Putative secondary active site of bovine pancreatic deoxyribonuclease I

Previous structural studies based on the co-crystal of a complex between bovine pancreatic deoxyribonuclease I (bpDNase I) and a double-stranded DNA octamer d(GCGATCGC)(2) have suggested the presence of a putative secondary active site near Ser43. In our present study, several crucial amino acid residues postulated in this putative secondary active site, including Thr14, Ser43, and His44 were selected for site-directed mutagenesis. A series of single, double and triple mutants were thus constructed and tested for their DNase I activity by hyperchromicity assay. Substitution of each or both of Thr14 and Ser43 by alanine results in mutant enzymes retaining 30-70% of WT bpDNase I activity. However, when His44 was replaced by aspartic acid, either in the single, double, or triple mutant, the enzyme activities were drastically decreased to 0.5-5% that of WT bpDNase I. Interestingly, when cysteine was substituted for Thr14 or Ser43, the specific DNase activities of the mutant enzymes were substantially increased by 1.5-100-fold, comparing to their alanine substitution mutant counterparts. Two other more sensitive DNase activity assay method, plasmid scission and zymogram analyses further confirm these observations. These results suggested that His44 may play a critical role in substrate DNA binding in this putative secondary active site, and introduction of sulfhydryl groups at Thr14 and Ser43 may facilitate Mn(2+)-coordination and further contribute to the catalytic activity of bpDNase I.     

Reassociation of deoxyribonuclease II with the lysosomal membrane isolated from porcine spleen

DNase II, bound to the lysosomal membrane of porcine spleen, can be extracted from the membrane with 0.4 M NaCl. Reassociation of DNase II with the salt-extracted lysosomal membrane is readily accomplished in 0.01 M sodium acetate (pH 4.5). The reassociable amount of DNase II is approximately equal to the extractable amount. The capacity of the lysosomal membrane to bind DNase II is unaffected by the subtilisin treatment of the membrane. Phosphatidyl serine can bind DNase II as well, but with a much higher capacity. The erythrocyte plasma membrane on the other hand binds only about 20% of DNase II bound to the lysosomal membrane. The DNase II activity can be eluted from a column of the lysosomal membrane entrapped in 2% agarose and the elution pattern is very similar to that of CM-cellulose chromatography of DNase II, suggesting that electrostatic interactions may play an important role in the binding. The pH-reassociation profile is bell-shaped and is similar to the pH-activity profile of DNase II, having a maximum near pH 5. Under the nondenaturing condition, the dissociated alpha and beta subunits of DNase II cannot be reassociated to regain the enzymatic activity with or without the lysosomal membrane.     

Deoxyribonuclease II purified from the isolated lysosomes of porcine spleen and from porcine liver homogenates. Comparison with deoxyribonuclease II purified from porcine spleen homogenates

Porcine spleen DNase II (EC 3.1.22.1), one of the best-characterized DNases II, is subcellularly located in lysosomes because the enzyme is co-sedimented with two of the lysosomal marker enzymes, cathepsin D and acid phosphatase. The physicochemical properties, including the subunit structure, sensitivity to iodoacetate inactivation, native molecular weight and chromatographic behavior, of the DNase II purified from the isolated lysosomes of porcine spleen are indistinguishable from those of the same enzyme purified from the whole porcine spleen homogenate. DNase II can also be extracted from porcine liver with 0.05 M H2SO4 or 0.1 M NaCl and purified from either extract by a series of column chromatographies. The purified liver DNase II from either extract has the same subunit structure (alpha-chain, Mr 35,000 and beta-chain, Mr 10,000) as the purified DNase II of porcine spleen. The two liver extracts as well as the extracts of spleen and gastric mucosa contain DNase II with very similar properties on Sephadex G-100 gel filtration, on acid polyacrylamide gel electrophoresis under non-denaturing conditions, and on isoelectric focusing. The data strongly suggest that, for the same species of animal, the DNase II activities in various tissues are associated with protein molecules of identical structure.     

