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Journal Issue - Volume 7 Issue 6 (June 1998)

Abstract Dihydroorotate dehydrogenases (DHODs) catalyze the oxidation of (S)‐dihydroorotate to orotate, the fourth step and only redox reaction in the de novo biosynthesis of pyrimidine nucleotides. A description is given of the crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A (DHODA) complexed with the product of the enzyme reaction orotate. The structure of the complex to 2.0 Å resolution has been compared with the...

Abstract The βγ‐crystallins form a superfamily of eye lens proteins comprised of multiple Greek motifs that are symmetrically organized into domains and higher assemblies. In the βB2‐crystallin dimer each polypeptide folds into two similar domains that are related to monomeric γ‐crystallin by domain swapping. The crystal structure of the circularly permuted two‐domain βB2 polypeptide shows that permutation converts intermolecular...

Abstract cis‐Biphenyl‐2,3‐dihydrodiol‐2,3‐dehydrogenase (BphB) is involved in the aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal structure of the NAD+‐enzyme complex was determined by molecular replacement and refined to an R‐value of 17.9% at 2.0 Å. As a member of the short‐chain alcohol dehydrogenase/reductase (SDR) family, the overall protein fold and positioning of the catalytic triad in BphB are very...

  • Crystal structure of human cathepsin S

  • Mary E. Mcgrath, James T. Palmer, Ddeter Brömme, John R. Somoza
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560070604 (p 1294-1302)

Abstract We have determined the 2.5 Å structure (Rcryst= 20.5%, Rfree = 28.5%) of a complex between human cathepsin S and the potent, irreversible inhibitor 4‐morpholinecarbonyl‐Phe‐hPhe‐vinyl sulfone‐phenyl. Noncrystallographic symmetry averaging and other density modification techniques were used to improve electron density maps which were nonoptimal due to systematically incomplete data. Methods that reduce the number of parameters were ...

Abstract Matrix metalloproteinases (MMPs) are a family of zinc endopeptidases, which have been implicated in various disease processes. Various classes of MMP inhibitors, including hydroxamic acids, phosphinic acids, and thiols, have been previously described. Most of these mimic peptides, and most likely bind analogous to the corresponding peptide substrates. Among the hydroxamic acids, malonic acid derivatives have been used as...

Abstract Cyclophilins are a family of proteins that exhibit peptidyl‐prolyl cis‐trans isomerase activity and bind the immuno‐suppressive agent Cyclosporin A (CsA). Brugia malayi is a filarial nematode parasite of humans, for which a cyclophilin‐like domain was identified at the N‐terminal of a protein containing 843 amino acid residues. There are two differences in sequence in the highly conserved CsA binding site: A histidine and a lysine...

Abstract Factor V (FV) is a large (2,196 amino acids) nonenzymatic cofactor in the coagulation cascade with a domain Organization (A1‐A2‐B‐A3‐C1‐C2) similar to the one of factor VIII (FVIII). FV is activated to factor Va (FVa) by thrombin, which cleaves away the B domain leaving a heterodimeric structure composed of a heavy chain (A1‐A2) and a light chain (A3‐C1‐C2). Activated protein C (APC), together with its cofactor protein S...

Abstract The crystal structure of the recombinant apo‐form of glycine N‐methyltransferase (GNMT) has been determined at 2.5 Å resolution. GNMT is a tetrameric enzyme (monomer Mr = 32,423Da, 292 amino acids) that catalyzes the transfer of a methyl group from S‐adenosylmethionine (AdoMet) to glycine with the formation of S‐adenosylmethionine (AdoHcy) and sarcosine (N‐methylglycine). GNMT is a regulatory enzyme, which is inhibited by...

Abstract Intestinal fatty acid‐binding protein (I‐FABP) is a cytosolic 15.1‐kDa protein that appears to function in the intracellular transport and metabolic trafficking of fatty acids. It binds a Single molecule of long‐chain fatty acid in an enclosed cavity surrounded by two five‐stranded antiparallel β‐sheets and a helix‐turn‐helix domain. To investigate the role of the helical domain, we engineered a variant of I‐FABP by...

Abstract Type IV collagen α1‐α6 chains have important roles in the assembly of basement membranes and are implicated in the pathogenesis of Goodpasture Syndrome, an autoimmune disorder, and Alport Syndrome, a hereditary renal disease. We report comparative sequence analyses and structural predictions of the noncollagenous C‐terminal globular NC1 domain (28 sequences). The inferred tree verified that type IV collagen sequences fall...

Abstract The thermal denaturation of recombinant human growth hormone (rhGH) was studied by differential scanning calorimetry and circular dichroism spectroscopy (CD). The thermal unfolding is reversible only below pH 3.5, and under these conditions a single two‐state transition was observed between 0 and 100°C. The magnitudes of the ΔH and ΔCP of this transition indicate that it corresponds to a partial unfolding of rhGH. This is also...

Abstract The interfacial activation of Rhizomucor miehei lipase (RmL) involves the motion of an α‐helical region (residues 82‐96) which acts as a “lid” over the active site of the enzyme, undergoing a displacement from a “closed” to an “open” conformation upon binding of substrate. Normal mode analyses performed in both low and high dielectric media reveal that low‐frequency vibrational modes contribute significantly to the ...

Abstract We made several statistical analyses in a large sample of nearly 4,000 helices (from 546 redundancy‐controlled PDB protein subunits), which give new insights into the helical properties of globular proteins. In a first experiment, the amino acid composition of the whole sample was compared with the composition of two helical sample subgroups (the “mainly‐α” and the “(α/β)8 barrel” domain classes); we reached the conclusion...

Abstract The crystal structure of Saccharomyces cerevisiae cytoplasmic aspartate aminotransferase (EC 2.6.1.1) has been determined to 2.05 Å resolution in the presence of the cofactor pyridoxal‐5′‐phosphate and the competitive inhibitor maleate. The structure was solved by the method of molecular replacement. The final value of the crystallographic R‐factor after refinement was 23.1% with good geometry of the final model. The yeast cytoplasmic...

Abstract Electrospray ionization time‐of‐flight mass spectrometry (ESI‐TOF MS) has been used to study noncovalent interactions between the trp apo‐repressor (TrpR), its co‐repressor tryptophan and its specific operator DNA. In 5 mM ammonium acetate, TrpR was detected as a partially unfolded monomer. In the presence of a 21‐base‐pair DNA possessing the two symmetrically arranged CTAG consensus sequences required for specific TrpR...

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