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1.
J Cell Mol Med ; 13(9B): 3343-57, 2009 Sep.
Article in English | MEDLINE | ID: mdl-19453521

ABSTRACT

Recent evidence suggests that regulatory pathways might control sustained high levels of FOXP3 in regulatory CD4(+)CD25(hi) T (T(reg)) cells. Based on transcriptional profiling of ex vivo activated T(reg) and helper CD4(+)CD25(-) T (T(h)) cells we have identified GARP (glycoprotein-A repetitions predominant), LGALS3 (lectin, galactoside-binding, soluble, 3) and LGMN (legumain) as novel genes implicated in human T(reg) cell function, which are induced upon T-cell receptor stimulation. Retroviral overexpression of GARP in antigen-specific T(h) cells leads to an efficient and stable re-programming of an effector T cell towards a regulatory T cell, which involves up-regulation of FOXP3, LGALS3, LGMN and other T(reg)-associated markers. In contrast, overexpression of LGALS3 and LGMN enhance FOXP3 and GARP expression, but only partially induced a regulatory phenotype. Lentiviral down-regulation of GARP in T(reg) cells significantly impaired the suppressor function and was associated with down-regulation of FOXP3. Moreover, down-regulation of FOXP3 resulted in similar phenotypic changes and down-regulation of GARP. This provides compelling evidence for a GARP-FOXP3 positive feedback loop and provides a rational molecular basis for the known difference between natural and transforming growth factor-beta induced T(reg) cells as we show here that the latter do not up-regulate GARP. In summary, we have identified GARP as a key receptor controlling FOXP3 in T(reg) cells following T-cell activation in a positive feedback loop assisted by LGALS3 and LGMN, which represents a promising new system for the therapeutic manipulation of T cells in human disease.


Subject(s)
Forkhead Transcription Factors/metabolism , Gene Expression Regulation , Membrane Proteins/metabolism , T-Lymphocytes, Regulatory/cytology , CD4-Positive T-Lymphocytes/cytology , Culture Media/metabolism , Down-Regulation , Green Fluorescent Proteins/chemistry , Humans , Interleukin-2 Receptor alpha Subunit/biosynthesis , Ionomycin/pharmacology , Models, Biological , Phenotype , Signal Transduction , Transcription, Genetic
2.
Appl Microbiol Biotechnol ; 56(5-6): 718-23, 2001 Sep.
Article in English | MEDLINE | ID: mdl-11601620

ABSTRACT

The amino acid analogue selenomethionine (SeMet) is shown to be efficiently incorporated into recombinant proteins expressed in Escherichia coli grown in a simple minimal medium without the addition of synthetic amino acids. Furthermore, satisfactory SeMet incorporation is obtained with a methionine-prototrophic strain transformed with commonly used vector systems. As examples, purified tryparedoxin 1 from Crithidia fasciculata, alkylhydroperoxide reductase (AhpC) from Mycobacterium marinum and the 16-kDa antigen from M. tuberculosis are shown to be efficiently labelled with SeMet, using the culture conditions and the host/vector systems described here. Enzymatic analysis reveals no differences between native and SeMet-labelled tryparedoxin 1 enzyme. Both proteins yield crystals under similar conditions. The culture conditions and host vector systems described greatly facilitate selenium-labelling of proteins for 3-D structure determination.


Subject(s)
Escherichia coli/growth & development , Escherichia coli/genetics , Genetic Vectors , Recombinant Proteins/metabolism , Selenomethionine/metabolism , Animals , Antigens, Bacterial/genetics , Antigens, Bacterial/metabolism , Crithidia fasciculata/metabolism , Culture Media , Escherichia coli/metabolism , Escherichia coli Proteins , Mycobacterium marinum/metabolism , Peroxidases/genetics , Peroxidases/metabolism , Peroxiredoxins , Recombinant Proteins/genetics , Thioredoxins/genetics , Thioredoxins/metabolism
3.
J Mol Biol ; 312(2): 405-18, 2001 Sep 14.
Article in English | MEDLINE | ID: mdl-11554796

