51
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Dunn MF, Biellmann J-F, Branlant G. Roles of zinc ion and reduced coenzyme in horse liver alcohol dehydrogenase catalysis. The mechanism of aldehyde activation. Biochemistry 1975; 14:3176-82. [PMID: 238585 DOI: 10.1021/bi00685a022] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
1,4,5,6-Tetrahydronicotinamide adenine dinucleotide (H2NADH) has been investigated as a reduced coenzyme analog in the reaction between trans-4-N,N-dimethylaminocinnamaldehyde (I) (lambdamax 398 nm, epsilonmax 3.15 X 10-4 M-minus 1 cm-minus 1) and the horse liver alcohol dehydrogenase-NADH complex. These equilibrium binding and temperature-jump kinetic studies establish the following. (i) Substitution of H2NADH for NADH limits reaction to the reversible formation of a new chromophoric species, lambdamax 468 nm, epsilonmax 5.8 x 10-4 M-minus 1 cm-minus 1. This chromophore is demonstrated to be structurally analogous to the transient intermediate formed during the reaction of I with the enzyme-NADH complex [Dunn, M. F., and Hutchison, J. S. (1973), Biochemistry 12, 4882]. (ii) The process of intermediate formation with the enzyme-NADH complex is independent of pH over the range 6.13-10.54. Although studies were limited to the pH range 5.98-8.72, a similar pH independence appears to hold for the H2NADH system. (iii) Within the ternary complex, I is bound within van der Waal's contact distance of the coenzyme nicotinamide ring. (iv) Formation of the transient intermediate does not involve covalent modification of coenzyme. Based on these findings, we conclude that zinc ion has a Lewis acid function in facilitating the chemical activation of the aldehyde carbonyl for reduction, and that reduced coenzyme plays a noncovalent effector role in this substrate activating step.
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52
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Brown LR, Bradbury JH. Proton-magnetic-resonance studies of the lysine residues of ribonuclease A. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 54:219-27. [PMID: 238843 DOI: 10.1111/j.1432-1033.1975.tb04131.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The amino groups of ribonuclease A (RNase-A) have been methylated with formaldehyde and borohydride to provide observable resonances for proton magnetic resonance (PMR) studies. Although enzymatic activity is lost, PMR difference spectroscopy and PMR studies of thermal denaturation show native conformation is largely preserved in methylated RNase-A. Resonances corresponding to the NH2-terminal alpha-amino and 10 xi-amino N-methyl groups are titrated at 220 MHz to obtain pK values. After correction for the effects of methylation, using values previously derived from model compound studies, a pK of 6.6 is found for the alpha-amino group, a pK of 8.6 for the xi-amino group of lysine-41 and pK values ranging from 10.6 to 11.2 for the other lysine xi-amino groups. Interactions between lysine-7 and lysine-41 or between the alpha-amino and xi-amino groups of lysine-1 have been proposed to account for deviations from simple titration behaviour. The correct continuities for the titration curves of the histidine H-2 proton resonances have been confirmed by selective deuteration of the H-2 protons. Titration curves for the H-2 proton resonances of histidine-12 and histidine-119 of methylated RNase-A show deviations from the titration curves for the native enzyme, indicating some alteration of the active-site conformation. In the presence of phosphate, titration curves for the H-2 proton resonances of histidine-12 and histidine-119 of methylated RNase-A indicate binding of phosphate at the active site, but these curves continue to show deviations from the titration behaviour of native RNase-A. The titration curve for the N-methyl resonance of lysine-41 is perturbed considerably by the presence of phosphate, which indicates a possible catalytic role for lysine-41.
