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L T Delbaere

Publications and source records attributed to L T Delbaere.

At least 37 records · Page 2Linked to original sources
PubMed1996

Crystal structure of Escherichia coli phosphoenolpyruvate carboxykinase: a new structural family with the P-loop nucleoside triphosphate hydrolase fold.

The crystal structure of ATP-dependent phosphoenolpyruvate carboxykinase (ATP-oxaloacetate carboxy-lyase, (transphosphorylating), E.C. 4.1.1.49; PCK) from Escherichia coli strain K12 has been determined using a combination of multiple isomorphous replacement, density modification, and partial model phase combination, and refined to a conventional R-index of 0.204 (Rfree = 0.244) at 1.9 A resolution. Each PCK molecule consists of a 275 residue N-terminal domain and 265 residue C-terminal or mononucleotide-binding domain, with the active site postulated to be within a cleft between the two domains. PCK is an open-faced, mixed alpha/beta protein, with each domain having an alpha/beta folding topology as found in several other mononucleoside-binding enzymes. The putative phosphate-binding site of ATP adopts the P-loop motif common to many ATP and GTP-binding proteins, and is similar in structure to that found within adenylate kinase. However, the beta-sheet topology within the mononucleotide-binding fold of PCK differs from all other families within the P-loop containing nucleoside triphosphate hydrolase superfamily, therefore suggesting it represents the first member in a new family of such proteins. The mononucleotide-binding domain is also different in structure compared to the classical mononucleotide-binding fold (CMBF) common to adenylate kinase, p21ras, and elongation factor-Tu. Several amino acid residues, including R65, K212, K213, H232, K254, D269, K288 and R333 appear to make up the active site of the enzyme, and are found to be absolutely conserved among known members of the ATP-dependent PCK family. A cysteine residue is located near the active-site, as has been suggested for other PCKs, although in the E. coli enzyme C233 is buried and so is most likely not involved in substrate binding or catalysis. Two binding sites of the calcium-analog TB3+ have been determined, one within the active site coordinating to the side-chain of D269, and the other within the C-terminal domain coordinating to the side-chains of E508 and E511.

Amino Acid Sequence↗
PubMed1996

Snapshot of an enzyme reaction intermediate in the structure of the ATP-Mg2+-oxalate ternary complex of Escherichia coli PEP carboxykinase.

We report the 1.8 A crystal structure of adenosine triphosphate (ATP)-magnesium-oxalate bound phosphoenolpyruvate carboxykinase (PCK) from Escherichia coli. ATP binding induces a 20 degree hinge-like rotation of the N- and C-terminal domains which closes the active-site cleft. PCK possesses a novel nucleotide-binding fold, particularly in the adenine-binding region, where the formation of a cis backbone torsion angle in a loop glycine residue promotes intimate contacts between the adenine-binding loop and adenine, while stabilizing a syn conformation of the base. This complex represents a reaction intermediate analogue along the pathway of the conversion of oxaloacetate to phosphoenolpyruvate, and provides insight into the mechanistic details of the chemical reaction catalysed by this enzyme.

Adenosine Triphosphate↗
PubMed1996

Complementarity determining region residues aspartic acid at H55, serine at H95 and tyrosines at H97 and L96 play important roles in the B72.3 antibody-TAG72 antigen interaction.

Structural analysis derived from the crystallographic study of the chimeric B72.3 antibody illustrated some major atomic interactions between complementarity determining region (CDR) residues. For example, hydrogen bonds are formed between H35/H95, L50/H97, H53/H55 and H96/L96 respectively. These CDR residues may play important roles in the B72.3-TAG72 (antibody-antigen) interaction either by direct interaction with the TAG72 antigen or by maintaining a CDR loop conformation through atomic interactions between CDR residues. In order to confirm these assumptions, we altered these CDR residues by site-directed mutagenesis and determined binding affinities of these mutant chimeric antibodies for the TAG72 antigen in a solid-phase radioimmunoassay. We found that H55, H95, H97 and L96 are important CDR residues for the B72.3-TAG72 interaction. Single amino acid substitutions of aspartic acid and serine by alanine at H55 of CDR2 and at H95 of CDR3 respectively and of tyrosine by phenylalanine at H97 and L96 of CDR3, significantly reduced the binding affinity for the TAG72 antigen by 20-, 8-, 16- and 45-fold respectively. Therefore, this study reveals some of the requirements for maintaining the integrity of the B72.3 antibody combining sites.