ABSTRACT

The molybdenum cofactor (Moco) consists of a unique and conserved pterin derivative, usually referred to as molybdopterin (MPT), which coordinates the essential transition metal molybdenum (Mo). Moco is required for the enzymatic activities of all Mo-enzymes, with the exception of nitrogenase and is synthesized by an evolutionary old multi-step pathway that is dependent on the activities of at least six gene products. In eukaryotes, the final step of Moco biosynthesis, i.e. transfer and insertion of Mo into MPT, is catalyzed by the two-domain proteins Cnx1 in plants and gephyrin in mammals. Gephyrin is ubiquitously expressed, and was initially found in the central nervous system, where it is essential for clustering of inhibitory neuroreceptors in the postsynaptic membrane. Gephyrin and Cnx1 contain at least two functional domains (E and G) that are homologous to the Escherichia coli proteins MoeA and MogA, the atomic structures of which have been solved recently. Here, we present the crystal structures of the N-terminal human gephyrin G domain (Geph-G) and the C-terminal Arabidopsis thaliana Cnx1 G domain (Cnx1-G) at 1.7 and 2.6 A resolution, respectively. These structures are highly similar and compared to MogA reveal four major differences in their three-dimensional structures: (1) In Geph-G and Cnx1-G an additional alpha-helix is present between the first beta-strand and alpha-helix of MogA. (2) The loop between alpha 2 and beta 2 undergoes conformational changes in all three structures. (3) A beta-hairpin loop found in MogA is absent from Geph-G and Cnx1-G. (4) The C terminus of Geph-G follows a different path from that in MogA. Based on the structures of the eukaryotic proteins and their comparisons with E. coli MogA, the predicted binding site for MPT has been further refined. In addition, the characterized alternative splice variants of gephyrin are analyzed in the context of the three-dimensional structure of Geph-G.


Subject(s)
Arabidopsis Proteins , Arabidopsis/chemistry , Calnexin , Carrier Proteins/chemistry , Carrier Proteins/metabolism , Coenzymes , Escherichia coli Proteins , Membrane Proteins/chemistry , Membrane Proteins/metabolism , Plant Proteins/chemistry , Plant Proteins/metabolism , Alternative Splicing/genetics , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Binding Sites , Carrier Proteins/genetics , Crystallization , Crystallography, X-Ray , Escherichia coli/chemistry , Escherichia coli/genetics , Genetic Complementation Test , Humans , Membrane Proteins/genetics , Metalloproteins/biosynthesis , Models, Molecular , Molecular Sequence Data , Molybdenum Cofactors , Mutation , Protein Structure, Secondary , Protein Structure, Tertiary , Pteridines , Receptors, Glycine/metabolism , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/metabolism , Sequence Alignment , Structure-Activity Relationship , Sulfurtransferases/chemistry , Surface Properties
4.
Biol Chem ; 382(3): 459-71, 2001 Mar.
Article in English | MEDLINE | ID: mdl-11347894

ABSTRACT

Tryparedoxins (TXNs) catalyse the reduction of peroxiredoxin-type peroxidases by the bis-glutathionyl derivative of spermidine, trypanothione, and are relevant to hydroperoxide detoxification and virulence of trypanosomes. The 3D-structures of the following tryparedoxins are presented: authentic tryparedoxin1 of Crithidia fasciculata, CfTXN1; the his-tagged recombinant protein, CfTXN1H6; reduced and oxidised CfTXN2, and an alternative substrate derivative of the mutein CfTXN2H6-Cys44Ser. Cys41 (Cys40 in TXN1) of the active site motif 40-WCPPCR-45 proved to be the only solvent-exposed redox active residue in CfTXN2. In reduced TXNs, its nucleophilicity is increased by a network of hydrogen bonds. In oxidised TXNs it can be attacked by the thiol of the 1N-glutathionyl residue of trypanothione, as evidenced by the structure of 1N-glutathionylspermidine-derivatised CfTXN2H6-Cys44Ser. Modelling suggests Arg45 (44), Glu73 (72), the Ile110 (109) cis-Pro111 (110)-bond and Arg129 (128) to be involved in the binding of trypanothione to CfTXN2 (CfTXN1). The model of TXN-substrate interaction is consistent with functional characteristics of known and newly designed muteins (CfTXN2H6-Arg129Asp and Glu73Arg) and the 1N-glutathionyl-spermidine binding in the CfTXN2H6-Cys44Ser structure.


