Biomedical subjects

W N Lipscomb

Publications and source records attributed to W N Lipscomb.

At least 91 records · Page 5Linked to original sources

PubMed1986

X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature.

A high-resolution x-ray crystallographic investigation of the complex between carboxypeptidase A (CPA; peptidyl-L-amino-acid hydrolase, EC 3.4.17.1) and the slowly hydrolyzed substrate glycyl-L-tyrosine was done at -9 degrees C. Although this enzyme-substrate complex has been the subject of earlier crystallographic investigation, a higher resolution electron-density map of the complex with greater occupancy of the substrate was desired. All crystal chemistry (i.e., crystal soaking and x-ray data collection) was performed on a diffractometer-mounted flow cell, in which the crystal was immobilized. The x-ray data to 1.6-A resolution have yielded a well-resolved structure in which the zinc ion of the active site is five-coordinate: three enzyme residues (glutamate-72, histidine-69, and histidine-196) and the carbonyl oxygen and amino terminus of glycyl-L-tyrosine complete the coordination polyhedron of the metal. These results confirm that this substrate may be bound in a nonproductive manner, because the hydrolytically important zinc-bound water has been displaced and excluded from the active site. It is likely that all dipeptide substrates of carboxypeptidase A that carry an unprotected amino terminus are poor substrates because of such favorable bidentate coordination to the metal ion of the active site.

Carboxypeptidases↗

PubMed1985

Substrate specificity and protonation state of ornithine transcarbamoylase as determined by pH studies.

The ornithine transcarbamoylase catalyzed reaction and its inhibition by L-norvaline have been investigated between pH 5.5 and 10.5. The steady-state turnover rate (kcat) of the enzyme from Escherichia coli increases with pH and plateaus above pH 9. Its change with pH conforms to a single protonation process with an apparent pKa of 7.3. The effect of pH on the apparent Michaelis constant (KMapp) of L-ornithine suggests that this diamino acid in its cationic form is not the substrate. Treating only the zwitterions of ornithine as substrate, the pH profile of the pseudo-first-order rate constant (kcat/KMz) of the reaction is a bell-shaped curve characterized by pKa's of 6.2 and 9.1 and asymptotic slopes of +/- 1. Similar pKa's (6.3 and 9.3) are obtained for the pKi profile of zwitterionic L-norvaline, a competitive inhibitor. The pKi profile further indicates that the alpha-amino group of the inhibitor must be charged for binding. Together, these pH profiles provide sufficient information to suggest that only the minor zwitterionic species of ornithine, H2N(CH2)3CH(NH3+)COO-, binds the enzyme productively. The selection of this substrate form by the enzyme leads to a Michaelis complex in which ornithine is poised for nucleophilic attack. Following such binding, the need for deprotonation of the delta-NH3+ group is avoided, and transcarbamoylation becomes energetically more feasible. Reaction schemes accounting for the effects of pH are proposed for the enzymic reaction.

Buffers↗

PubMed1985

Substrate specificity of aspartate transcarbamylase. Interaction of the enzyme with analogs of aspartate and succinate.

The ability of aspartate transcarbamylase from Escherichia coli to catalyze carbamylation of amino acids other than the natural substrate, L-aspartate, was examined. Cysteine, cysteate, cysteinesulfinate, and 3-nitroalanine showed kcat values at pH 7 of 0.16, 0.58, 5.2, and 62 s-1, respectively, while kcat with aspartate was 320 s-1. In a parallel study, competitive inhibition constants of 3-nitropropionate, 3-mercaptopropionate, 3-sulfopropionate, and 3-sulfinopropionate were found to be high, about 0.1 M, compared with that of succinate, 0.56 mM. Although cysteinesulfinate had low activity as a substrate, the pH dependences of kcat and kcat/Km in H2O and D2O observed with the compound closely paralleled those of aspartate. The results of these studies suggest that substrate specificity and reactivity are achieved in part by a strong, highly specific interaction of one or more active site residues with the beta-carboxylate of L-aspartate. Unlike the sigmoidal kinetics found with aspartate, saturation of native aspartate transcarbamylase by cysteine sulfinate showed a lack of cooperativity, even under conditions of activation of the reaction by ATP and inhibition by CTP. The cysteinesulfinate reaction was increased 9-fold by the bisubstrate analog N-phosphonacetyl-L-aspartate. These results were interpreted in terms of an inability of cysteinesulfinate to cause the allosteric conformational change promoted by aspartate.

Amino Acids↗

PubMed1985

Binding of a possible transition state analogue to the active site of carboxypeptidase A.

