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Biomedical subjects

Christian Oefner

Publications and source records attributed to Christian Oefner.

8 recordsLinked to original sources
PubMed2006

Mapping the active site of Escherichia coli malonyl-CoA-acyl carrier protein transacylase (FabD) by protein crystallography.

Malonyl-CoA-acyl carrier protein transacylase (FabD; EC 2.3.1.39) is a key enzyme in the fatty-acid biosynthesis pathway of bacteria, catalyzing the transfer of a malonyl moiety from malonyl-CoA to holo acyl carrier protein (ACP), generating malonyl-ACP and free CoASH. Malonyl-ACP, which is the product of this reaction, is the key building block for de novo fatty-acid biosynthesis. Various binary complex structures of the Escherichia coli enzyme are presented, including that of the natural substrate malonyl-CoA, indicating the functional role of the highly conserved amino acids Gln11, Ser92, Arg117 and His201 and the stabilizing function of the preformed oxyanion hole during the enzymatic reaction. Based on the presented structural data, a possible new catalytic enzyme mechanism is discussed. The data obtained could be used in aiding the process of rational inhibitor design.

Acyl-Carrier Protein S-Malonyltransferase↗
PubMed2005

The crystal structure of E.coli 1-deoxy-D-xylulose-5-phosphate reductoisomerase in a ternary complex with the antimalarial compound fosmidomycin and NADPH reveals a tight-binding closed enzyme conformation.

The key enzyme in the non-mevalonate pathway of isoprenoid biosynthesis, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) has been shown to be the target enzyme of fosmidomycin, an antimalarial, antibacterial and herbicidal compound. Here we report the crystal structure of selenomethionine-labelled Escherichia coli DXR in a ternary complex with NADPH and fosmidomycin at 2.2 A resolution. The structure reveals a considerable conformational rearrangement upon fosmidomycin binding and provides insights into the slow, tight binding inhibition mode of the inhibitor. Although the inhibitor displays an unusual non-metal mediated mode of inhibition, which is an artefact most likely due to the low metal affinity of DXR at the pH used for crystallization, the structural data add valuable information for the rational design of novel DXR inhibitors. Using this structure together with the published structural data and the 1.9 A crystal structure of DXR in a ternary complex with NADPH and the substrate 1-deoxy-D-xylulose 5-phosphate, a model for the physiologically relevant tight-binding mode of inhibition is proposed. The structure of the substrate complex must be interpreted with caution due to the presence of a second diastereomer in the active site.

Aldose-Ketose Isomerases↗
PubMed2004

Crystal structures of Staphylococcusaureus methionine aminopeptidase complexed with keto heterocycle and aminoketone inhibitors reveal the formation of a tetrahedral intermediate.

High-resolution crystal structures of Staphylococcus aureus methionine aminopeptidase I in complex with various keto heterocycles and aminoketones were determined, and the intermolecular ligand interactions with the enzyme are reported. The compounds are effective inhibitors of the S. aureus enzyme because of the formation of an uncleavable tetrahedral intermediate upon binding. The electron densities unequivocally show the enzyme-catalyzed transition-state analogue mimicking that for amide bond hydrolysis of substrates.

Amines↗
PubMed2004

Structural analysis of neprilysin with various specific and potent inhibitors.

Neutral endopeptidase (NEP) is the major enzyme involved in the metabolic inactivation of a number of bioactive peptides including the enkephalins, substance P, endothelin, bradykinin and atrial natriuretic factor. Owing to the physiological importance of NEP in the modulation of nociceptive and pressor responses, there is considerable interest in inhibitors of this enzyme as novel analgesics and antihypertensive agents. Here, the crystal structures of the soluble extracellular domain of human NEP (residues 52-749) complexed with various potent and competitive inhibitors are described. The structures unambiguously reveal the binding mode of the different zinc-chelating groups and the subsite specificity of the enzyme.

Binding, Competitive↗
PubMed2003

The 1.15A crystal structure of the Staphylococcus aureus methionyl-aminopeptidase and complexes with triazole based inhibitors.

Methionyl aminopeptidases (MetAPs) represent a unique class of protease that are responsible for removing the N-terminal methionine residue from proteins and peptides. There are two major classes of MetAPs (type I and type II) described and each class can be subdivided into two subclasses. Eukaryotes contain both the type I and type II MetAPs, whereas prokaryotes possess only the type I enzyme. Due to the physiological importance of these enzymes there is considerable interest in inhibitors to be used as antiangiogenic and antimicrobial agents. Here, we describe the 1.15A crystal structure of the Staphylococcus aureus MetAP-I as an apo-enzyme and its complexes with various 1,2,4-triazole-based derivatives at high-resolution. The protein has a typical "pita-bread" fold as observed for the other MetAP structures. The inhibitors bind in the active site with the N1 and N2 atoms of the triazole moiety complexing two divalent ions. The 1,2,4-triazols represent a novel class of potent non-peptidic inhibitors for the MetAP-Is.

Amino Acid Sequence↗
PubMed2003

High-resolution structure of human apo dipeptidyl peptidase IV/CD26 and its complex with 1-[([2-[(5-iodopyridin-2-yl)amino]-ethyl]amino)-acetyl]-2-cyano-(S)-pyrrolidine.

Dipeptidyl peptidase IV is a multifunctional type II transmembrane serine protease glycoprotein. The high-resolution crystal structure of the homodimeric human apo dipeptidyl peptidase IV has been determined at 1.9 A resolution. In addition, the structure of the binary complex with 1-[([2-[(5-iodopyridin-2-yl)amino]-ethyl]amino)-acetyl]-2-cyano-(S)-pyrrolidine has been solved, revealing the nature of the covalent interaction with the active-site serine.

Aminopyridines↗
PubMed2003

The protein as a variable in protein crystallization.

Strategies for growing protein crystals have for many years been essentially empirical, the protein, once purified to a certain homogeneity, being mixed with a selection of crystallization agents selected in a more or less trial-and-error fashion. Screening for the correct conditions has been made easier through automation and by the introduction of commercially available crystallization kits. Many parameters can be changed in these experiments, such as temperature, pH, and ionic strength, but perhaps the most important variable has been ignored, namely the protein. The crystallization properties of a protein vary greatly: some crystallize readily, whereas others have proven extremely difficult or even impossible to obtain in a crystalline state. The possibility of altering the intrinsic characteristics of a protein for crystallization has become a feasible strategy. Some historical perspectives and advances in this area will be reviewed.

Crystallization↗