Subject(s)
Glutathione/analogs & derivatives , Glutathione/chemistry , Spermidine/analogs & derivatives , Spermidine/chemistry , Thioredoxins/chemistry , Amino Acid Sequence , Animals , Catalytic Domain , Crithidia fasciculata , Crystallography, X-Ray/methods , Cysteine , Glutathione/metabolism , Models, Molecular , Molecular Sequence Data , Mutagenesis, Site-Directed , Protein Conformation , Sequence Homology, Amino Acid , Serine , Spermidine/metabolism , Thioredoxins/genetics , Thioredoxins/metabolism
5.
Biol Chem ; 381(3): 211-9, 2000 Mar.
Article in English | MEDLINE | ID: mdl-10782992

ABSTRACT

Tryparedoxins (TXN) are thioredoxin-related proteins which, as trypanothione:peroxiredoxin oxidoreductases, constitute the trypanothione-dependent antioxidant defense and may also serve as substrates for ribonucleotide reductase in trypanosomatids. The active site motif of TXN2, 40WCPPCR45, of Crithidia fasciculata was mutated by site-directed mutagenesis and eight corresponding muteins were expressed in E. coli as terminally His-tagged proteins, purified to homogeneity by nickel chelate chromatography, and characterized in terms of specific activity, specificity and, if possible, kinetics. Exchange of Cys41 and Cys44 by serine yielded inactive products confirming their presumed involvement in catalysis. Exchange of Arg45 by aspartate resulted in loss of activity, suggesting an activation of active site cysteines by the positive charge of Arg45. Substitution of Trp40 by phenylalanine or tyrosine resulted in moderate decrease of specific activity, as did exchange of Pro42 by glycine. Kinetic analysis of these three muteins revealed that primarilythe reaction with trypanothione is affected by the mutations. Simulation of thioredoxin or glutaredoxin-like active sites in TXN2 (P42G and W40T/P43Y, respectively) did not result in thioredoxin or glutaredoxin-like activities. These data underscore that TXNs, although belonging to the thioredoxin superfamily, represent a group of enzymes distinct from thioredoxins and glutaredoxins in terms of specificity, and appear attractive as molecular targets for the design of trypanocidal compounds.


Subject(s)
Protozoan Proteins/chemistry , Thioredoxins/chemistry , Animals , Binding Sites , Crithidia fasciculata , Models, Molecular , Mutagenesis, Site-Directed , Protozoan Proteins/genetics , Thioredoxins/genetics
6.
Biochem J ; 347(Pt 2): 553-9, 2000 Apr 15.
Article in English | MEDLINE | ID: mdl-10749686

ABSTRACT

The effects of mutation of key conserved active-site residues (Tyr-73, Phe-418, Trp-430, Arg-516, Asn-518, His-520 and His-563) of glucose oxidase from Penicillium amagasakiense on substrate binding were investigated. Kinetic studies on the oxidation of beta-D-glucose combined with molecular modelling showed the side chain of Arg-516, which forms two hydrogen bonds with the 3-OH group of beta-D-glucose, to be absolutely essential for the efficient binding of beta-D-glucose. The R516K variant, whose side chain forms only one hydrogen bond with the 3-OH group of beta-D-glucose, exhibits an 80-fold higher apparent K(m) (513 mM) but a V(max) only 70% lower (280 units/mg) than the wild type. The complete elimination of a hydrogen-bond interaction between residue 516 and the 3-OH group of beta-D-glucose through the substitution R516Q effected a 120-fold increase in the apparent K(m) for glucose (to 733 mM) and a decrease in the V(max) to 1/30 (33 units/mg). None of the other substitutions, with the exception of variant F418A, affected the apparent K(m) more than 6-fold. In contrast, the removal of aromatic or bulky residues at positions 73, 418 or 430 resulted in decreases in the maximum rates of glucose oxidation to less than 1/90. Variants of the potentially catalytically active His-520 and His-563 were completely, or almost completely, inactive. Thus, of the residues forming the active site of glucose oxidase, Arg-516 is the most critical amino acid for the efficient binding of beta-D-glucose by the enzyme, whereas aromatic residues at positions 73, 418 and 430 are important for the correct orientation and maximal velocity of glucose oxidation.


Subject(s)
Arginine/metabolism , Conserved Sequence/genetics , Glucose Oxidase/metabolism , Glucose/metabolism , Mutation/genetics , Penicillium/enzymology , Arginine/genetics , Binding Sites , Catalysis , Circular Dichroism , Escherichia coli , Glucose Oxidase/chemistry , Glucose Oxidase/genetics , Hydrogen Bonding , Kinetics , Models, Molecular , Penicillium/genetics , Protein Binding , Protein Conformation , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
9.
Protein Sci ; 8(11): 2406-17, 1999 Nov.
Article in English | MEDLINE | ID: mdl-10595543