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53
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54
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Shore JD, Santiago D. The role of metal in liver alcohol dehydrogenase catalysis. Spectral and kinetic studies with cobalt-substituted enzyme. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41676-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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55
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56
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Dunford HB. Kinetic exclusion rules applied to the study of pH-dependent enzyme reactions: application of the diffusion-controlled limit. J Theor Biol 1974; 46:467-79. [PMID: 4424632 DOI: 10.1016/0022-5193(74)90009-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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57
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Fan CC, Plaut GW. Functional Groups of Diphosphopyridine Nucleotide-linked Isocitrate Dehydrogenase from Bovine Heart. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42397-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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58
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Murakami H, Mori H, Taira S. Active centre model on the structure and function of the bleomycin molecule as the prototype of esteratic enzymes. J Theor Biol 1973; 42:443-60. [PMID: 4128957 DOI: 10.1016/0022-5193(73)90240-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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59
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60
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Ingraham LL. Mechanism of proton transfer. II. Transfers to and from imidazole. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 304:891-3. [PMID: 4742439 DOI: 10.1016/0304-4165(73)90238-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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61
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Robertus JD, Kraut J, Alden RA, Birktoft JJ. Subtilisin; a stereochemical mechanism involving transition-state stabilization. Biochemistry 1972; 11:4293-303. [PMID: 5079900 DOI: 10.1021/bi00773a016] [Citation(s) in RCA: 319] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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62
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63
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Wright CS. Comparison of the active site stereochemistry and substrate conformation in -chymotrypsin and subtilisin BPN'. J Mol Biol 1972; 67:151-63. [PMID: 5064999 DOI: 10.1016/0022-2836(72)90391-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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64
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Covalent Labeling of the Active Site of Human Carbonic Anhydrase B with N-Bromoacetylacetazolamide. J Biol Chem 1972. [DOI: 10.1016/s0021-9258(19)45107-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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65
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66
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Waara I, Lövgren S, Liljas A, Kannan KK, Bergstén PC. Functional aspects of the three-dimensional structure of the active site of carbonic anhydrase. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1972; 28:169-87. [PMID: 4628558 DOI: 10.1007/978-1-4684-3222-0_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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67
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Khalifah RG, Edsall JT. Carbon dioxide hydration activity of carbonic anhydrase: kinetics of alkylated anhydrases B and C from humans (metalloenzymes-isoenzymes-active sites-mechanism). Proc Natl Acad Sci U S A 1972; 69:172-6. [PMID: 4621546 PMCID: PMC427569 DOI: 10.1073/pnas.69.1.172] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A stop-flow kinetic study was performed on the carbon dioxide hydration activity of the human carbonic anhydrase B isoenzyme carboxymethylated at its histidine(200), and of the human C isoenzyme carboxyketoethylated at its histidine(63). The Michaelis-Menten parameters determined between pH 5.6 and 8.7 showed striking differences between the native and the alkylated enzymes, as well as between the modified enzymes themselves. The alkylations caused: (i) a decrease in the k(cat) values, particularly marked for the carboxymethylated B isoenzyme, (ii) a change in the apparent pK of the k(cat) curves, and (iii) a dependence of K(m) on pH, for the alkylated enzymes, in contrast to the pH-independent K(m) values of the native enzymes. The CO(2) hydration and esterase activities of the carboxymethyl B isoenzyme differ markedly in their pH dependence. A kinetic mechanism, which is found to be compatible with all the present observations, is proposed. The results indicate that the modifiable histidine residues do not play an essential role in the catalytic mechanism of the native carbonic anhydrases, but they may well influence the enzyme activity in a secondary role.
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68
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Usher DA, Erenrich ES, Eckstein F. Geometry of the first step in the action of ribonuclease-A (in-line geometry-uridine2',3'-cyclic thiophosphate- 31 P NMR). Proc Natl Acad Sci U S A 1972; 69:115-8. [PMID: 4500543 PMCID: PMC427556 DOI: 10.1073/pnas.69.1.115] [Citation(s) in RCA: 122] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Advantage was taken of the reversibility of the first step of ribonuclease-A action to synthesize the dinucleoside phosphorothioate Up(S)C from the crystalline isomer of uridine 2',3'-cyclic phosphorothioate [Up(S)] and cytidine. Cyclic phosphorothioate was then reformed from Up(S)C by a nonenzymic reaction known to proceed by an in-line mechanism. The geometry of the enzymic reaction was determined to be in-line by a comparison of the Up(S) product with the Up(S) originally used. By the principle of microscopic reversibility, the geometry of the first step in the action of ribonuclease-A is shown to be in-line.
