinucleotide (NADH). RESULTS: Here we describe the crystal structure of the recombinant cytochrome b reductase fragment of corn nitrate reductase, in complex with the cofactor FAD, determined to 2.5 A resolution. This catalytically competent fragment of nitrate reductase consists of two domains, the amino-terminal lobe, which binds FAD, and the carboxy-terminal lobe, which presumably binds NADH, connected by a linker region. CONCLUSIONS: Nitrate reductase belongs to the class of flavoprotein pyridine nucleotide cytochrome reductases, a subgroup in the family of ferredoxin reductase-like flavoproteins. Comparison with other members of this family reveals that large structural differences are found in the relative orientation of the cofactor binding lobes. This indicates that conformational changes might be important for biological function.

Amino Acid Sequence↗

PubMed1994

Site-directed mutagenesis of prostatic acid phosphatase. Catalytically important aspartic acid 258, substrate specificity, and oligomerization.

At the active site of rat prostatic acid phosphatase (rPAP), residue Asp258 is a suitable candidate to act as an acid/base catalyst during phosphoester hydrolysis. It was changed to Asn, Ser, and Ala by site-directed mutagenesis. All these mutants were inactive, indicating that Asp258 may act as a proton donor in catalysis. Tyr123 and Arg127 residues, located at the entrance of the active site surface in rPAP, are likely to be responsible for the substrate specificity of the enzyme. The corresponding residues in lysosomal acid phosphatase (LAP) are Lys and Gly. In order to clarify the roles of the Tyr123 and Arg127 residues, lysosomal type rPAP mutants (Y123K, R127G and Y123K,R127G) were generated. Sensitivity of Y123K,R127G to tartrate inhibition was similar to that observed in the case of LAP, indicating that these residues might be responsible for differences in substrate specificity between the enzymes of prostatic and lysosomal origin. However, unlike human LAP, the lysosomal type mutants hydrolyzed the suggested PAP-specific substrates, phosphocreatine and phosphocholine, showing that Tyr123 and Arg127 are not the only residues contributing to the substrate specificity of rPAP. The residues Trp106 and His112 appeared to be important in the dimerization of rPAP. Oligomerization mutants (W106E, H112D and W106E,H112D) existed in a monomeric form without catalytic activity or a tartrate binding ability.

Acid Phosphatase↗

PubMed1994

Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65 A resolution.

BACKGROUND: In Escherichia coli, the enzymes of the biotin biosynthesis pathway are encoded by the bio operon. One of these enzymes, ATP-dependent dethiobiotin synthetase, catalyzes the carboxylation of 7,8-diaminopelargonic acid leading to the formation of the ureido ring of biotin. The enzyme belongs to the class of ATP-dependent carboxylases and we present here the first crystal structure determined for this class of enzyme. RESULTS: We have determined the crystal structure of homodimeric dethiobiotin synthetase to 1.65 A resolution. The subunit consists of a seven-stranded parallel beta-sheet, surrounded by alpha-helices. The sheet contains the classical mononucleotide-binding motif with a fingerprint peptide Gly-X-X-X-X-X-Gly-Lys-Thr. The mononucleotide binding part of the structure is very similar to the GTP-binding protein H-ras-p21 and thus all GTP-binding proteins. A comparison reveals that some of the residues, which in H-ras-p21 interact with the nucleotide and the metal ion, are conserved in the synthetase. CONCLUSIONS: The three-dimensional structure of dethiobiotin synthetase has revealed that ATP-dependent carboxylases contain the classical mononucleotide-binding fold. Considerable similarities to the structure of the GTP-binding protein H-ras-p21 were found, indicating that both proteins might have evolved from a common ancestral mononucleotide-binding fold.

Adenosine Triphosphate↗

PubMed1994

Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 A resolution.

The crystal structure of transketolase from Saccharomyces cerevisiae has been refined to a crystallographic residual of 15.7% at 2.0 A resolution using the program package X-PLOR. The refined model of the transketolase homodimer, corresponding to 1356 amino acid residues in the asymmetric unit, consists of 10,396 protein atoms, 1040 solvent molecules, 52 thiamine diphosphate atoms and two calcium ions. All amino acid residues except for the two N-terminal residues of the two subunits are defined in the electron density maps and refined. The estimated root-mean-square (r.m.s.) error of the model is less than 0.2 A as deduced from Luzzati plots. The r.m.s. deviation from ideality is 0.017 A for bond distances and 3.1 degrees for bond angles. The main-chain torsion angles of non-glycine residues lie within the allowed regions of the Ramachandran plots. The model shows a very good fit to the electron density maps. The average B-factor for all protein atoms in the first subunit is 19 A2, and 15A2 in the second. The average B-factor for solvent atoms is 32A2. The two subunits of transketolase were refined independently and have nearly identical structures with an r.m.s. deviation of 0.24 A for C alpha atoms 3 to 680, and slightly less when aligning the individual domains. A few exceptions from the 2-fold symmetry are found, mostly in the surface residues. The thiamine diphosphate cofactors have identical conformations. The cofactor is shielded from solvent except for the C-2 atom of the thiazolium ring. A calcium ion is bound to the diphosphate group of thiamine and protein ligands. The metal binding site and the interactions of thiamine diphosphate with protein residues are described. A network of hydrogen bonds consisting of glutamic acid residues and internal water molecules connects the two thiamine diphosphate molecules. Its structure and possible functional implications are discussed.