ABSTRACT

The crystal structure of tyrosine aminotransferase (TAT) from the parasitic protozoan Trypanosoma cruzi, which belongs to the aminotransferase subfamily Igamma, has been determined at 2.5 A resolution with the R-value R = 15.1%. T. cruzi TAT shares less than 15% sequence identity with aminotransferases of subfamily Ialpha but shows only two larger topological differences to the aspartate aminotransferases (AspATs). First, TAT contains a loop protruding from the enzyme surface in the larger cofactor-binding domain, where the AspATs have a kinked alpha-helix. Second, in the smaller substrate-binding domain, TAT has a four-stranded antiparallel beta-sheet instead of the two-stranded beta-sheet in the AspATs. The position of the aromatic ring of the pyridoxal-5'-phosphate cofactor is very similar to the AspATs but the phosphate group, in contrast, is closer to the substrate-binding site with one of its oxygen atoms pointing toward the substrate. Differences in substrate specificities of T. cruzi TAT and subfamily Ialpha aminotransferases can be attributed by modeling of substrate complexes mainly to this different position of the cofactor-phosphate group. Absence of the arginine, which in the AspATs fixes the substrate side-chain carboxylate group by a salt bridge, contributes to the inability of T. cruzi TAT to transaminate acidic amino acids. The preference of TAT for tyrosine is probably related to the ability of Asn17 in TAT to form a hydrogen bond to the tyrosine side-chain hydroxyl group.


Subject(s)
Trypanosoma cruzi/enzymology , Tyrosine Transaminase/chemistry , Tyrosine Transaminase/metabolism , Amino Acid Sequence , Animals , Binding Sites , Crystallography, X-Ray/methods , Dimerization , Escherichia coli/enzymology , Humans , Macromolecular Substances , Models, Molecular , Molecular Sequence Data , Protein Conformation , Protein Structure, Secondary , Rats , Sequence Alignment , Sequence Homology, Amino Acid
10.
Free Radic Biol Med ; 27(9-10): 966-84, 1999 Nov.
Article in English | MEDLINE | ID: mdl-10569629

ABSTRACT

Thiol-dependent hydroperoxide metabolism in parasites is reviewed in respect to potential therapeutic strategies. The hydroperoxide metabolism of Crithidia fasciculata has been characterized to comprise a cascade of three enzymes, trypanothione reductase, tryparedoxin, and tryparedoxin peroxidase, plus two supportive enzymes to synthesize the redox mediator trypanothione from glutathione and spermidine. The essentiality of the system in respect to parasite vitality and virulence has been verified by genetic approaches. The system appears to be common to all genera of the Kinetoplastida. The terminal peroxidase of the system belongs to the protein family of peroxiredoxins which is also represented in Entamoeba and a variety of metazoan parasites. Plasmodial hydroperoxide metabolism displays similarities to the mammalian system in comprising glutathione biosynthesis, glutathione reductase, and at least one glutathione peroxidase homolog having the active site selenocysteine replaced by cysteine. Nothing precise is known about the antioxidant defence systems of Giardia, Toxoplasma, and Trichomonas species. Also, the role of ovothiols and mycothiols reportedly present in several parasites remains to be established. Scrutinizing known enzymes of parasitic antioxidant defence for suitability as drug targets leaves only those of the trypanosomatid system as directly or indirectly validated. By generally accepted criteria of target selection and feasibility considerations tryparedoxin and tryparedoxin peroxidase can at present be rated as the most appealing target structures for the development of antiparasitic drugs.


Subject(s)
Glutathione/analogs & derivatives , Glutathione/metabolism , Parasitic Diseases/metabolism , Peroxides/metabolism , Protozoan Proteins , Spermidine/analogs & derivatives , Amino Acid Sequence , Animals , Humans , Kinetoplastida/genetics , Kinetoplastida/metabolism , Malaria/metabolism , Models, Molecular , Molecular Sequence Data , NADH, NADPH Oxidoreductases/chemistry , NADH, NADPH Oxidoreductases/metabolism , Parasitic Diseases/drug therapy , Parasitic Diseases/parasitology , Peroxidases/chemistry , Peroxidases/genetics , Peroxidases/metabolism , Peroxiredoxins , Sequence Homology, Amino Acid , Spermidine/metabolism , Thioredoxins/chemistry , Thioredoxins/genetics , Thioredoxins/metabolism
11.
Eur J Biochem ; 264(2): 516-24, 1999 Sep.
Article in English | MEDLINE | ID: mdl-10491099

