Active site lysine

Two classes of aldolase enzymes are found in nature. Animal tissues produce a Class I aldolase, characterized by the formation of a covalent Schiff base intermediate between an active-site lysine and the carbonyl group of the substrate. Class I aldolases do not require a divalent metal ion (and thus are not inhibited by EDTA) but are inhibited by sodium borohydride, NaBH4, in the presence of substrate (see A Deeper Look, page 622). Class II aldolases are produced mainly in bacteria and fungi and are not inhibited by borohydride, but do contain an active-site metal (normally zinc, Zn ) and are inhibited by EDTA. Cyanobacteria and some other simple organisms possess both classes of aldolase. 

FIGURE 19.13 (a) A mechanism for the fructose-l,6-bisphosphate aldolase reaction. The Schlff base formed between the substrate carbonyl and an active-site lysine acts as an electron sink, Increasing the acidity of the /3-hydroxyl group and facilitating cleavage as shown. (B) In class II aldolases, an active-site Zn stabilizes the enolate Intermediate, leading to polarization of the substrate carbonyl group. 

These observations are explained by the mechanism shown in the figure. NaBH4 inactivates Class I aldolases by transfer of a hydride ion (H ) to the imine carbon atom of the enzyme-substrate adduct. The resulting secondary amine is stable to hydrolysis, and the active-site lysine is thus permanently modified and inactivated. NaBH4 inactivates Class I aldolases in the presence of either dihydroxyacetone-P or fructose-1,6-bisP, but inhibition doesn t occur in the presence of glyceraldehyde-3-P. 

FIGURE 23.3 Covalent linkage ( an active-site lysine in pyruvate carb... 

The transaldolase functions primarily to make a useful glycolytic substrate from the sedoheptulose-7-phosphate produced by the first transketolase reaction. This reaction (Figure 23.35) is quite similar to the aldolase reaction of glycolysis, involving formation of a Schiff base intermediate between the sedohep-tulose-7-phosphate and an active-site lysine residue (Figure 23.36). Elimination of the erythrose-4-phosphate product leaves an enamine of dihydroxyacetone, which remains stable at the active site (without imine hydrolysis) until the other substrate comes into position. Attack of the enamine carbanion at the carbonyl carbon of glyceraldehyde-3-phosphate is followed by hydrolysis of the Schiff base (imine) to yield the product fructose-6-phosphate. 

FIGURE 23.36 The transaldolas nism involves attack on the snbstrat active-site lysine. Departnre of eryth leaves the reactive enamine, which aldehyde carbon of glyceraldehyde- base hydrolysis yields the second pis frnctose-6-P. 

The active site lysine of ACS forms a Schiff base (internal aldimine) via its e-amino group with the bound PLP in the unliganded enzyme (Scheme 2(a)). 

The ct-amino group of the substrate SAM replaces that of active site lysine as the Schiff base partner of the cofactor (external aldimine. Scheme 2(b)) and the C-a proton of SAM is next abstracted by the e-NH2 function of active site lysine to form a quinoid intermediate (Scheme 2(c)). 

Scheme 2 Reaction mechanism of the conversion of SAM to ACC catalyzed by ACS. ACS-Lys denotes active site lysine of ACS, PLP denotes pyridoxai 5 -phosphate, and Opi-Op4 denotes oxygens of the pyridoxal 5 -phosphate moiety.

Aldolases have been classified into mechanistically distinct classes according to their mode of donor activation. Class 1 aldolases achieve stereospecific deprotonation via covalent imine/enamine formation at an active-site lysine residue, while Class II aldolases utilize a divalent transition metal cation for substrate coordination as an essential Lewis acid cofactor (usually Zn ) to facilitate deprotonation... 

The first step in this sequence is the binding of a molecule of acetaldehyde ( donor ) to the aldolase to form a Schiff base with the active site lysine followed by addition to CIAA, which acts as the acceptor aldehyde. This reaction delivers the mono-addition product, which then acts as an acceptor again to react with a second molecule of AA, yielding the double addition product which cyclizes spontaneously to the stable lactol 1 (Scheme 6.4). 

