PubMed Health⌕ Search

Biomedical subjects

J Delettré

Publications and source records attributed to J Delettré.

12 recordsLinked to original sources
PubMed2001

Crystal structures of the class D beta-lactamase OXA-13 in the native form and in complex with meropenem.

The therapeutic problems posed by class D beta-lactamases, a family of serine enzymes that hydrolyse beta-lactam antibiotics following an acylation-deacylation mechanism, are increased by the very low level of sensitivity of these enzymes to beta-lactamase inhibitors. To gain structural and mechanistic insights to aid the design of new inhibitors, we have determined the crystal structure of OXA-13 from Pseudomonas aeruginosa in the apo form and in complex with the carbapenem meropenem. The native form consisted of a dimer displaying an overall organisation similar to that found in the closely related enzyme OXA-10. In the acyl-enzyme complex, the positioning of the antibiotic appeared to be ensured mainly by (i) the covalent acyl bond and (ii) a strong salt-bridge involving the carboxylate moiety of the drug. Comparison of the structures of OXA-13 in the apo form and in complex with meropenem revealed an unsuspected flexibility in the region of the essential serine 115 residue, with possible consequences for the catalytic properties of the enzyme. In the apo form, the Ser115 side-chain is oriented outside the active site, whereas the general base Lys70 adopts a conformation that seems to be incompatible with the activation of the catalytic water molecule required for the deacylation step. In the OXA-13:meropenem complex, a 3.5 A movement of the backbone of the 114-116 loop towards the side-chain of Lys70 was observed, which seems to be driven by a displacement of the neighbouring 91-104 loop and which results in the repositioning of the side-chain hydroxyl group of Ser115 toward the catalytic centre. Concomitantly, the side-chain of Lys70 is forced to curve in the direction of the deacylating water molecule, which is then strongly bound and activated by this residue. However, a distance of ca 5 A separates the catalytic water molecule from the acyl carbonyl group of meropenem, a structural feature that accounts for the inhibition of OXA-13 by this drug. Finally, the low level of penicillinase activity revealed by the kinetic analysis of OXA-13 could be related to the specific presence in position 73 of a serine residue located close to the general base Lys70, which results in a decrease of the number of hydrogen-bonding interactions stabilising the catalytic water molecule.

Amino Acid Sequence↗
PubMed2000

The uteroglobin fold.

Uteroglobin (UTG) forms a fascinating homodimeric structure that binds small- to medium-sized ligands through an internal hydrophobic cavity, located at the interface between the two monomers. Previous studies have shown that UTG fold is not limited to the UTG/CC10 family, whose sequence/structure relationships are highlighted here, but can be extended to the cap domain of Xanthobacter autotrophicus haloalkane dehalogenase. We show here that UTG fold is adopted by several other cap domains within the alpha/beta hydrolase family, making it a well-suited "geode" structure allowing it to sequester various hydrophobic molecules. Additionally, some data about a new crystal form of oxidized rabbit UTG are presented, completing previous structural studies, as well as results from molecular dynamics, suggesting an alternative way for the ligand to reach the internal cavity.

Amino Acid Sequence↗
PubMed1999

Site-directed mutagenesis of residues 164, 170, 171, 179, 220, 237 and 242 in PER-1 beta-lactamase hydrolysing expanded-spectrum cephalosporins.

The class A beta-lactamase PER-1, which displays 26% identity with the TEM-type extended-spectrum beta-lactamases (ESBLs), is characterized by a substrate profile similar to that conferred by these latter enzymes. The role of residues Ala164, His170, Ala171, Asn179, Arg220, Thr237 and Lys242, found in PER-1, was assessed by site-directed mutagenesis. Replacement of Ala164 by Arg yielded an enzyme with no detectable beta-lactamase activity. Two other mutants, N179D and A164R+N179D, were also inactive. Conversely, a mutant with the A171E substitution displayed a substrate profile very similar to that of the wild-type enzyme. Moreover, the replacement of Ala171 by Glu in the A164R enzyme yielded a double mutant which was active, suggesting that Glu171 could compensate for the deleterious effect of Arg164 in the A164R+A171E enzyme. A specific increase in kcat for cefotaxime was observed with H170N, whereas R220L and T237A displayed a specific decrease in activity towards the same drug and a general increase in affinity towards cephalosporins. Finally, the K242E mutant displayed a kinetic behaviour very similar to that of PER-1. Based on three-dimensional models generated by homology modelling and molecular dynamics, these results suggest novel structure-activity relationships in PER-1, when compared with those previously described for the TEM-type ESBLs.

Amino Acids↗
PubMed1989

Structure and refinement of the oxidized P21 form of uteroglobin at 1.64 A resolution.