Amino Acid Sequence↗

PubMed1994

Crystallization and preliminary X-ray analysis of phenol hydroxylase from Trichosporon cutaneum.

Recombinant phenol hydroxylase from the soil yeast Trichosporon cutaneum has been crystallized with PEG 4000 as precipitant. The crystals are monoclinic, space group P2(1) with cell dimensions a = 101.8 A, b = 153.0 A, c = 116.0 A and beta = 114.8 degrees. The crystal asymmetric unit most likely contains two dimers of phenol hydroxylase corresponding to a packing density in the crystals of 2.54 A 3/Da. The self-rotation function is consistent with the packing of two dimers in the asymmetric unit. The observed diffraction pattern extends beyond 2.8 A resolution and the crystals are well suited for structural analysis by X-ray diffraction methods.

Crystallization↗

PubMed1994

Crystal structures of rat acid phosphatase complexed with the transition-state analogs vanadate and molybdate. Implications for the reaction mechanism.

The three-dimensional structures of complexes of recombinant rat prostatic acid phosphatase with the transition-state analogs vanadate and molybdate were determined to 0.3-nm resolution using protein crystallographic methods. The overall structure of the enzyme remains unchanged upon binding of the metal oxyanions; only local conformational differences in the positions of some side chains at the active site were found. The metal oxyanions bind in an identical fashion at the active site with trigonal bipyramidal coordination geometry. The metal ion is within coordination distance of the His12 side chain which is located at one of the axial positions. The three equatorial oxygen atoms interact with the conserved residues Arg11, Arg15, Arg79 and His257. Within hydrogen-bonding distance of the axial oxygen atom is the side chain of the conserved residue Asp258. The implications of these results for the catalytic mechanism of acid phosphatase are discussed.

Acid Phosphatase↗

PubMed1994

Ta6Br14 is a useful cluster compound for isomorphous replacement in protein crystallography.

The metal cluster Ta(6)Br(14) has been used to prepare heavy-metal derivatives of two large proteins, ribulose-1,5-bisphosphate carboxylase/oxygenase and transketolase. In both cases, this cluster compound produced a single-site derivative for which a difference Patterson map, calculated to 5.5 A resolution, could be solved straightforwardly. Ta(6)Br(14) provided enough phase information to unambiguously locate the heavy-atom positions in other multiple-site derivatives. In transketolase, the heavy-metal complex binds at the surface of the protein in a dominantly hydrophobic pocket. In ribulose bisphosphate carboxylase/oxygenase, it binds between two molecules in the crystal lattice. There are negatively charged glutamic and/or aspartic acid residues in the vicinity of the bound clusters. Ta(6)Br(14) is useful over a wide range of pH. For large proteins and/or large unit cells, this compound should be included in the initial screening for heavy-metal derivatives.

Journal Article↗

PubMed1993

Yeast TKL1 gene encodes a transketolase that is required for efficient glycolysis and biosynthesis of aromatic amino acids.

A gene encoding transketolase, TKL1, was cloned from the budding yeast Saccharomyces cerevisiae using oligonucleotide primers derived from protein sequence data. The TKL1 sequence predicts a 74-kDa polypeptide which is related to other transketolases. A sequence comparison revealed that the transketolases can be subdivided into three evolutionary branches. We also found that the transketolases are related to another vitamin B1-dependent enzyme: the E1 subunit of pyruvate dehydrogenase from Escherichia coli. Gene disruption and overexpression experiments were used to investigate the function of transketolase in yeast. We found that growth on fermentable carbon sources, but not on gluconeogenic carbon sources, is reduced in cells disrupted for TKL1. This suggests that the glycolytic efficiency is impaired. Growth on fermentable carbon sources is also reduced in cells that overexpress TKL1. Finally, we found that cells disrupted for TKL1 are unable to grow in the absence of aromatic amino acids. This is most likely due to the fact that transketolase is required for the synthesis of erythrose-4-P, a precursor of the aromatic amino acids.

Amino Acid Sequence↗

PubMed1993

A thiamin diphosphate binding fold revealed by comparison of the crystal structures of transketolase, pyruvate oxidase and pyruvate decarboxylase.

