Francisco J. Medrano

Insights into the Specificity of Thioredoxin Reductase-Thioredoxin Interactions. A Structural and Functional Investigation of the Yeast Thioredoxin System †

The enzymatic activity of thioredoxin reductase enzymes is endowed by at least two redox centers: a flavin and a dithiol/disulfide CXXC motif. The interaction between thioredoxin reductase and thioredoxin is generally species-specific, but the molecular aspects related to this phenomenon remain elusive. Here, we investigated the yeast cytosolic thioredoxin system, which is composed of NADPH, thioredoxin reductase (ScTrxR1), and thioredoxin 1 (ScTrx1) or thioredoxin 2 (ScTrx2). We showed that ScTrxR1 was able to efficiently reduce yeast thioredoxins (mitochondrial and cytosolic) but failed to reduce the human and Escherichia coli thioredoxin counterparts. To gain insights into this specificity, the crystallographic structure of oxidized ScTrxR1 was solved at 2.4 A resolution. The protein topology of the redox centers indicated the necessity of a large structural rearrangement for FAD and thioredoxin reduction using NADPH. Therefore, we modeled a large structural rotation between the two ScTrxR1 domains (based on the previously described crystal structure, PDB code 1F6M ). Employing diverse approaches including enzymatic assays, site-directed mutagenesis, amino acid sequence alignment, and structure comparisons, insights were obtained about the features involved in the species-specificity phenomenon, such as complementary electronic parameters between the surfaces of ScTrxR1 and yeast thioredoxin enzymes and loops and residues (such as Ser(72) in ScTrx2). Finally, structural comparisons and amino acid alignments led us to propose a new classification that includes a larger number of enzymes with thioredoxin reductase activity, neglected in the low/high molecular weight classification.

Crystallization and preliminary X-ray diffraction analysis of XAC1151, a small heat-shock protein from Xanthomonas axonopodis pv. citri belonging to the alpha-crystallin family.

The hspA gene (XAC1151) from Xanthomonas axonopodis pv. citri encodes a protein of 158 amino acids that belongs to the small heat-shock protein (sHSP) family of proteins. These proteins function as molecular chaperones by preventing protein aggregation. The protein was crystallized using the sitting-drop vapour-diffusion method in the presence of ammonium phosphate. X-ray diffraction data were collected to 1.65 angstroms resolution using a synchrotron-radiation source. The crystal belongs to the rhombohedral space group R3, with unit-cell parameters a = b = 128.7, c = 55.3 angstroms. The crystal structure was solved by molecular-replacement methods. Structure refinement is in progress.

Crystallization, data collection and phasing of infestin 4, a factor XIIa inhibitor.

Infestin is a protein from Triatoma infestans (kissing bug) composed of seven Kazal-type domains that is further processed to yield several serine protease inhibitors with varying specificities. Infestins 3 and 4 are the last two domains of the infestin gene and are found in vivo in the insects anterior midgut. The last domain, infestin 4, has been cloned, expressed and purified. Here, the crystallization of infestin 4 using the sitting-drop vapour-diffusion method with PEG 8000 as precipitant is described. Crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 25.89, b = 45.64, c = 57.41 A. X-ray diffraction data were collected to a maximum resolution of 1.8 A using a synchrotron-radiation source. Initial phases were calculated by molecular replacement using an edited rhodniin molecule as the search model. Structure refinement is in progress.

Crystallization and preliminary X-ray diffraction analysis of an oxidized state of Ohr from Xylella fastidiosa.

Xylella fastidiosa organic hydroperoxide-resistance protein (Ohr) is a dithiol-dependent peroxidase that is widely conserved in several pathogenic bacteria with high affinity for organic hydroperoxides. The protein was crystallized using the hanging-drop vapour-diffusion method in the presence of PEG 4000 as precipitant after treatment with organic peroxide (t-butyl hydroperoxide). X-ray diffraction data were collected to a maximum resolution of 1.8 A using a synchrotron-radiation source. The crystal belongs to the hexagonal space group P6(5)22, with unit-cell parameters a = b = 87.66, c = 160.28 A. The crystal structure was solved by molecular-replacement methods. The enzyme has a homodimeric quaternary structure similar to that observed for its homologue from Pseudomonas aeruginosa, but differs from the previous structure as the active-site residue Cys61 is oxidized. Structure refinement is in progress.

