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Representation of the external aldimine with atom labeling. is the C-CA-N-C4A dihedral angle that describes the relative orientation between substrate and cofactor.
Source publication
We report a hybrid quantum mechanics/molecular mechanics theoretical study on the reaction mechanism of mammalian histidine
decarboxylase that allows us to obtain valuable insights on the structure of the cofactor-substrate adduct (external aldimine)
in the active site of rat histidine decarboxylase. By means of molecular dynamics simulations, we t...
Contexts in source publication
Context 1
... mination leads to formation of the external aldimine, whereas the conserved lysine residue is released. This external aldimine can exist in different prototropic forms, although the predom- inant form seems to be that which presents the pyridine and the amide nitrogen atoms as protonated, whereas the 3-hydroxyl group is deprotonated (29) (see Fig. ...
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... groups were set to their normal ioniza- tion state at pH 7. Then, the protein was relaxed using a poten- tial restraining scheme with a low force constant (25 kcalmol 1 Å 2 ) applied only on the peptidic backbone. Finally, the optimized protein was solvated with a 24-Å radius sphere of TIP3P water molecules using atom C4 of the substrate (see Fig. 2 for atom numbering) as the geometrical center of the system. Water molecules that were within a distance of 2.5 Å of any non-hydrogen atom were removed. The resulting system was resolvated four more times using different relative orientations between the protein and the water sphere to ensure good sol- vation of the system. Then, water ...
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... performed in water, periodic boundary conditions were applied, making use of the same switched cut-off radius. The conformational changes and decarboxylation reactions were studied through computation of the corresponding potentials of mean force (PMFs) using the canonical ensemble (NVT). A PMF was traced using the dihedral angle (see Fig. 2) as the distinguished coordinate to investigate the relative orientation of the carbox- ylate group and the pyridine ring. A total of 12 simulation win- dows were run to cover coordinate values from 80 to 180 degrees for this transition. Each window was started from the final conformation of the previous window and consisted of 10 ps ...
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... of 10 ps of equilibration and 80 ps of production using a time step of 1 fs. Changes in the selected reaction coordinate were restrained using an umbrella potential with a force constant of 1.2 kcalmol 1 degree 2 and an additional biasing potential (39). A potential of mean force was also computed using the distance between CA and C (see Fig. 2) as the reaction coordi- nate. In this case we ran 17 windows to cover a reaction coor- dinate range from 1.4 to 3.0 Å. Each consecutive window con- sisted of 10 ps of production at 310 K, with a time step of 1 fs and a force constant of 500 kcalmol 1 Å 2 . In both cases, the refer- ence temperature was 310 K. The different values of ...
Citations
... As of today, the structure of the wild type enzyme has not been solved by any experimental method. A recombinant human fragment (512-N-terminus) of the native rat homodimer-with the maximum activity assayed in vitro [31]-is very instable and exhibit an extremely low Vmax [25,34], which suggest that an uncharacterized element could be stabilizing the native dimer conformation in vivo. In addition, further evidence indicates that HDC polypeptide length and the location where it performs is activity in the cell are key factors in the physiology of histamine-producing cells. ...
Histamine is a highly pleiotropic biogenic amine involved in key physiological processes including neurotransmission, immune response, nutrition, and cell growth and differentiation. Its effects, sometimes contradictory, are mediated by at least four different G-protein coupled receptors, which expression and signalling pathways are tissue-specific. Histamine metabolism conforms a very complex network that connect many metabolic processes important for homeostasis, including nitrogen and energy metabolism. This review brings together and analyses the current information on the relationships of the “histamine system” with other important metabolic modules in human physiology, aiming to bridge current information gaps. In this regard, the molecular characterization of the role of histamine in the modulation of angiogenesis-mediated processes, such as cancer, makes a promising research field for future biomedical advances.
... Epigallocatechin gallate (EGCG), a natural compound with promising anti-inflammatory activity, has been reported to bind mammalian HDC, changing the PLP conformation inside its catalytic site, thus inhibiting enzymatic activity by blocking its reaction with histidine [34,35]. Other researchers [36] have applied quantum mechanics (QM) and molecular mechanics (MM) simulations and found that the PLP-histidine complex was located in the HDC catalytic site. In the presence of natural substrates or synthetic analogues, local changes in the active site of HDC have been reported to affect its confirmation and enzymatic stability [37]. ...