Amino Acid Sequence↗
PubMed1995

Framework residues 71 and 93 of the chimeric B72.3 antibody are major determinants of the conformation of heavy-chain hypervariable loops.

Structural analysis derived from the crystallographic study of the chimeric B72.3 antibody illustrated that some heavy-chain framework residues having atomic interactions with heavy-chain CDR residues may directly affect the conformation of CDR loops. For example, an alanine residue at H71 provides room for packing CDR2/CDR1 and lysine residues at H73 and H93 contribute a salt-bridge to aspartic acid at H55 in CDR2 and a hydrogen bond to the carbonyl group at H96 in CDR3, respectively. We have analysed the contribution of these framework residues to the TAG72-binding affinity. We altered these framework residues by site-directed mutagenesis, and determined the affinity of these mutant chimeric antibodies for the TAG72 antigen by solid phase radioimmunoassay. We found that a single amino acid substitution of alanine by phenylalanine at H71 or lysine by isoleucine at H93, significantly reduced the binding affinity for the TAG72 antigen by 12 and 20-fold, respectively, whereas the substitution of lysine by alanine at H73 reduced the binding affinity only two-fold. Our results indicate that heavy-chain framework residues alanine at H71 and lysine at H93 of the chimeric B72.3 antibody are the major determinants of the conformation of heavy-chain CDR2/CDR1 and CDR3 loops, whereas the salt-bridge between lysine at H73 and aspartic acid at H55 is less important. The hydrogen bond between two framework residues, glutamine at H5 and serine at H25 does not affect any CDR conformation. Our results will thus be of importance especially when the humanized B72.3 antibody is constructed by grafting the CDR loops to a human framework. The important framework region interactions must be maintained in the final humanized antibody.

Amino Acid Sequence↗
PubMed1994

Crystallization of Ulex europaeus lectin I.

The lectin I from Ulex europaeus (UEAI) has a strong affinity for the H-type 2 human blood group determinant. Single crystals of UEAI have been grown in the monoclinic crystal system. Initial crystals were obtained after 11 months from a solution of 10 mg/ml protein, 40% 2,4-methylpentanediol and 0.1 N acetate buffer at pH 5.2. The technique of washing and reseeding was used to generate large suitable crystals. The space group is C2 with a = 78.84 A, b = 69.85 A, c = 120.62 A, beta = 108.74 degrees and Z = 4; there is one molecular dimer per asymmetric unit and the solvent content is estimated to be 58%. The crystals diffract to at least 2.8 A d spacings and are stable in the X-ray beam for more than three days.

Carbohydrate Sequence↗
PubMed1994

2',3'-Didehydro-2',3'-dideoxy-5-hydroxymethyluridine.

The furanose ring in C10H12N2O5 adopts the O(4')-endo envelope conformation (0E) and the glycosidic torsion angle C(2)--N(1)--C(1')--O(4'), chi, is 245.2 (3) degrees. The pseudo-rotational parameters are P = 102.7 degrees and tau m = 5.2 degrees. The CH2OH group on C(5') has the t conformation [gamma = 179.2 (2) degrees].

Antiviral Agents↗
PubMed1994

The 1.6 A structure of histidine-containing phosphotransfer protein HPr from Streptococcus faecalis.