Deoxyribose-5-P aldolase: subunit structure and composition of active site lysine region

Deoxyribose-5-P aldolase, a Class I aldolase, from Salmonella typhimurium has a molecular weight of 57,000 and is composed of two subunits of 28,500 molecular weight. Evidence from fingerprint analysis of tryptic digests and carboxypeptidase digestion suggests that the two subunits are identical. The COOH-terminal tyrosine residue which is removed by carboxypeptidase digestion appears to be necessary for catalytic activity but not for substrate binding. A tryptic peptide containing the “active site” lysyl residue modified by acetaldehyde has been purified and the following amino acid composition determined: (Ala₃, Gly₃, Thr₃, Asx₂, Ser, Ile, Phe, 1N-Lys)-Lys.     

1H NMR studies of porcine uteroferrin. Magnetic interactions and active site structure

Pink (reduced) uteroferrin exhibits well resolved paramagnetic NMR spectra with resonances ranging from 90 ppm downfield to 70 ppm upfield. The intensities of these signals depend on the degree of reduction and correlate well with the intensity of the EPR signals with gave = 1.74. Analyses of chemical shifts and the temperature dependence of the paramagnetically shifted resonances indicate that the Fe(III)-Fe(II) cluster in the reduced protein exhibits weak antiferromagnetic exchange coupling (-J approximately equal to 10 cm-1), in agreement with the estimate derived from the temperature dependence of the EPR signal intensity. Purple (oxidized) uteroferrin, on the other hand, exhibits no discernible paramagnetically shifted resonances, reflecting either strong antiferromagnetic coupling or an unfavorable electron spin-lattice relaxation time. Evans susceptibility comparisons between pink and purple uteroferrin show that the Fe(III)-Fe(III) cluster in the oxidized protein is more strongly coupled (-J greater than 40 cm-1). This value concurs with low temperature magnetic susceptibility measurements on both the porcine and splenic purple acid phosphatases. The isotropically shifted protons of tyrosine coordinated to the cluster are assigned by comparison with synthetic complexes. Tyrosine, earlier implicated as a ligand by resonance Raman spectroscopy, appears to coordinate only to the ferric site in pink uteroferrin. This is consistent with the relatively invariant extinction coefficients of uteroferrin in its oxidized and reduced forms and the ease of reduction of the nonchromophoric iron compared to its chromophoric partner. Other possible ligands to the cluster include histidine, suggested by the presence of downfield-shifted solvent-exchangeable resonances with appropriate isotropic shifts.     

The active site and partial sequence of cobra venom acetylcholinesterase

About 30% of the primary structure of acetylcholinesterase (AchE) from the cobraNaja naja oxiana has been determined. The sequence around the serine residue labeled by diisopropylfluorophosphate (DFP) was found to be TVTLFGESAGAASVGM which is similar to the active sites of AChE from other tissues. The part of the primary structure determined shows 76% identity with AChE from Torpedo and 42% identity with the Drosophila enzyme. A surprisingly large identity (42% in the sequence determined) was found with lysophospholipase from rat (Hanet al., 1987).     

Purification, characterization, and the complete amino acid sequence of porcine pancreatic deoxyribonuclease

Porcine pancreatic DNase has been purified to homogeneity. The polypeptide exhibits a single band of Mr = 34,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme is a glycoprotein containing glucosamine. The results of end group analyses show leucine at the NH2 terminus and alanine at the COOH terminus. The enzymatic properties of the purified porcine DNase are very similar to those of bovine and ovine DNases. The sequence data on the tryptic and chymotryptic peptides derived from CNBr fragments of porcine DNase, along with the results of automated Edman degradation of the intact polypeptide and of the two largest CNBr fragments, indicate the complete amino acid sequence of porcine DNase to be as follows:L-R- I-A-F-N-I-R-T-F-G-E-T-K-M-S-N-A-T-S-N-Y-I-V-R-I-L-S-R-Y-D-I-A-L-I-Q- E-V-R-D-S-H-L-T-A-V-G-K-L-L-N-E-L-N-Q-D-D-P-N-N-Y-H-H-V-V-S-E-P-L-G-R- S-T-Y-K-E-R-Y-L-F-V-F-R-P-N-Q-V-S-V-L-D-S-Y-L-Y-D-D-G-C-E-P-C-G-N-D-T- F-N-R-E-P-S-V-V-K-F-S-S-P-F-T-Q-V-K-E-F-A-I-V-P-L-H-A-A-P-S-D-A-A-A-E- I-N-S-L-Y-D-V-Y-L-N-V-R-Q-K-W-D-L-Q-D-I-M-L-M-G-D-F-N-A-G-C-S-Y-V-T- T-S-H-W-S-S-I-R-L-R-E-S-P-P-F-Q-W-L-I-P-D-T-A-D-T-T-V-S-S-H-T-C-A-Y- D-R-I-V-V-A-G-P-L-L-Q-R-A-V-V-P-D-S-A-A-P-F-D-F-Q-A-A-F-G-L-S-Q-E-T- A-L-A-I-S-D-H-Y-P-V-E-V-T-L-K-R-A. The polypeptide consists of 262 amino acid residues. One of the two disulfide loops links Cys-101 and Cys-104 and the other Cys-173 and Cys-209. Two carbohydrate side chains are attached at Asn-18 and Asn-106.     