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69
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Lee B. Conformation of penicillin as a transition-state analog of the substrate of peptidoglycan transpeptidase. J Mol Biol 1971; 61:463-9. [PMID: 4257008 DOI: 10.1016/0022-2836(71)90393-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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70
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71
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72
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73
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74
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5 Chymotrypsinogen: X-Ray Structure. ACTA ACUST UNITED AC 1971. [DOI: 10.1016/s1874-6047(08)60396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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75
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76
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Markland FS, Smith EL. 16 Subtilisins: Primary Structure, Chemical and Physical Properties. HYDROLYSIS: PEPTIDE BONDS 1971. [DOI: 10.1016/s1874-6047(08)60407-2] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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77
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7 Chymotrypsin-Chemical Properties and Catalysis. ACTA ACUST UNITED AC 1971. [DOI: 10.1016/s1874-6047(08)60398-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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78
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Liu TY, Elliott S. 17 Streptococcal Proteinase. ACTA ACUST UNITED AC 1971. [DOI: 10.1016/s1874-6047(08)60408-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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79
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Fruton JS. 4 Pepsin. ACTA ACUST UNITED AC 1971. [DOI: 10.1016/s1874-6047(08)60395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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80
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Usher DA, Richardson DI, Eckstein F. Absolute stereochemistry of the second step of ribonuclease action. Nature 1970; 228:663-5. [PMID: 5474937 DOI: 10.1038/228663a0] [Citation(s) in RCA: 113] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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81
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Vinogradov SN, Hudson RA, Scott RM. Models of intermolecular interactions involving proton transfer in biopolymers. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 214:6-27. [PMID: 5488951 DOI: 10.1016/0005-2795(70)90065-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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82
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Weintraub H, Baulieu EE. [Delta 5-4 3-oxosteroid isomerase. Characteristics of groups implicated in proton transfer]. EUROPEAN JOURNAL OF BIOCHEMISTRY 1970; 12:217-21. [PMID: 5459565 DOI: 10.1111/j.1432-1033.1970.tb00840.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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83
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Polgár L, Bender ML. The nature of general base-general acid catalysis in serine proteases. Proc Natl Acad Sci U S A 1969; 64:1335-42. [PMID: 5271756 PMCID: PMC223289 DOI: 10.1073/pnas.64.4.1335] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The high reactivity of the serine residue at the active site of serine proteases is often attributed to the formation of a hydrogen bond between this serine and a histidine residue. In the case of the serine protease subtilisin, the catalytic serine residue can be specifically replaced by a cysteine residue and this modified enzyme is called thiol-subtilisin. By studying the D(2)O effect on acyl-enzyme formation with subtilisin and thiol-subtilisin, we present evidence that thiol-subtilisin but not subtilisin may contain a hydrogen bond. Based on the comparison of the catalytic activities of subtilisin and thiol-subtilisin, a rigid active site model for the serine proteases is proposed in which the histidine residue operates in a fixed steric position both as a general base and as a general acid, and this, rather than the formation of a hydrogen bond, accounts for the high nucleophilicity of the serine residue.
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84
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Liu TY, Nomura N, Jonsson EK, Wallace BG. Streptococcal Proteinase-catalyzed Hydrolysis of Some Ester and Amide Substrates. J Biol Chem 1969. [DOI: 10.1016/s0021-9258(18)63622-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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85
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Roberts GC, Dennis EA, Meadows DH, Cohen JS, Jardetzky O. The mechanism of action of ribonuclease. Proc Natl Acad Sci U S A 1969; 62:1151-8. [PMID: 5256413 PMCID: PMC223627 DOI: 10.1073/pnas.62.4.1151] [Citation(s) in RCA: 107] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The possible mechanisms of action of bovine pancreatic ribonuclease are discussed in the light of the detailed knowledge of the geometry of the active site that has been derived from studies of inhibitor binding by X-ray diffraction and nuclear magnetic resonance. When combined with a knowledge of the mechanism of phosphate ester hydrolysis, this information imposes severe geometric constraints on possible mechanisms of action of the enzyme. Two types of mechanism can be distinguished, the linear and the pseudorotation. The linear mechanism includes a catalytic role for both histidine residues at the active site and does not involve pseudorotation of the intermediate. In contrast, in the pseudorotation mechanism one histidine residue performs all the catalytic functions, while the other serves only to bind the phosphate anion; this necessarily involves pseudorotation of the intermediate and specific protonation of the leaving group by the enzyme. The mode of binding of the product of the reaction, cytidine-3'-monophosphate, has been elucidated by X-ray diffraction and nuclear magnetic resonance. If the substrate binds in an analogous way, only the linear mechanism is possible. This mechanism is described in detail.
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86
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Abstract
The problem of the mechanism of pepsin action is considered in relation to recent data on the kinetics and specificity of the enzyme, as well as the finding, reported here, that pepsin exhibits a deuterium isotope effect in the cleavage of a peptide bond. The kinetic parameters for the hydrolysis of the Phe(NO(2))-Phe bond of Gly-Gly-Gly-Phe(NO(2))-Phe-OMe by pepsin have been determined in H(2)O and in D(2)O. The finding of a significant deuterium isotope effect (k(H2O)/k(D2O) = ca. 2) supports the hypothesis that the catalytic mechanism of pepsin involves the participation, in the rate-limiting step, of a proton donor (probably an enzymic carboxyl group) in addition to an enzymic carboxylate group acting as a nucleophile.
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87
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