Biomedical subjects

Camiel De Ranter

Publications and source records attributed to Camiel De Ranter.

8 recordsLinked to original sources

PubMed2004

Azospirillum irakense pectate lyase displays a toroidal fold.

The three-dimensional structure of Azospirillum irakense pectate lyase (PelA) has been determined at a resolution of 2.65 A. The crystals are hexagonal, belonging to space group P6(5)22, with unit-cell parameters a = b = 85.37, c = 231.32 angstroms. Phase information was derived from a multiple-wavelength anomalous dispersion (MAD) experiment using a Hg derivative. Refinement of the model converged to Rcryst = 20.08% and Rfree = 25.87%. The overall structure of PelA does not adopt the characteristic parallel beta-helix fold displayed by pectate lyases from polysaccharide lyase (PL) families PL1, PL3 and PL9. Instead, it displays a predominantly alpha-helical structure with irregular coils and short beta-strands, similar to the recently reported structure of the catalytic module of the Cellvibrio japonicus pectate lyase Pel10Acm. The topologies of the two structures have been compared. They show two 'domains' with the interface between them being a wide-open central groove in which the active site is located. The active sites of the crystal structures are also compared and their similarities and differences are discussed.

Amino Acid Sequence↗

PubMed2004

How calcium inhibits the magnesium-dependent enzyme human phosphoserine phosphatase.

The structure of the Mg(2+)-dependent enzyme human phosphoserine phosphatase (HPSP) was exploited to examine the structural and functional role of the divalent cation in the active site of phosphatases. Most interesting is the biochemical observation that a Ca(2+) ion inhibits the activity of HPSP, even in the presence of added Mg(2+). The sixfold coordinated Mg(2+) ion present in the active site of HPSP under normal physiological conditions, was replaced by a Ca(2+) ion by using a crystallization condition with high concentration of CaCl(2) (0.7 m). The resulting HPSP structure now shows a sevenfold coordinated Ca(2+) ion in the active site that might explain the inhibitory effect of Ca(2+) on the enzyme. Indeed, the Ca(2+) ion in the active site captures both side-chain oxygen atoms of the catalytic Asp20 as a ligand, while a Mg(2+) ion ligates only one oxygen atom of this Asp residue. The bidentate character of Asp20 towards Ca(2+) hampers the nucleophilic attack of one of the Asp20 side chain oxygen atoms on the phosphorus atom of the substrate phosphoserine.

Amino Acid Sequence↗

PubMed2003

Previtamin D3 with a trans-fused decalin CD-ring has pronounced genomic activity.

Deletion of C19 in the structure of 1 alpha,25-dihydroxyvitamin D3 [1,25(OH)2D3] does not substantially alter the biological potency but prevents the conversion between the vitamin and the previtamin form. Hence, this modification allows the study of locked previtamin and vitamin forms. The locked 19-nor-1,25(OH)2-previtamin D3 analog (19-nor-previtamin D) had a low biological activity and was a rather weak activator of the genomic signal transduction pathway. 19-Nor-trans-decalin-1,25(OH)2-vitamin D3 (19-nor-TD-vitamin D), characterized by the presence of a trans-fused decalin CD-ring system, was 10-fold more potent than the parent compound and was a potent activator of the genomic signal transduction pathway. Surprisingly, the previtamin, 19-nor-trans-decalin-1,25(OH)2-previtamin D3 (19-nor-TD-previtamin D), was as potent as 1,25(OH)2D3 in inhibiting cell proliferation and inducing cell differentiation and represents the first previtamin structure with pronounced vitamin D-like activity. Furthermore, this compound interacted as efficiently as 1,25(OH)2D3 with the vitamin D receptor (VDR), retinoid X receptor (RXR), coactivators, and DNA, which illustrated its potent ability to activate the genomic signal transduction pathway. Analysis of the transactivation potency of 12 VDR point mutants after stimulation with 19-nor-TD-previtamin D revealed that this analog used the same contact points within the receptor as did 1,25(OH)2D3. This could be confirmed by modeling analysis of this compound in the ligand binding pocket of VDR. In conclusion, a previtamin D3 analog is presented with genomic activities equivalent to 1,25(OH)2D3.

Amino Acid Substitution↗

PubMed2003

High-resolution structure of human phosphoserine phosphatase in open conformation.