The histidine-containing phosphocarrier protein (HPr) is a central component of the phosphoenolpyruvate: sugar phosphotransferase system (PTS) that transports carbohydrates across the cell membrane of bacteria. The three-dimensional structure of Gram-positive Streptococcus faecalis HPr has been determined using the method of multiple isomorphous replacement. The R factor for all data is 0.156 for S. faecalis HPr at 1.6 A resolution with very good geometry. The overall folding topology of HPr is a classical open-faced beta-sandwich, consisting of four antiparallel beta-strands and three alpha-helices. Remarkable disallowed Ramachandran torsion angles of Ala16 at the active center, revealed by the X-ray structure of S. faecalis HPr, demonstrate a unique example of torsion-angle strain that is likely involved directly in protein function. A brief report concerning the torsion-angle strain has been presented recently. A newly-determined pH 7.0 structure is shown to have the same open conformation of the active center and the same torsion-angle strain at Ala16, suggesting that pH is not responsible for the structural observations. The current structure suggests a role for residues 12 and 51 in HPr's function, since they are involved in the active center through direct and indirect hydrogen-bonding interactions with the imidazole ring of His15. It is found that Ser46, the regulatory site in HPr from Gram-positive bacteria, N-caps the minor alpha-B helix and is also involved in the Asn43-Ser46 beta-turn. This finding, in conjunction with the proposed routes of communication between the regulatory site Ser46 and the active center in S. faecalis HPr, provides new insight into the understanding of how Ser46 might function. The putative involvement of the C-terminal alpha-carboxyl group and the related Gly67-Glu70 reverse beta-turn with respect to the function of HPr are described.

Amino Acid Sequence↗
PubMed1994

Trifluoperazine-induced conformational change in Ca(2+)-calmodulin.

Here we show that, as a consequence of binding the drug trifluoperazine, a major conformational movement occurs in Ca(2+)-calmodulin (CaM). The tertiary structure changes from an elongated dumb-bell, with exposed hydrophobic surfaces, to a compact globular form which can no longer interact with its target enzymes. It is likely that inactivation of Ca(2+)-CaM by trifluoperazine is due to this major tertiary-structural alteration in Ca(2+)-CaM, which is initiated and stabilized by drug binding. This conformational change is similar to that which occurs on the binding of Ca(2+)-CaM to target peptides. Two hydrophobic binding pockets, created by amino acid residues adjacent to Ca(2+)-coordinating residues, form the key recognition sites on Ca(2+)-CaM for both inhibitors and target enzymes.

Amino Acid Sequence↗
PubMed1993

The 2.0-A resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPr. A redetermination.

The x-ray structure of Escherichia coli HPr has been redetermined at 2.0-A resolution. In contrast to the previous study (El-Kabbani, O. A. L., Waygood, E. B., and Delbaere, L. T. J. (1987) J. Biol. Chem. 262, 12926-12929), the overall structure is, in general, similar to other reported NMR and x-ray HPr structures, although there are some important differences in detail. The overall folding topology of HPr is a classical open-faced beta-sandwich, consisting of four antiparallel beta-strands and three alpha-helices. The least square refinement produced an R index of 0.135 for all measured unique data between 8.0 and 2.0 A resolution. The active center consists of His15 which is hydrogen bonded to a sulfate anion, and Arg17 which has a fully open conformation. This corresponds to the first observed "semi-closed" conformation of the active center of HPr. The Streptococcus faecalis HPr structure (Jia, Z., Vandonselaar, M., Quail, J. W., and Delbaere, L. T. J. (1993) Nature 361, 94-97) has the "open" conformation in which the side chains of His15 and Arg17 are directed as far away from each other as possible. The Bacillus subtilis HPr (Herzberg, O., Reddy, P., Sutrina, S., Saier, M. H., Jr., Reizer, J., and Kapadia, G. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 2499-2503) has the "closed" conformation in which the side chains of His15 and Arg17 are close together with a sulfate anion located in the active center. The open conformation represents the unphosphorylated form of HPr whereas the closed conformation likely resembles the phosphorylated form of HPr. The semi-closed conformation observed in the E. coli HPr structure could represent a structural intermediate on the phosphorylation/dephosphorylation pathway of HPr.

Amino Acid Sequence↗
PubMed1993

Evaluation of mutagenesis for epitope mapping. Structure of an antibody-protein antigen complex.

