Coenzyme amino acid complexes

Resonance forms of the coenzyme amino acid complex, A electromerio displacements indicated by the curly arrows. 

Pyridoxal phosphate is a coenzyme for many enzymes involved in amino acid metabolism, especially in transamination and decarboxylation. It is also the cofactor of glycogen phosphorylase, where the phosphate group is catalytically important. In addition, vitamin Bg is important in steroid hormone action where it removes the hormone-receptor complex from DNA binding, terminating the action of the hormones. In vitamin Bg deficiency, this results in increased sensitivity to the actions of low concentrations of estrogens, androgens, cortisol, and vitamin D. 

Another interesting example is SHMT. This enzyme catalyzes decarboxylation of a-amino-a-methylmalonate with the aid of pyridoxal-5 -phosphate (PLP). This is an unique enzyme in that it promotes various types of reactions of a-amino acids. It promotes aldol/retro-aldol type reactions and transamination reaction in addition to decarboxylation reaction. Although the types of apparent reactions are different, the common point of these reactions is the formation of a complex with PLP. In addition, the initial step of each reaction is the decomposition of the Schiff base formed between the substrate and pyridoxal coenzyme (Fig. 7-3). 

In mammals and in the majority of bacteria, cobalamin regulates DNA synthesis indirectly through its effect on a step in folate metabolism, catalyzing the synthesis of methionine from homocysteine and 5-methyltetrahydrofolate via two methyl transfer reactions. This cytoplasmic reaction is catalyzed by methionine synthase (5-methyltetrahydrofolate-homocysteine methyl-transferase), which requires methyl cobalamin (MeCbl) (253), one of the two known coenzyme forms of the complex, as its cofactor. 5 -Deoxyadenosyl cobalamin (AdoCbl) (254), the other coenzyme form of cobalamin, occurs within mitochondria. This compound is a cofactor for the enzyme methylmalonyl-CoA mutase, which is responsible for the conversion of T-methylmalonyl CoA to succinyl CoA. This reaction is involved in the metabolism of odd chain fatty acids via propionic acid, as well as amino acids isoleucine, methionine, threonine, and valine. 

The Schiff base can undergo a variety of reactions in addition to transamination, shown in Fig. 6.4 for example, racemization of the amino acid via the a-deprotonated intermediate. Many of these reactions are catalyzed by metal ions and each has its equivalent nonmetallic enzyme reaction, each enzyme containing pyridoxal phosphate as a coenzyme. Many ideas of the mechanism of the action of these enzymes are based on the behavior of the model metal complexes. 

This designed construct, as such, may not influence subsequent steps of transamination due to loss of the strong association between the coenzyme and the synthetic peptide after amino acid binding. However, the selectivity of the peptide for pyridoxal phosphate reveals the potential power of peptide design and the importance of secondary binding interactions for defining the formation of specific binary complexes. 

More recently, the Pam amino acid chimera has also been incorporated into a small j0j0a-motif peptide scaffold [28]. The family of BBA peptides was developed in our laboratory as structured platforms for the design of functional motifs. These motifs are attractive because they are small enough (23 residues) to be easily synthesized by standard solid phase synthesis methods. Additionally, the motifs appear to possess sufficient structural complexity to influence coenzyme properties while still being amenable to structural characterization by standard spectroscopic techniques [3, 29, 30]. The BBA peptides include a -hairpin domain with a type IT turn connected by a loop region to an a-heli-cal domain (Fig. 10). Packing of the sheet and helix against one another is accomplished by hydrophobic contacts created by a hydrophobic core of residues. 

The active center of an LDH subunit is shown schematically in Fig. 2. The peptide backbone is shown as a light blue tube. Also shown are the substrate lactate (red), the coenzyme NAD (yellow), and three amino acid side chains (Arg-109, Arg-171, and His-195 green), which are directly involved in the catalysis. A peptide loop (pink) formed by amino acid residues 98-111 is also shown. In the absence of substrate and coenzyme, this partial structure is open and allows access to the substrate binding site (not shown). In the enzyme lactate NAD"" complex shown, the peptide loop closes the active center. The catalytic cycle of lactate dehydrogenase is discussed on the next page. 

