Biomedical subjects

Ylva Lindqvist

Publications and source records attributed to Ylva Lindqvist.

23 records · Page 2Linked to original sources

PubMed2002

Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography.

The crystal structure of gluconate kinase from Escherichia coli has been determined to 2.0 A resolution by X-ray crystallography. The three-dimensional structure was solved by multi-wavelength anomalous dispersion, using a crystal of selenomethionine-substituted enzyme. Gluconate kinase is an alpha/beta structure consisting of a twisted parallel beta-sheet surrounded by alpha-helices with overall topology similar to nucleoside monophosphate (NMP) kinases, such as adenylate kinase. In order to identify residues involved in substrate binding and catalysis, structures of binary complexes with ATP, the ATP analogue adenosine 5'-(beta,gamma-methylene) triphosphate and the product, gluconate-6-phosphate have been determined. Significant conformational changes are induced upon binding of ATP to the enzyme. The largest changes involve a hinge-bending motion of the NMP(bind) part and a motion of the LID with adjacent helices, which opens the cavity to the second substrate, gluconate. Opening of the active site cleft upon ATP binding is the opposite of what has been observed in the NMP kinase family so far, which usually close their active site to prevent fortuitous hydrolysis of ATP. The conformational change positions the side-chain of Arg120 to stack with the purine ring of ATP and the side-chain of Arg124 is shifted to interact with the alpha-phosphate in ATP, at the same time protecting ATP from solvent water. The beta and gamma-phosphate groups of ATP bind in the predicted P-loop. A conserved lysine side-chain interacts with the gamma-phosphate group, and might promote phosphoryl transfer. Gluconate-6-phosphate binds with its phosphate group in a similar position as the gamma-phosphate of ATP, consistent with inline phosphoryl transfer. The gluconate binding-pocket in GntK is located in a different position than the nucleoside binding-site usually found in NMP kinases.

Adenosine Triphosphate↗

PubMed2002

Phosphatase and oxygen radical-generating activities of mammalian purple acid phosphatase are functionally independent.

Bone-resorbing osteoclasts and activated macrophages express large amounts of tartrate-resistant acid phosphatase (TRAP), an iron-containing enzyme with unknown biological function. We studied acid phosphatase (AcP) and reactive oxygen species (ROS)-generating activities of recombinant rat TRAP. pH optimum was 4.5 for AcP activity and 6.5 for ROS-generating activity. Replacement of His113 and His216 by site-directed mutagenesis severely inhibited AcP activity, but had no significant effects on ROS-generating activity. Substrate specificity was not affected by the mutations. These results suggest that AcP and ROS-generating activities of TRAP are functionally independent.

Acid Phosphatase↗

PubMed2002

Expression, purification, refolding and crystallization of the carbohydrate-recognition domain of p58/ERGIC-53, an animal C-type lectin involved in export of glycoproteins from the endoplasmic reticulum.

p58/ERGIC-53 is a mammalian calcium-dependent lectin that serves as a glycoprotein-sorting receptor between the endoplasmic reticulum (ER) and the Golgi complex. It is a type I transmembrane protein with two lumenal domains, one of which is a carbohydrate-recognition domain (CRD) and homologous to leguminous lectins. The CRD of p58, the rat homologue of human ERGIC-53, was overexpressed in insect cells and Escherichia coli, purified and crystallized using Li(2)SO(4) as a precipitant. The crystals belong to space group I222, with unit-cell parameters a = 49.6, b = 86.1, c = 128.1 A, and contain one molecule per asymmetric unit, corresponding to a packing density of 2.4 A(3)Da(-1). Knowledge of the structure of p58/ERGIC-53 will provide a starting model for understanding receptor-mediated glycoprotein sorting between the ER and the Golgi.

Animals↗

PubMed2002

Crystal structure of the carbohydrate recognition domain of p58/ERGIC-53, a protein involved in glycoprotein export from the endoplasmic reticulum.

p58/ERGIC-53 is an animal calcium-dependent lectin that cycles between the endoplasmic reticulum (ER) and the Golgi complex and appears to act as a cargo receptor for a subset of soluble glycoproteins exported from the ER. We have determined the crystal structure of the carbohydrate recognition domain (CRD) of p58, the rat homologue of human ERGIC-53, to 1.46 A resolution. The fold and ligand binding site are most similar to those of leguminous lectins. The structure also resembles that of the CRD of the ER folding chaperone calnexin and the neurexins, a family of non-lectin proteins expressed on neurons. The CRD comprises one concave and one convex beta-sheet packed into a beta-sandwich. The ligand binding site resides in a negatively charged cleft formed by conserved residues. A large surface patch of conserved residues with a putative role in protein-protein interactions and oligomerization lies on the opposite side of the ligand binding site. Together with previous functional data, the structure defines a new and expanding class of calcium-dependent animal lectins and provides a starting point for the understanding of glycoprotein sorting between the ER and the Golgi.

Amino Acid Sequence↗

PubMed2002

Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer.

Dihydroprymidine dehydrogenase catalyzes the first and rate-limiting step in pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds. The three-dimensional structures of a binary complex with the inhibitor 5-iodouracil and two ternary complexes with NADPH and the inhibitors 5-iodouracil and uracil-4-acetic acid were determined by x-ray crystallography. In the ternary complexes, NADPH is bound in a catalytically competent fashion, with the nicotinamide ring in a position suitable for hydride transfer to FAD. The structures provide a complete picture of the electron transfer chain from NADPH to the substrate, 5-iodouracil, spanning a distance of 56 A and involving FAD, four [Fe-S] clusters, and FMN as cofactors. The crystallographic analysis further reveals that pyrimidine binding triggers a conformational change of a flexible active-site loop in the alpha/beta-barrel domain, resulting in placement of a catalytically crucial cysteine close to the bound substrate. Loop closure requires physiological pH, which is also necessary for correct binding of NADPH. Binding of the voluminous competitive inhibitor uracil-4-acetic acid prevents loop closure due to steric hindrance. The three-dimensional structure of the ternary complex enzyme-NADPH-5-iodouracil supports the proposal that this compound acts as a mechanism-based inhibitor, covalently modifying the active-site residue Cys-671, resulting in S-(hexahydro-2,4-dioxo-5-pyrimidinyl)cysteine.

Animals↗