The location and description of epitopes on proteins describe the basis of immunological specificity. The 2.8-A structure of the phosphocarrier protein, HPr from Escherichia coli, complexed to the Fab fragment of the monoclonal antibody, Jel42, has been determined. This allows the first comparison of epitope predictions from extensive site-directed mutagenesis experiments, coupled with biological activity studies (Sharma, S., Georges, F., Klevit, R. E., Delbaere, L. T. J., Lee, J. S., and Waygood, E. B. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 4877-4881), with those from x-ray analysis. There are 14 amino acid residues of E. coli HPr that interact with the Jel42 antigen-binding site. Nine of these were correctly assigned by the mutagenesis studies. Of the 5 remaining residues, Met-1 could not be altered; two others appear to have critical roles in determining protein conformation; the other 2 residues have a minimal effect on antibody binding since they are located on the periphery of the epitope with one face of their side chains in van der Waals contact with the antibody and the other face in contact with solvent. Four residues were incorrectly assigned to the epitope. These residues were located adjacent to epitope residues that were likely perturbed by these mutations. This study demonstrates that mutations which caused greater than 10-fold changes in antibody binding affinity were correctly assigned to the epitope by the mutagenesis experiments. Guidelines are also presented in order to minimize incorrect assignments.

Amino Acid Sequence↗
PubMed1993

Structures of the lectin IV of Griffonia simplicifolia and its complex with the Lewis b human blood group determinant at 2.0 A resolution.

The structures of the fourth lectin isolated from Griffonia simplicifolia (GS4) and its complex with the methyl-glycoside of the Lewis b human blood group determinant (Le(b)-OMe) are reported at high resolution. The native GS4 crystal is isomorphous with the complexed GS4 crystal. The space group is P4(2)2(1)2 with unit cell dimensions a = 78.9 A, c = 89.1 A with one subunit of the lectin (bound to 1 Le(b)-OMe in the complex) in the crystallographic asymmetric unit. The native GS4 structure was solved by the molecular replacement technique and least-squares refined (PROLSQ and X-PLOR). The orientation of the Le(b)-OMe tetrasaccharide in the complex was established from a 2.8 A difference map with coefficients (Fcomplex--Fnative) and calculated phase angles from the native model. Both the final native and complex GS4 models consist of 1904 protein non-hydrogen atoms, one sulfate ion, one Ca ion, one Mn ion and three covalently-bound sugar residues N-linked to Asn18. In addition, the complex model has 47 Le(b)-OMe non-hydrogen atoms. The two structures have 135 water molecules in common in addition to eight and nine unique water molecules in the native and complex structures, respectively. The root-mean-square deviations from ideal bond distances and angles are 0.016 A, 3.2 degrees and 0.016 A, 3.0 degrees, for the native and complexed GS4, respectively. The R index for all unique data from 8 to 2.0 A is 0.187 for the native (19,204 reflections) and 0.181 for the complex (19,212 reflections). The tertiary structure of each subunit is similar to that of other leguminous lectins but the quaternary structure of the molecular dimer is different from that of any other lectin reported to date. The co-ordination about the Ca ion is pentagonal bipyramidal (with 1 long Ca(2+)-oxygen bond) and the co-ordination about the Mn ion is octahedral. Two conserved residues (Asp149 and Ser155) appear to be important because they are hydrogen-bonded to each other and to groups that co-ordinate the Mn ion. There are three cis-peptides in the polypeptide chain; two involve non-proline residues, one of which is homologous with other leguminous lectins and the other is unique to GS4. The two non-proline cis-peptides are located in the carbohydrate-binding site and are important for the specificity of the lectin. The molecular recognition of Le(b)-OMe by GS4 involves both polar and extensive non-polar interactions.(ABSTRACT TRUNCATED AT 400 WORDS)

Binding Sites↗
PubMed1993

Active-centre torsion-angle strain revealed in 1.6 A-resolution structure of histidine-containing phosphocarrier protein.