The crystal structure of human phosphoserine phosphatase (HPSP) in the open conformation has been determined at a resolution of 1.53 A. The crystals are orthorhombic, belonging to space group C222(1), with unit-cell parameters a = 49.03, b = 130.25, c = 157.29 A. The asymmetric unit contains two molecules. Phase information was derived from a multiwavelength anomalous dispersion (MAD) experiment conducted at three wavelengths using a selenomethionine-derivative crystal of HPSP. The structure was refined using CNS to a final crystallographic R value of 21.6% (R(free) = 23.4%). HPSP is a dimeric enzyme responsible for the third and final step of the l-serine biosynthesis pathway. It catalyses the Mg2+-dependent hydrolysis of l-phosphoserine. Recently, the structure of HPSP in complex with an inhibitor bound to the active site has been reported to be the open conformation of the enzyme. Here, the structure of HPSP is reported in the absence of substrate in the active site. Evidence is presented that HPSP in an uncomplexed form is in an even more open conformation than in the inhibitor complex. In this state, the enzyme is partially unfolded to allow the substrate to enter the active site. Binding of the substrate causes HPSP to shift to the closed conformation by stabilizing the partially unfolded region. In the present structure a Ca2+ ion is bound to the active site and an explanation is given why HPSP is not active when in the active site Mg2+ is replaced by a Ca2+ ion.

Amino Acid Sequence↗

PubMed2003

Actin-DBP: the perfect structural fit?

The multifunctional vitamin D binding protein (DBP) is an actin-sequestering protein present in blood. The crystal structure of the actin-DBP complex was determined at 2.4 A resolution. DBP binds to actin subdomains 1 and 3 and occludes the cleft at the interface between these subdomains. Most remarkably, DBP demonstrates an unusually large actin-binding interface, far exceeding the binding-interface areas reported for other actin-binding proteins such as profilin, DNase I and gelsolin. The fast-growing side of actin monomers is blocked completely through a perfect structural fit with DBP, demonstrating how DBP effectively interferes with actin-filament formation. It establishes DBP as the hitherto best actin-sequestering protein and highlights its key role in suppressing and preventing extracellular actin polymerization.

Actins↗

PubMed2002

Crystallization and preliminary X-ray diffraction analysis of a novel pectate lyase from Azospirillum irakense.

The PelA gene from the N(2)-fixing plant-associated bacterium Azospirillum irakense encodes a pectate lyase. Analysis of the corresponding amino-acid sequence revealed no homology to other bacterial, plant and fungal pectinases of known published structure, resulting in the classification of the enzyme in a new pectate lyase family. The A. irakense PelA has been crystallized using the hanging-drop vapour-diffusion method at 277 K. The crystals are hexagonal, with unit-cell parameters a = b = 85.55, c = 230.13 A, gamma = 120 degrees, and belong to space group P6(5)22 or P6(1)22, having one molecule per asymmetric unit. Diffraction data to a resolution of 1.97 A were collected at synchrotron facilities, as well as a three-wavelength MAD data set from an Hg-derivative crystal to a resolution of 2.6 A.

Azospirillum↗

PubMed2002

A structural basis for the unique binding features of the human vitamin D-binding protein.

The human serum vitamin D-binding protein (DBP) has many physiologically important functions, ranging from transporting vitamin D3 metabolites, binding and sequestering globular actin and binding fatty acids to functioning in the immune system. Here we report the 2.3 A crystal structure of DBP in complex with 25-hydroxyvitamin D3, a vitamin D3 metabolite, which reveals the vitamin D-binding site in the N-terminal part of domain I. To more explicitly explore this, we also studied the structure of DBP in complex with a vitamin D3 analog. Comparisons with the structure of human serum albumin, another family member, reveal a similar topology but also significant differences in overall, as well as local, folding. These observed structural differences explain the unique vitamin D3-binding property of DBP.

Amino Acid Sequence↗

PubMed2001

Purification, crystallization and preliminary X-ray diffraction analysis of human phosphoserine phosphatase.

Phosphoserine phosphatase (PSP), a human enzyme involved in the L-serine biosynthesis pathway, has been crystallized using the hanging-drop vapour-diffusion method at 277 K. The crystals are orthorhombic, belonging to space group C222(1), with unit-cell parameters a = 49.03 A, b = 130.25 A, c = 157.29 A. Calculation of the Matthews coefficient indicates that there are two molecules in the asymmetric unit. A complete native data set to a resolution of 1.53 A has been collected at 100 K using synchrotron radiation.

Crystallization↗