The mode of binding of the competitive inhibitor 2-benzyl-3-formylpropanoic acid to the active site of carboxypeptidase A has been studied by x-ray diffraction methods to a resolution of 1.7 A. The actual species bound to the enzyme was determined to be the gem-diol resulting from covalent hydration at the aldehyde carbonyl. Details relating to the process of association of inhibitor with enzyme are unknown at this time: the free aldehyde could initially bind to the enzyme and subsequently undergo catalytic hydration; or, the hydrate itself could be the species initially binding to the enzyme, because it does exist to a high degree (25%) in aqueous solution. Nevertheless, the structure of the complex reported is reminiscent of a possible tetrahedral intermediate that would be encountered in a general base hydrolytic mechanism. Of course, other mechanistic proposals, such as the anhydride pathway, cannot be ruled out simply on the basis of the structure of this enzyme-inhibitor complex.

Binding Sites↗

PubMed1985

Structure at 2.9-A resolution of aspartate carbamoyltransferase complexed with the bisubstrate analogue N-(phosphonacetyl)-L-aspartate.

In an x-ray diffraction study by the isomorphous replacement method, the structure of the complex of aspartate carbamoyltransferase (EC 2.1.3.2) bound to the bisubstrate analogue N-(phosphonacetyl)-L-aspartate has been solved to 2.9-A resolution (R = 0.24). The large quaternary structural changes previously deduced by molecular replacement methods have been confirmed: the two catalytic trimers (c3) move apart by 12 A and mutually reorient by 10 degrees, and the regulatory dimers (r2) reorient each about its twofold axis by about 15 degrees. In this, the T-to-R transition, new polar interactions develop between equatorial domains of c chains and the Zn domain of r chains. Within the c chain the two domains, one binding the phosphonate moiety (polar) and the other binding the aspartate moiety (equatorial) of the inhibitor N-(phosphonacetyl)-L-aspartate, move closer together. The Lys-84 loop makes a large relocation so that this residue and Ser-80 bind to the inhibitor of an adjacent catalytic chain within c3. A very large change in tertiary structure brings the 230-245 loop nearer the active site, allowing Arg-229 and Gln-231 to bind to the inhibitor. His-134 is close to the carbonyl group of the inhibitor, and Ser-52 is adjacent to its phosphonate group. However, no evidence exists in the literature for phosphorylation of serine in the mechanism. Residues studied by other methods, including Cys-47, Tyr-165, Lys-232, and Tyr-240, are too far from the inhibitor to have a direct interaction.

Aspartate Carbamoyltransferase↗

PubMed1984

Leucine aminopeptidase from bovine lens and hog kidney. Comparison using immunological techniques, electron microscopy, and X-ray diffraction.

The crystallization of leucine aminopeptidase from hog kidney is reported for the first time. The crystals which diffract to 4-A resolution have the space group P2(1)2(1)2(1) (a = 186.3 A, b = 223.2 A, and c = 80.5 A) and contain four hexamers per unit cell, or one per asymmetric unit. Electron micrographic images of hog kidney leucine aminopeptidase are indistinguishable from micrographs of beef leucine aminopeptidase taken under the same conditions (10). These reveal an equilateral triangle of about 85 A per side, seemingly made of three 40-A diameter spheres. This triangle is circumscribed by another concentric, less-dense triangle of 120 A per side which is rotated 60 degrees with respect to the inner triangle. Immunodiffusion and microcomplement fixation assays indicate that the two enzymes share greater than 90% amino acid sequence homology. This similarity is corroborated by peptide maps of tryptic fragments of the radioiodinated enzymes. The model of the quaternary structure proposed to explain the appearance of electron micrographs of single molecule and crystalline bovine lens enzyme also describes the hog kidney enzyme equally well. That the model of leucine aminopeptidase originally proposed for the beef enzyme also can be used to describe hog kidney leucine aminopeptidase crystal packing in the highly anisometric unit cell provides further corroboration that leucine aminopeptidase in these two species is a hexamer based on two trimers each made of three bilobal promoters.

Animals↗

PubMed1984

Structure of unligated aspartate carbamoyltransferase of Escherichia coli at 2.6-A resolution.

The three-dimensional structure of the allosteric enzyme aspartate carbamoyltransferase (EC 2.1.3.2) has been refined to a crystallographic R-factor of 0.24 at 2.6-A resolution in the space group P321, where a and b are 122.1 A and c is 142.2 A. This structure is isomorphous to the form of the enzyme complexed to the allosteric inhibitor cytidine triphosphate. All sources of sequence information have been evaluated against the electron density. The corrected amino acid sequences of the catalytic and regulatory proteins have been incorporated in the model, and three regions in the active site are described: (i) near arginine-105, histidine-134, and arginine-167, (ii) near lysine-232 and arginine-229, and (iii) near lysine-83 and lysine-84.

Amino Acid Sequence↗

PubMed1984

Effects of pH on the structure and function of carboxypeptidase A: crystallographic studies.

High-resolution crystal structures are described for carboxypeptidase A (EC 3.4.17.1) in crystals grown at pH 8.5, 9.0, and 9.5 and compared with the structure at pH 7.5. The comparison shows that in the pH range of 7.5-9.5 the enzyme structure is practically unchanged, and, most importantly, that the flexible side chain of Tyr-248 remains exclusively in the "up" position, away from the Zn atom, throughout the pH range. There is no evidence for binding of Tyr-248 to Zn at any of these pH values. We conclude that the interaction of Tyr-248 with Zn is not an essential part of the mechanism of carboxypeptidase A and that its occurrence is an artifact of chemical modification of Tyr-248. It is also suggested that Tyr-248 is not uniquely associated with the observed high pK of the enzymatic hydrolysis.