ABSTRACT

Tryparedoxin peroxidase (TXNPx), recently identified as the hydroperoxide-detoxifying enzyme of trypanosomatidae [Nogoceke, E., Gommel, D. U., Kiess, M., Kalisz, H. M. & Flohé, L. (1997) Biol. Chem. 378, 827-836], is a member of the peroxiredoxin family and is characterized by two VCP motifs. Based on a consensus sequence of TXNPx and peroxiredoxin-type peroxidases, eight TXNPx variants were designed, heterologously expressed in Escherichia coli, checked for alpha-helix content by CD and kinetically analysed. The variant Q164E was fully active, C52S, W87D and R128E were inactive and C173S, W87H, W177E and W177H showed reduced activity. Wild-type TXNPx and Q164E exhibit ping-pong kinetics with infinite maximum velocities, whereas saturation kinetics were observed with C173S and W177E. The data comply with a mechanism in which C52, primarily activated by R128 and possibly by W87, is first oxidized by hydroperoxide to a sulfenic acid derivative. C173, supported by W177, then forms an intersubunit disulfide bridge with C52. If C173 is exchanged with a redox-inactive residue (Ser) or is insufficiently activated, the redox shuttle remains restricted to C52. The shift in the kinetic pattern and decrease in specific activity of C173S and W177E may result from a limited accessibility of the oxidized C52 to tryparedoxin, which in the oxidized wild-type TXNPx presumably attacks the C173 sulfur of the disulfide bridge. The proposed mechanism of action of TXNPx is consistent with that deduced for the homologous thioredoxin peroxidase of yeast [Chae, H. Z., Uhm, T. B. & Rhee, S. G. (1994) Proc. Natl Acad. Sci. USA 91, 7022-7026] and is supported by molecular modelling based on the structure of the human peroxiredoxin 'hORF6' [Choi, H.-J., Kang, S. W. Yang, C.-H., Rhee, S. G. & Ryu, S.-E. (1998) Nat. Struct. Biol. 5, 400-406].


Subject(s)
Crithidia fasciculata/enzymology , Peroxidases/chemistry , Peroxidases/metabolism , Animals , Binding Sites , Circular Dichroism , DNA Primers , Disulfides/chemistry , Enzyme Activation , Escherichia coli , Kinetics , Models, Molecular , Mutagenesis, Site-Directed , Peroxidases/genetics , Peroxides/metabolism , Protein Structure, Secondary , Protozoan Proteins/chemistry , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Thioredoxin-Disulfide Reductase/chemistry , Yeasts/enzymology
12.
Acta Crystallogr D Biol Crystallogr ; 55(Pt 5): 969-77, 1999 May.
Article in English | MEDLINE | ID: mdl-10216293

ABSTRACT

Glucose oxidase is a flavin-dependent enzyme which catalyses the oxidation of beta-D-glucose by molecular oxygen to delta-gluconolactone and hydrogen peroxide. The structure of the enzyme from Aspergillus niger, previously refined at 2.3 A resolution, has been refined at 1.9 A resolution to an R value of 19.0%, and the structure of the enzyme from Penicillium amagasakiense, which has 65% sequence identity, has been determined by molecular replacement and refined at 1.8 A resolution to an R value of 16.4%. The structures of the partially deglycosylated enzymes have an r.m.s. deviation of 0.7 A for main-chain atoms and show four N-glycosylation sites, with an extended carbohydrate moiety at Asn89. Substrate complexes of the enzyme from A. niger were modelled by force-field methods. The resulting model is consistent with results from site-directed mutagenesis experiments and shows the beta-D-glucose molecule in the active site of glucose oxidase, stabilized by 12 hydrogen bonds and by hydrophobic contacts to three neighbouring aromatic residues and to flavin adenine dinucleotide. Other hexoses, such as alpha-D-glucose, mannose and galactose, which are poor substrates for the enzyme, and 2-deoxy-D-glucose, form either fewer bonds or unfavourable contacts with neighbouring amino acids. Simulation of the complex between the reduced enzyme and the product, delta-gluconolactone, has provided an explanation for the lack of product inhibition by the lactone.


Subject(s)
Aspergillus niger/enzymology , Bacterial Proteins/chemistry , Glucose Oxidase/chemistry , Models, Molecular , Penicillium/enzymology , Amino Acid Sequence , Bacterial Proteins/metabolism , Crystallography, X-Ray , Flavin-Adenine Dinucleotide/chemistry , Flavin-Adenine Dinucleotide/metabolism , Glucose Oxidase/metabolism , Kinetics , Molecular Sequence Data , Monosaccharides/chemistry , Monosaccharides/metabolism , Oxidation-Reduction , Protein Conformation , Substrate Specificity
13.
Acta Crystallogr D Biol Crystallogr ; 55(Pt 3): 696-8, 1999 Mar.
Article in English | MEDLINE | ID: mdl-10089473