Allergy is an immunological disorder that develops in response to exposure to an allergen, and histamines mediate these effects via histidine decarboxylase (HDC) activity at the intracellular level. In the present study, we developed a 3D model of Klebsiella pneumoniae histidine decarboxylase (HDC) and analyzed the HDC inhibitory potential of cinnamaldehyde (CA) and subsequent anti-allergic potential using a bacterial and mammalian mast cell model. A computational and in vitro study using K. pneumonia revealed that CA binds to HDC nearby the pyridoxal-5′-phosphate (PLP) binding site and inhibited histamine synthesis in a bacterial model. Further study using a mammalian mast cell model also showed that CA decreased the levels of histamine in the stimulated RBL-2H3 cell line and attenuated the release of β-hexoseaminidase and cell degranulation. In addition, CA treatment also significantly suppressed the levels of pro-inflammatory cytokines TNF-α and IL-6 and the nitric oxide (NO) level in the stimulated mast cells. A gene expression and Western blotting study revealed that CA significantly downregulated the expressions of MAPKp38/ERK and its downstream pro-allergic mediators that are involved in the signaling pathway in mast cell cytokine synthesis. This study further confirms that CA has the potential to attenuate mast cell activation by inhibiting HDC and modifying the process of allergic disorders.
... Epigallocatechin gallate (EGCG), a natural compound with promising anti-inflammatory activity, has been reported to bind mammalian HDC, changing the PLP conformation inside its catalytic site, thus inhibiting enzymatic activity by blocking its reaction with histidine [34,35]. Other researchers [36] have applied quantum mechanics (QM) and molecular mechanics (MM) simulations and found that the PLP-histidine complex was located in the HDC catalytic site. In the presence of natural substrates or synthetic analogues, local changes in the active site of HDC have been reported to affect its confirmation and enzymatic stability [37]. ...
Allergy is an immunological disorder that develops in response to exposure to an allergen, and histamines mediate these effects via histidine decarboxylase (HDC) activity at the intracellular level. In the present study, we developed a 3D model of Klebsiella pneumoniae histidine decarboxylase (HDC) and analyzed the HDC inhibitory potential of cinnamaldehyde (CA) and subsequent anti-allergic potential using a bacterial and mammalian mast cell model. A computational and in vitro study using K. pneumonia revealed that CA binds to HDC nearby the pyridoxal-5′-phosphate (PLP) binding site and inhibited histamine synthesis in a bacterial model. Further study using a mammalian mast cell model also showed that CA decreased the levels of histamine in the stimulated RBL-2H3 cell line and attenuated the release of β-hexoseaminidase and cell degranulation. In addition, CA treatment also significantly suppressed the levels of pro-inflammatory cytokines TNF-α and IL-6 and the nitric oxide (NO) level in the stimulated mast cells. A gene expression and Western blotting study revealed that CA significantly downregulated the expressions of MAPKp38/ERK and its downstream pro-allergic mediators that are involved in the signaling pathway in mast cell cytokine synthesis. This study further confirms that CA has the potential to attenuate mast cell activation by inhibiting HDC and modifying the process of allergic disorders.
... The action mechanism of mammalian PLP-dependent L-amino acid decarboxylases has been previously described [54,55]. Briefly, it involves two transaldamination reactions from the PLP-enzyme complex to the L-amino acid-enzyme complex, which is decarboxylated in the substrate α-carboxylic group to form a covalent amine product-enzyme complex. ...
... Important changes in the global decarboxylase conformation have been observed for both mammalian HDC and DDC during catalysis [56,57]. The quaternary structure of HDC and DDC only differs in tautomeric forms of intermediates along the reaction, most probably due to slight differences in the active dimer conformation [54,55]. In fact, both enzymes can share substrates (i.e., L-histidine, but with different affinities) and inhibitors (for instance, epigallocathechine-3-gallate). ...
... Mammalian HDC and DDC share the catalytic mechanism explained above for HDC [54,90]. However, at least in the case of the purified recombinant wild proteins, mammalian DDC seems to be a more efficient enzyme according to their respective catalytic constant values obtained in silico and in vitro [54,55]. In the case of DDC, slight modifications of the catalytic site environment seem to induce important changes in catalytic constant (k cat ) values [90]. ...
Biogenic amines derived from basic and aromatic amino acids (B/A-BAs), polyamines, histamine, serotonin, and catecholamines are a group of molecules playing essential roles in many relevant physiological processes, including cell proliferation, immune response, nutrition and reproduction. All these physiological effects involve a variety of tissue-specific cellular receptors and signalling pathways, which conforms to a very complex network that is not yet well-characterized. Strong evidence has proved the importance of this group of molecules in the gastrointestinal context, also playing roles in several pathologies. This work is based on the hypothesis that integration of biomedical information helps to reach new translational actions. Thus, the major aim of this work is to combine scientific knowledge on biomolecules, metabolism and physiology of the main B/A-BAs involved in the pathophysiology of the gastrointestinal tract, in order to point out important gaps in information and other facts deserving further research efforts in order to connect molecular information with pathophysiological observations.