Enzymes, like other proteins, have molecular weights ranging from about 12,000 to more than 1 million. Some enzymes require no chemical groups for activity other than their amino acid residues. Others require an additional chemical component called a cofactor—either one or more inorganic ions, such as Fe2+, Mg2+, Mn2+, or Zn2+ (Table 6-1), or a complex organic or metalloorganic molecule called a coenzyme (Table 6-2). Some enzymes require both a coenzyme... 

The amino acid units that make up a protein molecule are joined together in a precise sequence when the protein is made on a ribosome. The chain is then folded, often into a very compact form. Sometimes the chain is then cut in specific places. Pieces may be discarded and parts may be added. A metal ion, a coenzyme derived from a vitamin, or even a single methyl group may be attached to form the biologically active protein. The final product is a complex and sophisticated machine, often with moving parts, that is exquisitely designed for its particular role. 

A detailed study of amino acid sequences and mechanistic similarities in various polyketide synthase (PKS) enzymes has led to two main types being distinguished. Type I enzymes consist of one or more large multifunctional proteins that possess a distinct active site for every enzyme-catalysed step. On the other hand, Type II enzymes are multienzyme complexes that carry out a single set of repeating activities. Like fatty acid synthases, PKSs catalyse the condensation of coenzyme A esters of simple carboxylic acids. However, the variability at each step in... 

The NADP-IDH from Escherichia coli has been thoroughly studied. It is a dimeric protein of two identical 40-kDa subunits. High-resolution X-ray crystal structures have been determined for the enzyme with and without substrate [16,17], and for the pseudo-Michaelis complex of the enzyme with isocitrate and NADP [18], Structures of sequential intermediates formed during the catalytic action of IDH are also available [19], Additionally, the kinetic and catalytic mechanisms have been determined in detail [20], Amino acid residues which are involved in interactions with substrate, coenzyme, metal ions, and catalysis have been identified [10,21],... 

The chromophoric pyridoxal phosphate coenzyme provides a useful spectrophotometric probe of catalytic events and of conformational changes that occur at the pyridoxal phosphate site of the P subunit and of the aiPi complex. Tryptophan synthase belongs to a class of pyridoxal phosphate enzymes that catalyze /3-replacement and / -elimination reactions.3 The reactions proceed through a series of pyridoxal phosphate-substrate intermediates (Fig. 7.6) that have characteristic spectral properties. Steady-state and rapid kinetic studies of the P subunit and of the aiPi complex in solution have demonstrated the formation and disappearance of these intermediates.73-90 Fig. 7.7 illustrates the use of rapid-scanning stopped-flow UV-visible spectroscopy to investigate the effects of single amino acid substitutions in the a subunit on the rate of reactions of L-serine at the active site of the P subunit.89 Formation of enzyme-substrate intermediates has also been observed with the 012P2 complex in the crystalline state.91 ... 

Biotin, an essential water-soluble B-complex vitamin, is the coenzyme for four human carboxylases (Fig. 12-2) These include the three mitochondrial enzymes pyruvate carboxylase, which converts pyruvate to oxaloacetate and is the initial step of gluconeogenesis propionyl-CoA carboxylase, which catabolizes several branched-chain amino acids and odd-chain fatty acids and 3-methylcrotonyl-CoA carboxylase, which is involved in the catabolism of leucine and the principally cytosolic enzyme, acetyl-CoA carboxylase, which is responsible for the... 

The mammalian synthesis of methionine is more complex and requires cobalamin, a coenzyme form of vitamin B12. Note that because methionine is an essential amino acid, it must be supplied in the diet methionine that is used for methylation (Fig. 15-20) is degraded to homocysteine, and this is remethylated to give methionine. These reactions merely recycle methionine and do not constitute a means of net synthesis. 

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