The histidine-containing phosphocarrier protein (HPr) is a central component of the phosphoenolpyruvate: sugar phosphotransferase system that transports carbohydrates across the cell membrane of bacteria. A typical phosphotransfer sequence is phosphoenolpyruvate-->enzyme I-->HPr-->enzyme II/IIIsugar-->sugar. This is thermodynamically favourable owing to the participation of the high-energy phosphoenolpyruvate. We report here the structure of HPr from Streptococcus faecalis determined at 1.6 A resolution. Remarkable disallowed Ramachandran torsion angles at the active centre, revealed by the X-ray structure, demonstrate a unique example of torsion-angle strain that is probably directly involved in protein function. During phosphorylation, the active-centre torsion-angle strain should facilitate the phosphotransfer reaction by lowering the activation-energy barrier. A recently reported Bacillus subtilis HPr structure, which represents the phosphorylated state of HPr with no torsion-angle strain, provides direct evidence supporting our hypothesis that torsion-angle strain plays a direct part in the function of HPr. An HPr phosphotransfer cycling mechanism is proposed, based primarily on the structures of HPr and other phosphotransferase system proteins.

Bacterial Proteins↗
PubMed1993

Differences in antigen-binding affinity caused by a single amino acid substitution in the variable region of the heavy chain.

Site-directed mutagenesis has been used to examine the importance of histidine-99 in the VH CDR3 region of a mouse/human chimeric anti-TAG72 antibody, cB72.3-1-3. The expression vectors mpSV2neo-EP1-V-m4-10C gamma 1, containing seven different mutant VH region fragments (Vm4-10) in association with the immunoglobulin enhancer (E), promoter (P1) and human genomic C gamma 1 region fragments, were transfected into a heavy chain loss mutant cell line B72.3 Mut(K), respectively. Mutant chimeric antibodies cB72.3m4-10 were purified from the transfectant supernates, and their binding affinities for the TAG72 antigen relative to that of the original cB72.3-1-3 antibody were compared. Substitution of histidine-99 by glutamine resulted in a higher affinity antibody (cB72.3m4) whereas substitution by isoleucine resulted in a lower affinity antibody (cB72.3m9). The binding affinity of these mutant antibodies varied nearly eight-fold. It was concluded that the residue at position 99 in the VH CDR3 region is in a 'contact' position in the B72.3/TAG72 antibody-combining site. The polar side-chains of glutamine and asparagine or the ionized side-chains of histidine, arginine or glutamic acid contribute to higher binding affinity, whereas the hydrophobic side-chains of isoleucine, leucine or phenylalanine resulted in a lower binding affinity for the TAG72 antigen.

Amino Acid Sequence↗
PubMed1993

The tyrosine residue at position 97 in the VH CDR3 region of a mouse/human chimeric anti-colorectal carcinoma antibody contributes hydrogen bonding to the TAG72 antigen.

One amino acid, tyrosine at position 96 and 97 in the VH CDR3 region of a mouse/human chimeric anti-TAG72 antibody cB72.3m4 was substituted by the phenylalanine residue and by a number of amino acids from different amino acid groups by the site-directed mutagenesis technique. The expression vector mpSV2neo-EP1-Vm11-16C1 containing mutant VH region fragments (Vm11-16) as well as the immunoglobulin enhances (E), promoter (P1) and the human genomic C1 region fragments, were transfected into a heavy-chain-loss mutant cell line B72.3Mut(K), respectively. Mutant chimeric cB72.3m11-16 antibodies were purified from the transfectant supernates and compared based upon their binding affinity for the TAG72 antigen relative to that of the original cB72.3m4 antibody. The data showed that a single amino acid substitution of tyrosine by phenylalanine and a number of amino acids including serine, asparagine, histidine and arginine at position 97 in the VH CDR3 region all resulted in approximate 18-fold lower binding affinity, whereas the substitution of tyrosine by phenylalanine at position 96 in the VH CDR3 region did not affect the binding affinity of the cB72.3m4 antibody. This suggests that the tyrosine residue at position 97 in the VH CDR3 region is in a contact position in the B72.3/TAG72 antibody/antigen interaction, and that the terminal hydroxyl group of the position 97 tyrosine side-chain contributes hydrogen bonding to the TAG72 antigen, whereas the position 96 tyrosine side-chain does not.