ABSTRACT

The thioredoxin-related protein tryparedoxin I from Crithidia fasciculata has been crystallized using PEG 4000 as a precipitant. The enzyme forms long needle-shaped crystals which diffract to at least 1.7 A. A native data set has been collected at the DESY synchrotron from a flash-frozen crystal at 90 K to 1.7 A resolution. The data set shows that the crystals belong to the orthorhombic space group P212121 and have unit-cell parameters a = 37.94, b = 51. 39, c = 71.46 A. Tryparedoxin I is involved in a trypanothione-dependent peroxide metabolic pathway specific for trypanosomatids and may therefore be a suitable candidate for the design of drugs for the specific treatment of a variety of important tropical diseases caused by these parasites.


Subject(s)
Crithidia fasciculata/enzymology , Thioredoxins/chemistry , Animals , Crystallization , Crystallography, X-Ray
14.
Eur J Biochem ; 259(3): 789-94, 1999 Feb.
Article in English | MEDLINE | ID: mdl-10092865

ABSTRACT

Tryparedoxin (TXN) has recently been discovered as a constituent of the complex peroxidase system in the trypanosomatid Crithidia fasciculata [Nogoceke et al. (1997) Biol. Chem. 378, 827-836] where it catalyzes the reduction of a peroxiredoxin-type peroxidase by trypanothione. Here we report on the full-length DNA sequence of the TXN previously isolated from C. fasciculata (TXN1). The deduced amino acid sequence comprises 147 residues and matches with all the peptide sequences of fragments obtained from TXN1. It shares a characteristic sequence motif YFSAxWCPPCR with some thioredoxin-related proteins of unknown function. This motif is homologous with the CXXC motif, which characterizes the thioredoxin superfamily of proteins and is known to catalyze disulfide reductions. Sequence conservations between TXNs and the typical thioredoxins are restricted to the intimate environment of the CXXC motif and three more remote residues presumed to contribute to the folding pattern of the thioredoxin-type proteins. The TXNs thus form a distinct molecular clade within the thioredoxin superfamily. TXN1 was expressed in Escherichia coli BL21 (DE3)pLysS as a C-terminally extended and His-tagged protein, isolated by chelate chromatography and characterized functionally. The recombinant product exhibited a kinetic pattern identical with, and kinetic parameters similar to those of the authentic enzyme in the trypanothione/peroxiredoxin oxidoreductase assay. The recombinant TXN1 can therefore be considered a valuable tool for the screening of specific inhibitors as potential trypanocidal agents.


Subject(s)
Crithidia fasciculata/chemistry , Protozoan Proteins/chemistry , Thioredoxins/chemistry , Amino Acid Sequence , Animals , Base Sequence , Cloning, Molecular , Disulfides/metabolism , Kinetics , Models, Molecular , Molecular Sequence Data , Protozoan Proteins/genetics , Recombinant Proteins/genetics , Sequence Alignment , Sequence Analysis, DNA , Thioredoxins/genetics
15.
Acta Crystallogr D Biol Crystallogr ; 54(Pt 1): 105-7, 1998 Jan 01.
Article in English | MEDLINE | ID: mdl-9761826

ABSTRACT

Tyrosine aminotransferase from Trypanosoma cruzi has been crystallized from PEG 4000 at pH 6.8. The crystals belong to the monoclinic space group P21 and have lattice constants of a = 59.1, b = 103.0, c = 77.8 A, beta = 113.1 degrees for a data set measured at 138 K. The presence of a non-crystallographic twofold axis together with a Matthews parameter Vm of 2.5 A3 Da-1 indicates that the asymmetric unit contains one dimeric molecule. The crystals diffract to at least 2.7 A and are stable in the X-ray beam in a shock-frozen state. Native data sets have been collected at temperatures of 285 and 138 K using a Siemens X1000 detector on a rotating-anode generator.