In the presence of PPi, known to bind strongly to the enzyme active site (Section III,E), there was a weak protective effect. The experimental points fell in the shaded area of Fig. 6, and the data were analyzed with equations developed by Scrutton and Utter (45). The results of this treatment led to the conclusion that TNBS can react with both free enzyme and enzyme-PPi complex to cause catalytic inactivation the differences are only quantitative (45). Either TNBS can displace PP, from an active site lysine or TNBS modifies a different lysine, apart from the active site, and the presence of PPi on the enzyme partially protects against TNBS inactivation by some indirect mechanism. Unfortunately, as discussed above, this issue cannot be settled with these kinetic analyses. Furthermore, because all of the enzyme lysines are to some extent reactive with TNBS (Fig. 5), the single super-reactive lysine whose modification leads to inactivation cannot be isolated and identified, as, for example, in a particular peptide fragment. A variety of interpretations are possible, as discussed elsewhere (45). 

RNase A is completely inhibited if either of two histidine residues (His 12 or His 119) is modified by car-boxymethylation with iodoacetate (fig. 8.13) suggesting that these histidines play important roles in the active site. In support of this conclusion, the reaction of iodoacetate with His 12 or His 119 is inhibited by cytidine-3 -phosphate and other small molecules that bind at the active site. Lysine 41 has been implicated similarly in the active site by the observation that enzymatic activity is destroyed by the reaction of... 

Aldolases such as fructose-1,6-bisphosphate aldolase (FBP-aldolase), a crucial enzyme in glycolysis, catalyze the formation of carbon-carbon bonds, a critical process for the synthesis of complex biological molecules. FBP-aldolase catalyzes the reversible condensation of dihydroxyacetone phosphate (DHAP) and glyceralde-hyde-3-phosphate (G3P) to form fructose-1,6-bisphosphate. There are two classes of aldolases the first, such as the mammalian FBP-aldolase, uses an active-site lysine to form a Schiff base, whereas the second class features an active-site zinc ion to perform the same reaction. Acetoacetate decarboxylase, an example of the second class, catalyzes the decarboxylation of /3-keto acids. A lysine residue is required for good activity of the enzyme the -amine of lysine activates the substrate carbonyl group by forming a Schiff base. 

The new aldolase differs from all other existing ones with respect to the location of its active site in relation to its secondary structure and still displays enantiofacial discrimination during aldol addition. Modification of substrate specificity is achieved by altering the position of the active site lysine from one /3-strand to a neighboring strand rather than by modification of the substrate recognition site. Determination of the 3D crystal structure of the wild type and the double mutant demonstrated how catalytic competency is maintained despite spatial reorganization of the active site with respect to substrate. It is possible to perturb the active site residues themselves as well as surrounding loops to alter specificity. 

Highbarger, L.A., Gerlt, J.A. and Kenyon, G.L. (1996) Mechanism of the reaction catalyzed by acetoacetate decarboxylase. Importance of lysine 116 in determining the pFQ of active-site lysine 115. Biochemistry, 35, 41. 

For the proline- and proline congener-catalyzed aldol reaction [23, 24], a mechanism based on enamine formation is proposed [25], Scheme 7. The catalytic process starts with condensation of the secondary amino group of proline with a carbonyl substrate leading to a nucleophilic enamine intermediate, which mimics the condensation of the active-site lysine residue with a carbonyl substrate in type I aldolases. The adjacent carboxylic acid group of the enamine intermediate... 

The probes of this type were shown to selectively label at least 75% of human kinases in crude cell lysates, thus demonstrating their selectivity and promiscuity for kinases [101]. As a follow up, the labeled kinases were subjected to proteolytic digestion, and the biotinylated peptides purified on avidin beads and analyzed by LC-MS/MS. This analysis demonstrated that the site of probe labeling was indeed the conserved active-site lysine as predicted. In contrast to the promiscuity demonstrated by the acyl phosphate probes, several selective covalent inhibitors of protein kinases have been used as ABPP probes. Wortmannin is a natural product derived from the fungus Penicillium funiculosum. It is a potent and specific covalent inhibitor of phosphoinositide 3-kinase (PI3K) and the PI3K-related kinase (PIKK) families [102, 103]. The use of natural products in relation to ABPP is covered by Breinbauer et al. [104]. 