Animals↗
PubMed1991

Crystallization of the calcium-activated phosphoenolpyruvate carboxykinase from Escherichia coli K12.

Single crystals of phosphoenolpyruvate carboxykinase from Escherichia coli K12 have been grown in the orthorhombic crystal system. Single crystals developed to a maximum size of 0.25 mm x 0.25 mm x 1.5 mm by the technique of washing and reseeding. The space group is P2(1)2(1)2(1), with a = 77.24 A, b = 89.18 A, c = 93.24 A and Z = 4; there is one enzyme molecule per crystallographic asymmetric unit and the solvent content is estimated to be 59%. The crystals diffract to at least 2.8 A d spacings and decompose in the X-ray beam after approximately two days of exposure.

Calcium↗
PubMed1991

Epitope mapping by mutagenesis distinguishes between the two tertiary structures of the histidine-containing protein HPr.

Thirty-four of the 85 residues of the histidine-containing protein HPr of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system have been changed by site-directed mutagenesis. Many of the mutations have wild-type activity suggesting an unaltered tertiary structure but have altered binding to three monoclonal antibodies: Jel42, Jel44, and Jel323. This altered binding defines the residues that are involved in the epitopes of HPr. At present, two different three-dimensional structures have been determined for HPr, one from two-dimensional nuclear magnetic resonance spectra and the other from x-ray diffraction of HPr crystals. The epitope mapping for Jel42 does not distinguish between the tertiary structures. However, only the HPr structure derived from two-dimensional nuclear magnetic resonance spectra is consistent with a contiguous surface binding site that can be defined as the epitope for Jel44. Thus the x-ray structure may represent a partially unfolded HPr.

Amino Acid Sequence↗
PubMed1991

Involvement of water in host-guest interactions.

As predicted by inhibition studies the X-ray crystal structure of the complex formed between the tetrasaccharide alpha-L-Fuc(1----2)-beta-D-Gal(1----3) [alpha-L-Fuc-(1----4)]-beta-D-GlcNAc- OMe (Leb-OMe) and the lectin IV of Griffonia simplicifolia (GS-IV) shows three hydroxyl groups (referred to as the polar key) hydrogen bonded within the combining site and flanked by hydrophobic surfaces. Apart from OH-6 of the beta-D-GlcNAc unit, the six other hydroxyl groups reside at or near the periphery of the combining site. Linear enthalpy-entropy compensation is observed for complex formation with monodeoxy and other derivatives of Leb-OMe involving one of these six hydroxyl groups. Decreases in both the thermodynamic parameters (- delta H 0 and - delta S 0) are largest when a hydroxyl group is in contact with water at the periphery of the combining site. The experimental evidence indicates that the binding reactions involve very similar if not identical changes in the conformations of both the lectin and the ligands; it is therefore proposed that the enthalpy-entropy compensations arise because water molecules hydrogen bonded to the amphiphilic surfaces of the unbound oligosaccharide and the protein are more mobile (higher entropy content) and less strongly hydrogen bonded than are water molecules in bulk solution. Monte Carlo simulations of the hydration of Leb-OMe appear to support this idea. In accordance with this proposal the association of complementary amphiphilic molecular surfaces from aqueous solution is driven by the release of the water molecules from both non-polar and polar regions of the amphiphiles to form stronger hydrogen bonds in bulk water. In the case of highly amphiphilic molecules such as the oligosaccharide Leb-OMe the negative contributions to entropy change dominate positive contributions that may arise from hydrophobic effects. The GS-IV(Leb-OMe)2 complex is stabilized by the hydrogen-bonding networks involving an asparate, an asparagine and a serine residue within the combining site and the above-mentioned key hydroxyl groups. Improved packing of the molecules may also be involved.

Carbohydrate Metabolism↗