Subject(s)
Trypanosoma cruzi/enzymology , Tyrosine Transaminase/chemistry , Animals , Crystallization , Crystallography, X-Ray , Trypanosoma cruzi/growth & development , Trypanosoma cruzi/ultrastructure
16.
Appl Environ Microbiol ; 64(9): 3290-9, 1998 Sep.
Article in English | MEDLINE | ID: mdl-9726873

ABSTRACT

Muconate cycloisomerases play a crucial role in the bacterial degradation of aromatic compounds by converting cis,cis-muconate, the product of catechol ring cleavage, to (4S)-muconolactone. Chloromuconate cycloisomerases catalyze both the corresponding reaction and a dehalogenation reaction in the transformation of chloroaromatic compounds. This study reports the first thorough examination of the substrate specificity of the muconate cycloisomerases from Pseudomonas putida PRS2000 and Acinetobacter "calcoaceticus" ADP1. We show that they transform, in addition to cis,cis-muconate, 3-fluoro-, 2-methyl-, and 3-methyl-cis, cis-muconate with high specificity constants but not 2-fluoro-, 2-chloro-, 3-chloro-, or 2,4-dichloro-cis,cis-muconate. Based on known three-dimensional structures, variants of P. putida muconate cycloisomerase were constructed by site-directed mutagenesis to contain amino acids found in equivalent positions in chloromuconate cycloisomerases. Some of the variants had significantly increased specificity constants for 3-chloro- or 2,4-dichloromuconate (e.g., A271S and I54V showed 27- and 22-fold increases, respectively, for the former substrate). These kinetic improvements were not accompanied by a change from protoanemonin to cis,cis-dienelactone as the product of 3-chloro-cis,cis-muconate conversion. The rate of 2-chloro-cis,cis-muconate turnover was not significantly improved, nor was this compound dehalogenated to any significant extent. However, the direction of 2-chloro-cis,cis-muconate cycloisomerization could be influenced by amino acid exchange. While the wild-type enzyme discriminated only slightly between the two possible cycloisomerization directions, some of the enzyme variants showed a strong preference for either (+)-2-chloro- or (+)-5-chloromuconolactone formation. These results show that the different catalytic characteristics of muconate and chloromuconate cycloisomerases are due to a number of features that can be changed independently of each other.


Subject(s)
Acinetobacter calcoaceticus/enzymology , Intramolecular Lyases/genetics , Intramolecular Lyases/metabolism , Pseudomonas putida/enzymology , Sorbic Acid/analogs & derivatives , Acinetobacter calcoaceticus/genetics , Biodegradation, Environmental , Escherichia coli/genetics , Intramolecular Lyases/isolation & purification , Kinetics , Lactones/metabolism , Mutagenesis, Site-Directed , Plasmids/genetics , Pseudomonas putida/genetics , Recombinant Proteins/metabolism , Sorbic Acid/metabolism , Substrate Specificity
17.
Protein Sci ; 7(6): 1286-93, 1998 Jun.
Article in English | MEDLINE | ID: mdl-9655331

ABSTRACT

cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is involved in the aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal structure of the NAD+-enzyme complex was determined by molecular replacement and refined to an R-value of 17.9% at 2.0 A. As a member of the short-chain alcohol dehydrogenase/reductase (SDR) family, the overall protein fold and positioning of the catalytic triad in BphB are very similar to those observed in other SDR enzymes, although small differences occur in the cofactor binding site. Modeling studies indicate that the substrate is bound in a deep hydrophobic cleft close to the nicotinamide moiety of the NAD+ cofactor. These studies further suggest that Asn143 is a key determinant of substrate specificity. A two-step reaction mechanism is proposed for cis-dihydrodiol dehydrogenases.


Subject(s)
Oxidoreductases/chemistry , Polychlorinated Biphenyls/metabolism , Asparagine , Binding Sites , Crystallization , Crystallography, X-Ray , Hydrogen Bonding , Macromolecular Substances , Models, Molecular , NAD/metabolism , Oxidoreductases/metabolism , Protein Folding , Substrate Specificity
18.
J Mol Biol ; 279(4): 889-900, 1998 Jun 19.
Article in English | MEDLINE | ID: mdl-9642069

ABSTRACT

The structures of cofactor-free haloperoxidases from Streptomyces aureofaciens, Streptomyces lividans, and Pseudomonas fluorescens have been determined at resolutions between 1.9 A and 1.5 A. The structures of two enzymes complexed with benzoate or propionate identify the binding site for the organic acids which are required for the haloperoxidase activity. Based on these complexes and on the structure of an inactive variant, a reaction mechanism is proposed for the halogenation reaction with peroxoacid and hypohalous acid as reaction intermediates. Comparison of the structures suggests that a specific halide binding site is absent in the enzymes but that hydrophobic organic compounds may fit into the active site pocket for halogenation at preferential sites.