BACKGROUND: The crystal structures of three thiamin diphosphate-dependent enzymes that catalyze distinct reactions in basic metabolic pathways are known. These enzymes--transketolase, pyruvate oxidase and pyruvate decarboxylase--also require metal ions such as Ca2+ and Mg2+ as cofactors and have little overall sequence similarity. Here, the crystal structures of these three enzymes are compared. RESULTS: The three enzymes share a similar pattern of binding of thiamin diphosphate and the metal ion cofactors. The enzymes function as multisubunit proteins, with each polypeptide chain folded into three alpha/beta domains. Two of these domains are involved in binding of the thiamin diphosphate and the metal ion. These domains have the same topology of six parallel beta-strands and surrounding alpha-helices. The thiamin diphosphate is bound in a cleft, formed by two domains from two different subunits. Only a few residues are conserved in all three enzymes and these are responsible for proper binding of the cofactors. CONCLUSIONS: Despite considerable differences in quaternary structure and lack of overall sequence homology, thiamin diphosphate binds to the three enzymes in a very similar fashion, and a general thiamin-binding fold can be revealed.

Amino Acid Sequence↗

PubMed1993

Three-dimensional structure of rat acid phosphatase in complex with L(+)-tartrate.

The crystal structure of recombinant rat prostatic acid phosphatase in complex with the inhibitor L(+)-tartrate was determined to 3-A resolution with protein crystallographic methods. The inhibitor binds at the carboxyl end of the parallel strands of the alpha/beta domain. One of the carboxyl groups of the tartrate molecule interacts with the conserved residues Arg-11, His-12, and Arg-15, which form part of the phosphate binding site. Furthermore, the C2 and C3 hydroxyl groups interact with His-257 and Arg-79. The second carboxyl group is close to Arg-79 but makes no direct hydrogen bonds to the protein. A sequence comparison between tartrate-sensitive and -resistant acid phosphatases suggests that these enzymes have different three-dimensional structures.

Acid Phosphatase↗

PubMed1993

Crystal structure of apo-glycolate oxidase.

The crystal structure of the apoform of the alpha/beta-barrel enzyme glycolate oxidase has been determined to 2.6 A resolution. Removal of the tightly bound cofactor FMN has a very strong influence on the protein structure; it is converted into a very flexible state, verging on a molten globule type of structure. The asymmetric unit contains two subunits with different conformations to each other and to the holo-enzyme. The secondary structures are preserved, but their mutual arrangement has changed to some extent introducing cavities into the protein. The largest structural shifts are, however, found in the loops.

Alcohol Oxidoreductases↗

PubMed1993

Crystal structure of transketolase in complex with thiamine thiazolone diphosphate, an analogue of the reaction intermediate, at 2.3 A resolution.

The crystal structure of the complex of transketolase and thiamine thiazolone diphosphate has been determined at 2.3 A resolution. The complex has a structure which closely resembles that of this enzyme with the cofactor ThDP. This is consistent with the observation that the binding of the analogue to transketolase involves ground state rather than transition state interactions. Since thiamine thiazolone diphosphate resembles an expected intermediate in the catalytic pathway, the structure of the intermediate was modelled from the crystal structure. Based on this model, enzymic groups responsible for binding of the intermediate and proton transfer during catalysis are suggested.

Binding Sites↗

PubMed1993

Role of tyrosine 129 in the active site of spinach glycolate oxidase.

The enzymatic properties and the three-dimensional structure of spinach glycolate oxidase which has the active-site Tyr129 replaced by Phe (Y129F glycolate oxidase) has been studied. The structure of the mutant is unperturbed which facilitates interpretation of the biochemical data. Y129F glycolate oxidase has an absorbance spectrum with maxima at 364 and 450 nm (epsilon max = 11400 M-1 cm-1). The spectrum indicates that the flavin is in its normal protonated form, i.e. the Y129F mutant does not lower the pKa of the N(3) of oxidized flavin as does the wild-type enzyme [Macheroux, P., Massey, V., Thiele, D. J., and Volokita, M. (1991) Biochemistry 30, 4612-4619]. This was confirmed by a pH titration of Y129F glycolate oxidase which showed that the pKa is above pH 9. In contrast to wild-type glycolate oxidase, oxalate does not perturb the absorbance spectrum of Y129F glycolate oxidase. Moreover oxalate does not inhibit the enzymatic activity of the mutant enzyme. Typical features of wild-type glycolate oxidase that are related to a positively charged lysine side chain near the flavin N(1)-C(2 = O), such as stabilization of the anionic flavin semiquinone and formation of tight N(5)-sulfite adducts, are all conserved in the Y129F mutant protein. Y129F glycolate oxidase exhibited about 3.5% of the wild-type activity. The lower turnover number for the mutant of 0.74 s-1 versus 20 s-1 for the wild-type enzyme amounts to an increase of the energy of the transition state of about 7.8 kJ/mol. Steady-state analysis gave Km values of 1.5 mM and 7 microM for glycolate and oxygen, respectively. The Km for glycolate is slightly higher than that found for wild-type glycolate oxidase (1 mM) whereas the Km for oxygen is much lower. As was the case for wild-type glycolate oxidase, reduction was found to be the rate-limiting step in catalysis, with a rate of 0.63 s-1. The kinetic properties of Y129F glycolate oxidase provide evidence that the main function of the hydroxyl group of Tyr129 is the stabilization of the transition state.