... 2 The effects of histamine on the body are well studied and include such processes as allergic reactions, gastric acid secretion, smooth muscle contractions, vasodilation, circadian rhythm regulation, cell growth, memory, inflammation, bone loss, tumor progression, learning deficiencies, epilepsy, and intracellular communication. [3][4][5][6] Histidine is an essential amino acid which plays a vital role in cellular metabolism. ...
Histidine decarboxylase (HDC) is an enzyme that converts histidine to histamine. Inhibition of HDC has several medical applications, and HDC inhibitors are of considerable interest for the study of histidine metabolism. (S)-α-Fluoromethylhistidine di-hydrochloride (α-FMH) is a potent HDC inhibitor that is commercially available at high cost in small amounts only. Here we report a novel, inexpensive, and efficient method for synthesis of α-FMH using methyl 2-aziridinyl-3-(N-triphenylmethyl-4-imidazolyl) propionate and HF/pyridine, with experimental yield of 57%. To identify novel targets for α-FMH, we developed a three step in silico work-flow for identifying physically plausible protein targets. The work-flow resulted in 21 protein target hits, including several enzymes involved in glutathione metabolism, and notably, two isozymes of the glutathione S-transferase (GST) superfamily, which plays a central role in drug metabolism. In view of this predictive data, the efficacy of α-FMH as a GST inhibitor was investigated in vitro. α-FMH was demonstrated to be an effective inhibitor of GST at micromolar concentration, suggesting that off-target effects of α-FMH may limit physiological drug metabolism and elimination by GST-dependent mechanisms. The present study therefore provides new avenues for obtaining α-FMH and for studying its biochemical effects, with potential implications for drug development.
... which is active as a homodimer. It shares a common catalytic mechanism with other PLP-dependent decarboxylases ( Fig. 1 step a-c; Olmo et al. 2002;Eliot and Kirsch 2004;Moya-García et al. 2008). The reported L-histidine K m values range from 0.11 to 0.5 mM (Tagushi et al. 1984;Tanase et al. 1985;Mamune-Sato et al. 1990;Engel et al. 1996). ...
... The first structural model of rat HDC (rHDC) was obtained by comparative modeling (Rodríguez-Caso et al. 2003a) and it has been extensively evaluated to reproduce previously published experimental data (Moya-García et al. 2008). Recently, the structure of the active human histidine decarboxylase (hHDC) complexed with HME was solved by X-ray diffraction (Komori et al. 2012). ...
... As depicted in Fig. 4, O-IMHA at 10 lM concentration is able to reduce hHDC activity by more than 80 % at any of the assayed PLP concentrations. The imidazole group of L-histidine has pKa 6.0 and anchoring of the substrate in the binding site is achieved by a system of hydrogen bonds and hydrophobic interactions (Moya-García et al. 2008), which are also established as in the case of O-IMHA. However, protonated amino groups of APA/AEA cannot participate in such types of interactions and this explains the great differences in the activities of O-IMHA and APA/AEA. ...
Histamine plays highlighted roles in the development of many common, emergent and rare diseases. In mammals, histamine is formed by decarboxylation of L-histidine, which is catalyzed by pyridoxal-5'-phosphate (PLP) dependent histidine decarboxylase (HDC, EC 4.1.1.22). The limited availability and stability of the protein have delayed the characterization of its structure-function relationships. Our previous knowledge on mammalian HDC, derived from both in silico and experimental approaches, indicates that an effective competitive inhibitor should be capable to form an "external aldimine-like structure" and have an imidazole group, or its proper mimetic, which provides additional affinity of PLP-inhibitor adduct to the HDC active center. This is confirmed using HEK-293 cells transfected to express human HDC and the aminooxy analog of histidine, 4(5)-aminooxymethylimidazole (O-IMHA, IC50 ≈ 2 × 10(-7) M) capable to form a PLP-inhibitor complex (oxime) in the enzyme active center. Taking advantage of the availability of the human HDC X-ray structure, we have also determined the potential interactions that could stabilize this oxime in the active site of mammalian HDC.
... the transition state of decarboxylation (Fig. 8). Previous simulation studies based on rat HDC suggested that histidine binds to PLP with the side chain on the re-face of the PLP cofactor (37). The reason for the difference between the present study and the previous simulation is not clear, but this difference might explain why the catalytic efficiency was remarkably different between hHDC 2-477 and rat HDC as shown in Table 2. ...
Histamine is an important chemical mediator for a wide variety of physiological reactions. l-Histidine decarboxylase (HDC) is the primary enzyme responsible for histamine synthesis and produces histamine from histidine
in a one-step reaction. In this study, we determined the crystal structure of human HDC (hHDC) complexed with the inhibitor
histidine methyl ester. This structure shows the detailed features of the pyridoxal-5′-phosphate inhibitor adduct (external
aldimine) at the active site of HDC. Moreover, a comparison of the structures of hHDC and aromatic l-amino acid (l-DOPA) decarboxylase showed that Ser-354 was a key residue for substrate specificity. The S354G mutation at the active site
enlarged the size of the hHDC substrate-binding pocket and resulted in a decreased affinity for histidine, but an acquired
ability to bind and act on l-DOPA as a substrate. These data provide insight into the molecular basis of substrate recognition among the group II pyridoxal-5′-phosphate-dependent
decarboxylases.