Animals↗

PubMed1983

Refined crystal structure of carboxypeptidase A at 1.54 A resolution.

The crystal structure of bovine carboxypeptidase A (Cox) has been refined at 1.54 A resolution using the restrained least-squares algorithm of Hendrickson & Konnert (1981). The crystallographic R factor (formula; see text) for structure factors calculated from the final model is 0.190. Bond lengths and bond angles in the carboxypeptidase A model have root-mean-square deviations from ideal values of 0.025 A and 3.6 degrees, respectively. Four examples of a reverse turn like structure (the "Asx" turn) requiring an aspartic acid or asparagine residue are observed in this structure. The Asx turn has the same number of atoms as a reverse turn, but only one peptide bond, and the hydrogen bond that closes the turn is between the Asx side-chain CO group and a main-chain NH group. The distributions of CO-N and NH-O hydrogen bond angles in the alpha-helices and beta-sheet structures of carboxypeptidase A are centered about 156 degrees. A total of 192 water molecules per molecule of enzyme are included in the final model. Unlike the hydrogen bonding geometry observed in the secondary structure of the enzyme, the CO-O(wat) hydrogen bond angle is distributed about 131 degrees, indicating the role of the lone pair electrons of the carbonyl oxygen in the hydrogen bond interaction. Twenty four solvent molecules are observed buried within the protein. Several of these waters are organized into hydrogen-bonded chains containing up to five waters. The average temperature factor for atoms in carboxypeptidase A is 8 A2, and varies from 5 A2 in the center of the protein, to over 30 A2 at the surface.

Amino Acid Sequence↗

PubMed1983

Unexpected similarity of the structures of the weakly toxic amanitin (S)-sulfoxide and the highly toxic (R)-sulfoxide and sulfone as revealed by proton nuclear magnetic resonance and X-ray analysis.

The three-dimensional structures of the slightly toxic diastereomeric (S)-sulfoxide of 6'-O-methyl-alpha-amanitin [6'-O-Me-alpha-ama (S)-sulfoxide, 4] and of the corresponding highly toxic sulfone 5 have been determined by X-ray diffraction analysis. The same derivatives along with 6'-O-methyl-alpha-amanitin [O-Me-alpha-ama (R)-sulfoxide, 3] and the corresponding thioether (O-Me-alpha-ama sulfide, 6] have been investigated in dimethyl sulfoxide solutions by 360-MHz 1H NMR spectroscopy including nuclear Overhauser effects (NOE). In addition alpha-amanitin (2) has been reinvestigated by this high-resolution method involving the identification of the ABMX systems of the tryptophan, cysteine, and asparagine and discrimination between the glycine residues. The structures of compounds 2-6 are compared with the structure of beta-amanitin which was solved previously by X-ray structure analysis. The results are (1) the structures in the crystalline state of the (S)-sulfoxide 4 and sulfone 5 are practically identical and (2) in dimethyl sulfoxide solution the structures of compounds 4 and 5 are likewise identical with each other and with those of the (R)-sulfoxide 3 and the thioether 6. The general structure of the peptide backbone of the alpha-amanitin derivatives investigated here almost corresponds to that of beta-amanitin (1), the main difference being a rotated plane of the peptide bond between the asparagine and cysteine residue. In order to explain the lack of high toxicity in the (S)-sulfoxide 4 we tentatively suggest alternative hydrogen bonding of a donor from the protein, or displacement of the R oxygen to the S oxygen of a hydrogen bond donor. This alternative bonding or displacement might not occur in the sulfoxide 4. Other explanations which include local conformational changes in the inhibitors or a difference between the SO and SO2 local dipoles are also possible.

Amanitins↗

PubMed1983

Crystallographic studies on apocarboxypeptidase A and the complex with glycyl-L-tyrosine.

The crystal structures of zinc-free carboxypeptidase A (apocarboxypeptidase A) and the complex of glycyl-L-tyrosine with apocarboxypeptidase A are described and compared to the corresponding structures of the zinc-containing enzyme. Only small conformational changes in the zinc ligands accompany removal of the metal. Interactions between the tyrosine residue of glycyl-L-tyrosine and apocarboxypeptidase A are similar to those observed in the complex with the holoenzyme. However, in the absence of zinc, the carbonyl oxygen of the glycyl moiety now receives a hydrogen bond from the side chain of arginine-127. Although not as yet observed, a similar shift of the carbonyl oxygen of a susceptible bond from the zinc to arginine-127 could stabilize tetrahedral intermediates generated during the hydrolysis of substrates by carboxypeptidase.

Apoenzymes↗

PubMed1983