Subject(s)
Bacterial Proteins/chemistry , Chloride Peroxidase/chemistry , Pseudomonas/enzymology , Streptomyces/enzymology , Amino Acid Sequence , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Chloride Peroxidase/genetics , Chloride Peroxidase/metabolism , Crystallography, X-Ray , Molecular Sequence Data , Protein Conformation , Sequence Alignment , Sequence Analysis , Structure-Activity Relationship
19.
Eur J Biochem ; 252(1): 90-9, 1998 Feb 15.
Article in English | MEDLINE | ID: mdl-9523716

ABSTRACT

The complete amino acid sequence of glucose oxidase from Penicillium amagasakiense was determined by Edman degradation and mass spectrometry of peptide fragments derived from three different specific proteolytic digests and a cyanogen bromide cleavage. The complete sequence of each monomer comprises 587 amino acid residues, contains three cysteine residues, and seven potential N-glycosylation sites, of which at least five were confirmed to be glycosylated. Glucose oxidase from P. amagasakiense shows a high degree of identity (66%) and 79% similarity to glucose oxidase from Aspergillus niger, and is a member of the glucose-methanol-choline (GMC) oxidoreductase family. The tertiary structures of glucose oxidase from A. niger and cholesterol oxidase from Brevibacterium sterolicum were superimposed to provide a template for the sequence comparison of members of the GMC family. The general topology of the GMC oxidoreductases is conserved, with the exception of the presence of an active site lid in cholesterol oxidase and the insertion of additional structural elements in the substrate-binding domain of alcohol oxidase. The overall structure can be divided into five distinct sequence regions: FAD-binding domain, extended FAD-binding domain, flavin attachment loop and intermediate region, FAD covering lid, and substrate-binding domain. The FAD-binding and the extended FAD-binding domains are composed of several separate sequence regions. The other three regions each comprise a single contiguous sequence. Four major consensus patterns have been identified, including the nucleotide-binding consensus sequence close to their N-termini. The functions of the two motifs recently selected by the Genetics Computer Group, Madison, Wisconsin, as additional signature patterns of the GMC oxidoreductases are discussed. The other consensus patterns belong to either the FAD-binding or the extended FAD-binding domain. In addition, the roles of conserved residues are discussed wherever possible.


Subject(s)
Glucose Oxidase/chemistry , Penicillium/enzymology , Amino Acid Sequence , Bacterial Proteins/chemistry , Binding Sites/genetics , Flavoproteins/chemistry , Fungal Proteins/chemistry , Mass Spectrometry , Models, Molecular , Molecular Sequence Data , Oxidoreductases/chemistry , Peptide Fragments/analysis , Protein Structure, Secondary , Protein Structure, Tertiary , Sequence Analysis , Sequence Homology, Amino Acid
20.
Structure ; 5(2): 187-202, 1997 Feb 15.
Article in English | MEDLINE | ID: mdl-9032074

ABSTRACT

BACKGROUND: . The interfacial activation of lipases results primarily from conformational changes in the enzymes which expose the active site and provide a hydrophobic surface for interaction with the lipid substrate. Comparison of the crystallization conditions used and the structures observed for a variety of lipases suggests that the enzyme conformation is dependent on solution conditions. Pseudomonas cepacia lipase (PCL) was crystallized in conditions from which the open, active conformation of the enzyme was expected. Its three-dimensional structure was determined independently in three different laboratories and was compared with the previously reported closed conformations of the closely related lipases from Pseudomonas glumae (PGL) and Chromobacterium viscosum (CVL). These structures provide new insights into the function of this commercially important family of lipases. RESULTS: . The three independent structures of PCL superimpose with only small differences in the mainchain conformations. As expected, the observed conformation reveals a catalytic site exposed to the solvent. Superposition of PCL with the PGL and CVL structures indicates that the rearrangement from the closed to the open conformation involves three loops. The largest movement involves a 40 residue stretch, within which a helical segment moves to afford access to the catalytic site. A hydrophobic cleft that is presumed to be the lipid binding site is formed around the active site. CONCLUSIONS: . The interfacial activation of Pseudomonas lipases involves conformational rearrangements of surface loops and appears to conform to models of activation deduced from the structures of fungal and mammalian lipases. Factors controlling the conformational rearrangement are not understood, but a comparison of crystallization conditions and observed conformation suggests that the conformation of the protein is determined by the solution conditions, perhaps by the dielectric constant.


Subject(s)
Bacterial Proteins/chemistry , Burkholderia cepacia/enzymology , Lipase/chemistry , Protein Conformation , Amino Acid Sequence , Bacterial Proteins/metabolism , Binding Sites , Calcium/metabolism , Crystallography, X-Ray , Lipase/metabolism , Models, Molecular , Molecular Sequence Data , Solvents , Water
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