Investigation of the functional role of active site loop II in a hypoxanthine phosphoribosyltransferase

Hypoxanthine phosphoribosyltransferases (HPRTs) are of biomedical interest because defects in the enzyme from humans can result in gouty arthritis or Lesch-Nyhan syndrome, and in parasites these enzymes are potential targets for antiparasite chemotherapy. In HPRTs, a long flexible loop (active site loop II) closes over the active site during the enzyme catalyzed reaction. Functional roles for this loop have been proposed but have yet to be substantiated. For the present study, seven amino acids were deleted from loop II of the HPRT from Trypanosoma cruzi to probe the functional role of this active site loop in catalysis. The mutant enzyme (Deltaloop II) was expressed in bacteria, purified by affinity chromatography, and kinetic constants were determined for substrates of both forward (purine salvage) and reverse (pyrophosphorolysis) reactions catalyzed by the enzyme. Loop II deletion resulted in moderate (0.6-2.7-fold) changes in the Michaelis constants (K(m)s) for substrates other than pyrophosphate (PP(i)), for which there was a 5.8-fold increase. In contrast, k(cat) values were severely affected by loop deletion, with rates that were 240-840-fold below those for the wild-type enzyme. Together with previously reported structural data, these results are consistent with active site loop II participating in transition-state stabilization by precise positioning of the substrates for in line nucleophilic attack and in the liberation of PP(i) as a product of the salvage reaction.

Crystallization and preliminary X-ray diffraction analysis of NADPH-dependent thioredoxin reductase I from Saccharomyces cerevisiae

Thioredoxin reductase 1 (Trr1) from Saccharomyces cerevisiae is a member of the family of pyridine nucleotide-disulfide oxidoreductases capable of reducing the redox-active disulfide bond of the cytosolic thioredoxin 1 (Trx1) and thioredoxin 2 (Trx2). NADPH, Trr1 and Trx1 (or Trx2) comprise the thioredoxin system, which is involved in several biological processes, including the reduction of disulfide bonds and response to oxidative stress. Recombinant Trr1 was expressed in Escherichia coli as a His6-tagged fusion protein and purified by nickel-affinity chromatography. The protein was crystallized using the hanging-drop vapour-diffusion method in the presence of PEG 3000 as precipitant after treatment with hydrogen peroxide. X-ray diffraction data were collected to a maximum resolution of 2.4 A using a synchrotron-radiation source. The crystal belongs to the centred monoclinic space group C2, with unit-cell parameters a = 127.97, b = 135.41, c = 75.81 A, beta = 89.95 degrees. The crystal structure was solved by molecular-replacement methods and structure refinement is in progress.

Expression, purification, crystallization and preliminary X-ray analysis of YaeQ (XAC2396) from Xanthomonas axonopodis pv. citri

Xanthomonas axonopodis pv. citri YaeQ (XAC2396) is a member of a family of bacterial proteins conserved in several Gram-negative pathogens. Here, the cloning, expression, purification and crystallization of the 182-residue (20.6 kDa) YaeQ protein are described. Recombinant YaeQ containing selenomethionine was crystallized in space group P2(1) and crystals diffracted to 1.9 A resolution at a synchrotron source. The unit-cell parameters are a = 39.75, b = 91.88, c = 48.03 A, beta = 108.37 degrees. The calculated Matthews coefficient suggests the presence of two YaeQ molecules in the asymmetric unit. Initial experimental phases were calculated by the multiple-wavelength anomalous dispersion technique and an interpretable electron-density map was obtained.

Crystallization, data collection and phasing of black-eyed pea trypsin/chymotrypsin inhibitor in complex with bovine β-trypsin

The black-eyed pea trypsin and chymotrypsin inhibitor (BTCI) is a Bowman-Birk-type inhibitor from Vigna unguiculata seeds. A complex of BTCI with bovine beta-trypsin was crystallized by the hanging-drop vapour-diffusion method with ammonium sulfate as precipitant. Crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 59.3, b = 61.8, c = 80.0 A. Diffraction data were collected to 2.36 A resolution and were processed to give an overall R(sym) of 0.137. The Matthews coefficient for one complex per asymmetric unit is 2.2 A(3) Da(-1), with a corresponding solvent content of 43%. After molecular replacement and initial refinement, the model gives an R(cryst) of 0.361 and an R(free) of 0.432.

Crystallization and preliminary X-ray diffraction analysis of HeLp, a heme lipoprotein from the hemolymph of the cattle tick Boophilus microplus

The main protein present in the hemelymph of the cattle tick Boophilus microplus is a lipoprotein able to bind heme (HeLp). It has an apparent molecular weight of 354 000 Da and is composed of two polypeptide chains found in stoichiometric amounts. It contains 33% lipids. The protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 1,6-hexanediol as a precipitant. X-ray diffraction data were collected to 2.1 A resolution using a synchrotron-radiation source. The crystal belongs to the triclinic space group P1, with unit-cell parameters a = 90.58, b = 105.50, c = 116.14 A, alpha = 112.40, beta = 111.64, gamma = 91.35 degrees. Owing to the lack of information about the amino-acid sequence, the structure of HeLp will be solved by the use of heavy atoms. Several possible derivatives have been collected and analysis is under way.