pH Dependence of the kinetic parameters for the pyrophosphate-dependent phosphofructokinase reaction supports a proton-shuttle mechanism

Biochemistry ◽  
1989 ◽  
Vol 28 (10) ◽  
pp. 4155-4160 ◽  
Author(s):  
Yong Kweon Cho ◽  
Paul F. Cook
Keyword(s):  
Kinetic Parameters ◽  
Ph Dependence

scholarly journals Treponema denticola cystalysin exhibits significant alanine racemase activity accompanied by transamination: mechanistic implications1

2003 ◽  
Vol 371 (2) ◽  
pp. 473-483 ◽  
Author(s):  
Mariarita BERTOLDI ◽  
Barbara CELLINI ◽  
Alessandro PAIARDINI ◽  
Martino Di SALVO ◽  
Carla BORRIVOLTATTORNI
Keyword(s):  
Kinetic Parameters ◽  
Binding Sites ◽  
Ph Dependence ◽  
Catalytic Efficiency ◽  
Partition Ratio ◽  
Side Reactions ◽  
Treponema Denticola ◽  
Steady State Kinetic ◽  
Reaction Specificity ◽  
State Kinetic

To obtain information on the reaction specificity of cystalysin from the spirochaete bacterium Treponema denticola, the interaction with l- and d-alanine has been investigated. Binding of both alanine enantiomers leads to the appearance of an external aldimine absorbing at 429nm and of a band absorbing at 498nm, indicative of a quinonoid species. Racemization and transamination reactions were observed to occur with both alanine isomers as substrates. The steady-state kinetic parameters for racemization, kcat and Km, for l-alanine are 1.05±0.03s−1 and 10±1mM respectively, whereas those for d-alanine are 1.4±0.1s−1 and 10±1mM. During the reaction of cystalysin with l- or d-alanine, a time-dependent loss of β-elimination activity occurs concomitantly with the conversion of the pyridoxal 5′-phosphate (PLP) coenzyme into pyridoxamine 5′-phosphate (PMP). The catalytic efficiency of the half-transamination of l-alanine is found to be 5.3×10−5 mM−1·s−1, 5-fold higher when compared with that of d-alanine. The partition ratio between racemization and half-transamination reactions is 2.3×103 for l-alanine and 1.4×104 for d-alanine. The pH dependence of the kinetic parameters for both the reactions shows that the enzyme possesses a single ionizing residue with pK values of 6.5–6.6, which must be unprotonated for catalysis. Addition of pyruvate converts the PMP form of the enzyme back into the PLP form and causes the concomitant recovery of β-elimination activity. In contrast with other PLP enzymes studied so far, but similar to alanine racemases, the apoform of the enzyme abstracted tritium from C4′ of both (4′S)- and (4′R)-[4′-3H]PMP in the presence of pyruvate. Together with molecular modelling of the putative binding sites of l- and d-alanine at the active site of the enzyme, the implications of these studies for the mechanisms of the side reactions catalysed by cystalysin are discussed.

scholarly journals Chemical mechanism of D-amino acid oxidase from Rhodotorula gracilis: pH dependence of kinetic parameters

1998 ◽  
Vol 330 (1) ◽  
pp. 311-314 ◽  
Author(s):  
F. RAMÓN ◽  
M. P. CASTILLÓN ◽  
I. DE LA MATA ◽  
C. ACEBAL
Keyword(s):  
Amino Acid ◽  
Kinetic Parameters ◽  
Ph Dependence ◽  
Competitive Inhibitor ◽  
Chemical Mechanism ◽  
Acid Oxidase ◽  
Protonation State ◽  
Amino Acid Oxidase ◽  
Basic Group ◽  
Rhodotorula Gracilis