Revised structure of the active form of human deoxyribonuclease IIalpha

Deoxyribonuclease IIalpha (DNase IIalpha) is an acid endonuclease found in lysosomes, nuclei, and various secretions. Murine DNase IIalpha is required for digesting the DNA of apoptotic cells after phagocytosis and for correct development and viability. DNase IIalpha purified from porcine spleen was previously shown to contain three peptides, two of which were thiol crosslinked, all derived by processing of a single polypeptide. Commercial bovine protein is consistent with this structure. However, screening of 18 human cell lines failed to demonstrate this processing, rather a 45 kDa protein was consistently observed. Incubation of cells with the N-glycosylation inhibitor tunicamycin resulted in a 37 kDa protein, which is close to the predicted formula weight. The protein also contains at least one thiol crosslink. Similar results were obtained with overexpressed DNase IIalpha. These results suggest that active DNase IIalpha consists of one contiguous polypeptide. We suggest the previous structure reflects proteolysis during protein purification.     

Isolation and partial amino acid sequence of three subunit species of porcine spleen ferritin: evidence of multiple H subunits

A partial amino acid sequence for three different subunits of the iron storage protein, ferritin, has been determined. Ferritin (Mr approximately 480,000) was isolated from porcine spleen and dissociated into its component subunits (Mr approximately 20,000). The subunits, in turn, were separated into three fractions by reversed-phase HPLC. The fractions appeared to be of equal size by sedimentation velocity, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and size-exclusion chromatography in 6 M guanidinium chloride. All three fractions were shown to be monomeric and to have no covalently attached carbohydrate (J. F. Collawn et al. (1984) Arch. Biochem. Biophys. 233, 260-266). Determination of the amino acid sequence of the C-terminal 70-80 residues from each of the fractions demonstrated three different sequences. Comparison with human liver H and L subunit sequences indicates that two of the porcine ferritin subunits are H-type subunits and one is an L-type subunit. Application of the Chou-Fasman algorithm on the three partial sequences suggests that these respective regions from each of the three subunits would probably adopt the same conformation.     

The volume and structure of the chymotrypsin active site

It was found that the chymotrypsin active site is located in the largest cleft on the enzyme surface approximated by a sphere with a radius of 20 angstroms. The active site cleft volume is about 2 nm3, as computed by the Monte-Carlo method. The size and shape of the active site cleft-- the intersection of two unequal spheres--are sufficient for large (about 1 nm3) fragments of substrate molecules to enter the active site. The active site bottom and the adjacent narrow section are about 600 angstroms3 in volume and may serve as a combustion chamber of a water-substrate mixture during the operation of the enzyme machinery. Intrinsic water molecules inside the combustion chamber can take part in heat exchange during different steps of the enzymatic process.     

Amino acid sequence of porcine spleen cathepsin D light chain

The complete amino acid sequence of the light chain of cathepsin D from porcine spleen has been determined. The light chain consists of a single polypeptide chain with 97 amino acid residues. The sequence is: (formula; see text) The molecular weight of the light chain was calculated from this sequence to be 10,548 (without carbohydrates). A single disulfide bond links two half-cystine residues between positions 46 and 53. A cysteine residue is located at position 27. The light chain sequence is extensively homologous to the NH2-terminal sequence of other aspartyl proteases. It shows a 59% identity with the sequence of mouse submaxillary gland renin and a 49% identity with that of porcine pepsin. A single glycosylation site is located at residue 70 of the cathepsin D light chain. This site corresponds to position 67 of pepsin by homology. The active site aspartyl residue, corresponding to Asp-32 of pepsin, is located at residue 33 in the cathepsin D light chain.