Alcohol Oxidoreductases↗

PubMed1993

Rat acid phosphatase: overexpression of active, secreted enzyme by recombinant baculovirus-infected insect cells, molecular properties, and crystallization.

Rat prostatic acid phosphatase (rPAP; orthophosphoric-monoester phosphohydrolase (acid optimum), EC 3.1.3.2) was expressed in the baculovirus expression vector system. Recombinant protein was secreted into the medium at a high yield by infected insect cells, which were cultured at high density in a 30-liter bioreactor allowing high oxygen content for rapidly growing cells. About 20% of the cell protein produced was rPAP. Partial sequence determination of the N terminus of the purified recombinant secreted protein revealed identity to the native secreted protein, showing that the signal peptide is recognized and properly cleaved in insect cells. The enzyme was purified by using L-(+)-tartrate affinity chromatography. The purified protein had a high specific activity of 2620 mumol.min-1.mg-1 with p-nitrophenyl phosphate at the substrate, and it also showed phosphotyrosine phosphatase activity. The molecular mass of the recombinant rPAP was 155 kDa. Two subunits of 46 kDa and 48 kDa could be detected in SDS/PAGE, but only one subunit of 41 kDa was present after digestion with N-glycosidase. The active enzyme is a trimer of subunits differing only in glycosylation. When recombinant rPAP was crystallized with polyethylene glycol 6000 as the precipitant, the crystals were trigonal (space group P3(1)21) with cell dimensions a = 89.4 A and c = 152.0 A. The observed diffraction pattern extends to a resolution of at least 3 A.

Acid Phosphatase↗

PubMed1993

Three-dimensional structure of rat acid phosphatase.

The crystal structure of recombinant rat prostatic acid phosphatase was determined to 3 A resolution with protein crystallographic methods. The enzyme subunit is built up of two domains, an alpha/beta domain consisting of a seven-stranded mixed beta-sheet with helices on both sides of the sheet and a smaller alpha domain. Two disulfide bridges between residues 129-340 and 315-319 were found. Electron density at two of the glycosylation sites for parts of the carbohydrate moieties was observed. The dimer of acid phosphatase is formed through two-fold interactions of edge strand 3 from one subunit with strand 3 from the second subunit, thus extending the beta-sheet from seven to 14 strands. Other subunit-subunit interactions involve conserved residues from loops between helices and beta-strands. The fold of the alpha/beta domain is similar to the fold observed in phosphoglycerate mutase. The active site is at the carboxy end of the parallel strands of the alpha/beta domain. There is a strong residual electron density at the phosphate binding site which probably represents a bound chloride ion. Biochemical properties and results from site-directed mutagenesis experiments of acid phosphatase are correlated to the three-dimensional structure.

Acid Phosphatase↗

PubMed1993

Insulin-like growth factor II in the mink (Mustela vison): determination of a cDNA nucleotide sequence and developmental regulation of its expression.

Mink cDNA for insulin-like growth factor II (IGF-II) has been isolated by cDNA synthesis from bulk mRNA and subsequent PCR-screening. Positive clones were sequenced and analyzed. Analysis of a cDNA revealed that, compared with human, the mature mink IGF-II peptide contains 68 instead of 67 amino acids with a serine insertion at residue 40. With this exception, the homology between the human and mink mature peptide is 100% and is 94% between rat and mink. Comparing IGF-II transcripts in fetal and adult mink liver, fetal tissue contains three transcripts of 5.8, 4.5, and 4.0 kb. In contrast, adult liver expresses low levels of a 4.6-kb transcript.

Aging↗

PubMed1992

Three-dimensional structure of apotransketolase. Flexible loops at the active site enable cofactor binding.

The structure determination of apotransketolase and the comparison of its three-dimensional structure with that of the holoenzyme has revealed that no large conformational changes are associated with cofactor binding. Two loops at the active site are flexible in the apoenzyme which enables ThDP to reach its binding site. Binding of the cofactor induces defined conformations for these two loops at the active site. One of these loops is directly involving in binding of the cofactors, Ca2+ and ThDP. This loop acts like a flap which closes off the diphosphate binding site. After binding of the cofactor, residues of this loop form interactions to residues of loop 383-398 from the second subunit. These interactions stabilize the conformation of the two loops from a flexible to a 'closed' conformation.

Apoproteins↗