The variation of kinetic parameters of D-amino acid oxidase from Rhodotorula gracilis with pH was used to gain information about the chemical mechanism of the oxidation of D-amino acids catalysed by this flavoenzyme. D-Alanine was the substrate used. The pH dependence of Vmax and Vmax/Km for alanine as substrate showed that a group with a pK value of 6.26-7.95 (pK1) must be unprotonated and a group with a pK of 10.8-9.90 (pK2) must be protonated for activity. The lower pK value corresponded to a group on the enzyme involved in catalysis and whose protonation state was not important for binding. The higher pK value was assumed to be the amino group of the substrate. Profiles of pKi for D-aspartate as competitive inhibitor showed that binding is prevented when a group on the enzyme with a pK value of 8.4 becomes unprotonated; this basic group was not detected in Vmax/Km profiles suggesting its involvement in binding of the β-carboxylic group of the inhibitor.

The Catalytic Mechanism of Tyrosine Phenol-Lyase from Erwinia herbicola: The Effect of Substrate Structure on pH-Dependence of Kinetic Parameters in the Reactions with Ring-Substituted Tyrosines

1996 ◽  
Vol 51 (5-6) ◽  
pp. 363-370 ◽  
Author(s):  
N. G. Faleev ◽  
S.N. Spirina ◽  
V. S. Ivoilov ◽  
T. V. Demidkina ◽  
R. S. Phillips
Keyword(s):  
Kinetic Parameters ◽  
Aromatic Ring ◽  
Catalytic Mechanism ◽  
Ph Dependence ◽  
Phenolic Hydroxyl ◽  
New Method ◽  
Erwinia Herbicola ◽  
Substrate Structure ◽  
Tyrosine Phenol Lyase ◽  
Additional Base

Abstract Apparently homogeneous tyrosine phenol-lyase (TPL) from Erwinia herbicola has been prepared by a new method. The pH-dependencies of the main kinetic parameters for the reactions of Erwinia TPL with tyrosine, 2-fluorotyrosine, 3-fluorotyrosine, 2-chlorotyrosine, and 3.4-dihydroxyphenylalanine (DOPA ) have been studied. The pattern of pH-dependence of Vmax depends on the nature of the substituent in the aromatic ring. For the substrates bearing small substituents (H, 2-F, 3-F) Kmax values were found to be pH-independent. For 2-chlorotyrosine and DOPA Vmax decreased at lower pH, the effect being described by equation with one pKa. Generally two bases are reflected in the pH dependence of Vmax/Km. The first base, probably is responsible for the abstraction of a-proton, while the second one, interacts with the phenolic hydroxyl at the stage of binding. The reaction of TPL with DOPA differs from the reactions with other tyrosines by the requirement of an additional base which is reflected in the pH-profiles of both and Vmax/Km. For the reaction of TPL from Citrobacter intermedins with DOPA only Vmax/Km values could be determined. The activity of Citrobacter enzyme towards DOPA is considerably less than that of E. herbicola enzyme, and its maximal value is attained at higher pH.

Chemical mechanism of β-xylosidase from Trichoderma reesei QM 9414: pH-dependence of kinetic parameters

Biochimie ◽  
2001 ◽  
Vol 83 (10) ◽  
pp. 961-967 ◽  
Author(s):  
María Gómez ◽  
Pablo Isorna ◽  
Marta Rojo ◽  
Pilar Estrada
Keyword(s):  
Kinetic Parameters ◽  
Trichoderma Reesei ◽  
Ph Dependence ◽  
Chemical Mechanism

Chemical mechanism of penicillin V acylase from Streptomyces lavendulae: pH-dependence of kinetic parameters

2001 ◽  
Vol 16 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Raquel Torres-Guzmán ◽  
Isabel de la Mata ◽  
Jesús Torres-Bacete ◽  
Miguel Arroyo ◽  
Marı́a Pilar Castillón ◽  
...  
Keyword(s):  
Kinetic Parameters ◽  
Ph Dependence ◽  
Chemical Mechanism ◽  
Penicillin V ◽  
Streptomyces Lavendulae ◽  
Penicillin V Acylase
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