... 1.22). In gram-positive bacteria, HDC activity is pyruvoyl-dependent, whereas in gram-negative bacteria and in animals, this is a pyridoxal 5-phosphate (PLP)-dependent enzyme [2,3]. ...
... In a recent study comprised of several members of the same family, it was observed that each family member presented a premature termination codon in the HDC gene at the position coding for residue 317 [65]. Our group have generated and validated the first structural model of the active conformation of mammalian HDC [2,3]. In this truncated version, the enzyme lacks important residues involved in the formation of the binding pocket and the establishment of the proper catalytic environment, leading to a decrease in the production of Hia in the CNS. ...
Histamine is a biogenic amine performing pleiotropic effects in humans, involving tasks within the immune and neuroendocrine systems, neurotransmission, gastric secretion, cell life and death, and development. It is the product of the histidine decarboxylase activity, and its effects are mainly mediated through four different G-protein coupled receptors. Thus, histamine-related effects are the results of highly interconnected and tissue-specific signalling networks. Consequently, alterations in histamine-related factors could be an important part in the cause of multiple rare/orphan diseases. Bearing this hypothesis in mind, more than 25 rare diseases related to histamine physiopathology have been identified using a computationally assisted text mining approach. These newly integrated data will provide insight to elucidate the molecular causes of these rare diseases. The data can also help in devising new intervention strategies for personalized medicine for multiple rare diseases.
... The initial review of the structure-function relationship of mammalian HDC integrated all the previous information about this enzyme based on its structural characteristics (Moya-Garcia et al., 2005). More recently, the decarboxylation reaction (the rate-limiting step for histamine synthesis) has been analysed by applying a combined strategy of quantum mechanics (QM) and molecular mechanics (MM) simulations on the external aldimine (PLP-histidine) complex located in the catalytic site of the enzyme (Moya- Garcia et al., 2008). Therefore, the exact location of all residues involved in this reaction and their behaviour along the reaction is now known, facilitating the search for new potential inhibitory compounds for this reaction. ...
... Our group has applied simulation techniques and MD techniques, by using the hybrid methodology QM/MM, to unravel the basis of the mammalian HDC catalytic mechanism (Moya-Garcia et al., 2008). In this study, we examined the decarboxylation of the intermediate cofactor-substrate adduct (the external aldimine) in the enzymatic environment (catalysed reaction) and in an aqueous environment. ...
... It shows the relevant structural features and reliably reproduces the behaviour of the enzyme. We were able to reveal key amino acids for the activity and stability of HDC (Rodriguez-Caso et al., 2003a;Fleming et al., 2004b) and we discern particular features of the reaction mechanism, with full atomic details (Moya-Garcia et al., 2008). Nevertheless, we submitted our model to an additional validation test to check whether it can be used to discover new HDC inhibitors with potential pharmacological use. ...
For a long time the structural and molecular features of mammalian histidine decarboxylase (EC 4.1.1.22), the enzyme that produces histamine, have evaded characterization. We overcome the experimental problems for the study of this enzyme by using a computer-based modelling and simulation approach, and have now the conditions to use histidine decarboxylase as a target in histamine pharmacology. In this review, we present the recent (last 5 years) advances in the structure-function relationship of histidine decarboxylase and the strategy for the discovery of new drugs.
The catalytic mechanism of histidine decarboxylase (HDC), a pyridoxal-5'-phosphate (PLP)-dependent enzyme, was studied by using a computational QM/MM approach following the scheme M06-2X/6-311++G(3df,2pd):Amber. The reaction involves two sequential steps: the decarboxylation of l-histidine and the protonation of the generated intermediate from which results histamine. The rate-limiting step is the first one (ΔG(≠) =17.6 kcal mol(-1) ; ΔGr =13.7 kcal mol(-1) ) and agrees closely with the available experimental kcat (1.73 s(-1) ), which corresponds to an activation barrier of 17.9 kcal mol(-1) . In contrast, the second step is very fast (ΔG(≠) =1.9 kcal mol(-1) ) and exergonic (ΔGr =-33.2 kcal mol(-1) ). Our results agree with the available experimental data and allow us to explain the role played by several active site residues that are considered relevant according to site-directed mutagenesis studies, namely Tyr334B, Asp273A, Lys305A, and Ser354B. These results can provide insights regarding the catalytic mechanism of other enzymes belonging to family II of PLP-dependent decarboxylases.