The alanine racemization catalyzed by alanine racemase is considered to be initiated by the transaldimination (Fig. 8.5).26) In this step, PLP bound to the active-site lysine residue forms the external Schiff base with a substrate alanine (Fig. 8.5, 1). The following a-proton abstraction produces the resonance-stabilized carbanion intermediates (Fig. 8.5, 2). If the reprotonation occurs on the opposite face of the substrate-PLP complex on which the proton-abstraction proceeds, the antipodal aldimine is formed (Fig. 8.5,3). The subsequent hydrolysis of the aldimine complex gives the isomerized alanine and PLP-form racemase. The random return of hydrogen to the carbanion intermediate is the distinguishing feature that differentiates racemization from reactions catalyzed by other pyridoxal enzymes such as transaminases. Transaminases catalyze the transfer of amino group between amino acid and keto acid, and the reaction is initiated by the transaldimination, followed by the a-proton abstraction from the substrate-PLP aldimine to form a resonance-stabilized carbanion. This step is common to racemases and transaminases. However, in the transamination the abstracted proton is then tranferred to C4 carbon of PLP in a highly stereospecific manner The re-protonation occurs on the same face of the PLP-substrate aldimine on which the a-proton is abstracted. With only a few exceptions,27,28) each step of pyridoxal enzymes-catalyzed reaction proceeds on only one side of the planar PLP-substrate complex. However, in the amino acid racemase... 

Results. Lee and Houk were the first to model part of the ODCase active site when they calculated decarboxylation energetics for orotate in the presence of methylammonium ion as a mimic of the key active site lysine. Based on their conclusion that 4-protonation is an energetically favorable pathway (see above), they calculated the energy of reaction of orotate (la) plus Cf NHj to form a carbene-methylamine complex plus C02 (equation 1). 

Like transketolase, transaldolase (TA, E.C. 2.2.1.2) is an enzyme in the oxidative pentose phosphate pathway. TA is a class one lyase that operates through a Schiff-base intermediate and catalyzes the transfer of the C(l)-C(3) aldol unit from D-sedoheptulose 7-phosphate to glyceraldehyde-3-phosphate (G3P) to produce D-Fru 6-P and D-erythrose 4-phosphate (Scheme 5.59). TA from human as well as microbial sources have been cloned.110 111 The crystal structure of the E. coliu and human112 transaldolases have been reported and its similarity to the aldolases is apparent, since it consists of an eight-stranded (o /(3)s or TIM barrel domain as is common to the aldolases. As well, the active site lysine residue that forms a Schiff base with the substrate was identified.14112 Thus, both structurally and mechanistically it is related to the type I class of aldolases. 

The actual pKa value of an active site catalytic group will be influenced by the particular microenvironment of the active site, which could raise or lower the pKa. For example, the enzyme acetoacetate decarboxylase contains an active site lysine residue that forms an imine link with its substrate its pKa value was found to be 5.9, which is much less than the expected value of 9. Adjacent to this residue in the active site is a second lysine residue, which in protonated form destabflizes the protonated amine and, therefore, reduces the pKa. Conversely, aspartic acid or glutamic acid residues that are positioned in hydrophobic active sites can have increased pKa values near 7 because the anionic form of the side chain is destabilized. 

The a -amino group of the amino acid substrate displaces the e-amino group of the active-site lysine residue. In other words, an internal aldimine becomes an external aldimine. The amino acid-PLP Schiff base that is formed remains tightly bound to the enzyme by multiple noncovalent interactions. 

Transaldolase catalyzes the transfer of a C3 unit. The reaction occurs via an aldol cleavage similar to that seen with aldolase there is a schiff base intermediate formed with an active site lysine. The difference between aldolase and transaldolase is in the acceptor groups in aldolase the acceptor is a proton, in transaldolase it is another sugar. This reaction yields a F-6-P, which can go to Glycolysis, and an E-4-P which reacts with Xu-5-P catalyzed by the same transketolase seen above. This second transketolase reaction yields F-6-P and Ga-3-P, both intermediates of Glycolysis and the end products of the Pentose-P pathway. 

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