One of the monoclinic P21 forms of uteroglobin, a progesterone-binding protein secreted by the rabbit uterus, was crystallized and subjected to X-ray diffraction analysis at 1.64 A resolution. The analysis was refined to an R factor of 0.19 and the 1096 non-hydrogen atomic positions are known to an accuracy of about 0.18 A. The average isotropic temperature factor B was 10.4 A2. Uteroglobin is a dimer of two independent polypeptide chains of 70 residues linked by two disulfide bridges and related by a pseudo binary axis. Each monomer is folded into four alpha-helices. An oblong hydrophobic pocket is observed inside the dimer, and the possibility that it represents a progesterone-binding site is discussed. The present model includes 165 possible sites for water molecules, of which six are located in the hydrophobic pocket. Polar groups are involved in hydrogen bonding (intramolecular, intermolecular or with water molecules).

Amino Acid Sequence↗
PubMed1988

[Crystalline structure of L-leucyl-L-leucyl-L-tyrosine chlorhydrate].

C21H34N3O5+.Cl-, Mr = 444.0, orthorhombic, P2(1)2(1)2(1), a = 26.074 (5), b = 17.591 (4), c = 5.224 (2) A, V = 2396.1 (10) A3, Z = 4, Cu K alpha, lambda = 1.5418 A, mu = 1.71 mm-1, F(000) = 952, D chi = 1.231 Mg m-3, room temperature, final R = 0.080 and wR = 0.070 for 2439 reflections [(sin theta)/lambda greater than 0.03 A-1]. The peptide groups are planar; torsion angles (-101 and -88 degrees) indicate a roughly helical structure. The peptide bonds have a trans conformation. The crystal structure is stabilized by a network of hydrogen bonds.

Amino Acid Sequence↗
PubMed1988

[Crystalline structure of L-glycyl-L-leucyl-L-phenylalanine hemihydrate].

C17H25N3O4.1/2H2O, Mr = 344.4, monoclinic, B2, a = 18.299 (6), b = 18.781 (6), c = 5.917 (3) A, gamma = 110.65 (3) degrees, V = 1902.9 (10) A3, Z = 4, Cu K alpha, lambda = 1.54178 A, mu = 0.73 mm-1, F(000) = 740, D chi = 1.202 Mg m-3, room temperature, final R = 0.048 and wR = 0.048 for all (1470) reflections. The molecules are stacked in layers along the alpha axis. There are five intermolecular hydrogen bonds.

Amino Acid Sequence↗
PubMed1987

Towards the mapping of the progesterone and androgen receptors.

At a time when the secondary structures of receptor proteins are being predicted from sequence data by modeling techniques, knowledge of the ligand characteristics compatible with high-affinity binding to the receptor and with efficient receptor function is indispensable. We have already compared progesterone receptor (PR) ligands in attempts to map the PR hormone-binding site. In the present study, the relative binding affinities (RBAs) of 33 steroid ligands for the cytosol androgen receptor (AR) of rat prostate, measured in a routine screening system, have been compared. Special emphasis has been given to the effects of modifications (unsaturation, methylation, substitution by halogens) that might influence AR recognition by the ring A carbonyl and also to the consequences of these changes on binding specificity. Nonsteroid antiandrogens are reputed to compete with labelled testosterone (or methyltrienolone) binding to AR. Their RBAs, however, are very low compared to those of steroid antiandrogens. It is feasible that such molecules might occupy and interact with the AR site that binds hormone. The solvent accessible surface of one Anandron conformer is highly similar to that of testosterone and this conformer can be adequately superimposed upon the structure of testosterone and of antiandrogenic Des-A steroid derivatives. The nitro group might assume the role of the ring A carbonyl of steroids; reduction of this group to an amine or a hydroxylamine completely suppresses binding. These observations, however, do not eliminate the hypothesis of interference with AR function, and consequent antiandrogenic activity, by interaction with other (adjacent) sites on AR.

Androgen Antagonists↗
PubMedDate not supplied

Purification, crystallization, and preliminary X-Ray diffraction analysis of the carbapenem-hydrolyzing class A beta-lactamase Sme-1 from Serratia marcescens.

The carbapenem-hydrolyzing class A beta-lactamase Sme-1 from Serratia marcescens S6 was expressed in Escherichia coli and purified by ion-exchange chromatography and gel filtration. Crystals of the purified enzyme were obtained by the hanging drop vapor diffusion method using polyethylene glycol 4000 as precipitant. The crystals belong to the monoclinic space group P21 with unit cell parameters a = 81.48 A, b = 51.76 A, c = 71.81 A, alpha = gamma = 90 degrees, and beta = 118.71 degrees. There are two monomers in the asymmetric unit and the calculated Matthew's volume is 2.26 A3/Da. The crystals, which diffract to at least 2.3 A resolution, are suitable for X-ray structure analysis.

Bacterial Proteins↗