Structural Basis of Perturbed pKa Values of Catalytic Groups in Enzyme Active Sites

Harris, Thomas K.; Turner, George J.

doi:10.1080/15216540211468

Cited by 485 publications

(634 citation statements)

References 80 publications

Supporting

Mentioning

587

Contrasting

Unclassified

Order By: Relevance

“…The formation of the subsequent diphenylalanyl enzyme intermediate implies that the ammonium group of the phenylalanyl enzyme intermediate has to be deprotonated by a catalytic base to perform the nucleophilic attack on the incoming carbonyl of the second substrate. The nearby E182 may fulfill this role 13,18,19 . This residue is essential to the catalytic reaction and is involved in catalytic steps following amino-acyl formation [4][5][6] .…”

Section: Resultsmentioning

confidence: 99%

Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases

et al. 2014

View full text Add to dashboard Cite

Cyclodipeptide synthases form cyclodipeptides from two aminoacyl transfer RNAs. They use a ping-pong mechanism that begins with transfer of the aminoacyl moiety of the first aminoacyl tRNA onto a conserved serine, yielding an aminoacyl enzyme. Combining X-ray crystallography, site-directed mutagenesis and affinity labelling of the cyclodipeptide synthase AlbC, we demonstrate that the covalent intermediate reacts with the aminoacyl moiety of the second aminoacyl tRNA, forming a dipeptidyl enzyme, and identify the aminoacyl-binding sites of the aminoacyl tRNAs.

show abstract

Section: Resultsmentioning

confidence: 99%

Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases

et al. 2014

View full text Add to dashboard Cite

show abstract

“…In addition, pK a calculations continue to provide a significant challenge to computations. [49][50][51][52] In the present work, we have investigated pK a values of three tyrosine residues (Tyr188, Tyr 398 and Tyr 435) and the dopamine molecule within MAO B active site. Both the free enzyme and the enzyme complexed with dopamine were considered.…”

Section: Introductionmentioning

confidence: 99%

Computational Study of the pK_aValues of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B

Borštnar

Repič

Kamerlin

et al. 2012

J. Chem. Theory Comput.

View full text Add to dashboard Cite

Monoamine oxidase (MAO), which exists in two isozymic forms, MAO A and MAO B, is an important flavoenzyme responsible for the metabolism of amine neurotransmitters such as dopamine, serotonin and norepinephrine. Despite extensive research effort, neither the catalytic nor the inhibition mechanisms of MAO have been completely understood. There has also been dispute with regard to the protonation state of the substrate upon entering the active site, as well as the identity of residues that are important for the initial deprotonation of irreversible acetylenic inhibitors, in accordance with the recently proposed mechanism. Therefore, in order to investigate features essential for the modes of action of MAO, we have calculated pK a values of three relevant tyrosine residues in the MAO B active site, with and without dopamine bound as the substrate (as well as the pK a of the dopamine itself in the active site). The calculated pK a values for Tyr188, Tyr398 and Tyr435 in the complex are found to be shifted upwards to 13.0, 13.7 and 14.7, respectively, relative to 10.1 in aqueous solution, ruling out the likelihood that they are viable proton acceptors. The altered tyrosine pK a values could be rationalized as an interplay of two opposing effects: insertion of positively charged bulky dopamine that lowers tyrosine pK a values, and subsequent removal of water molecules from the active site that elevates tyrosine pK a values, in which the latter prevails. Additionally, the pK a value of the bound dopamine (8.8) is practically unchanged compared to the corresponding value in aqueous solution (8.9), as would be expected from a charged amine placed in a hydrophobic active site consisting of aromatic moieties. We also observed potentially favorable cation-π interactions between -NH 3 + group on dopamine and aromatic moieties, which provide stabilizing effect to the charged fragment. Thus, we offer here theoretical evidence that the amine is most likely to be present in the active site in its protonated form, which is similar to the conclusion from experimental studies of MAO A (Jones et al. J. Neural Trans. 2007, 114, 707-712). However, the free energy cost of 3 transferring the proton from the substrate to the bulk solvent is only 1.9 kcal mol -1 , leaving open the possibility that the amine enters the chemical step in its neutral form. In conjunction with additional experimental and computational work, the data presented here should lead towards a deeper understanding of mechanisms of the catalytic activity and irreversible inhibition of MAO B, which can allow for the design of novel and improved MAO B inhibitors.

show abstract

“…Acutohaemolysin was crystallized at pH 5.6 (a little lower than the dissociation pK a value) so that the environment was appropriate for the protonation of both the N␦ 1 and the N⑀ 2 atoms. However, it should be remembered that the pK a values of amino acid residues located at the surface of proteins are known to be highly dependent on the local chemical environment (43). The protonation of the N⑀ 2 atom is favored by its role as hydrogen-bond donor to the negatively charged carboxylate of Asp 99 .…”

Section: Calcium-binding Loop-the Calcium-binding Loop Illustrated Inmentioning

confidence: 99%

The Crystal Structure of a Novel, Inactive, Lysine 49 PLA2 from Agkistrodon acutus Venom

Liu

Huang

Teng

et al. 2003

Journal of Biological Chemistry

View full text Add to dashboard Cite

The crystal structure of acutohaemolysin, a lysine 49 phospholipase A2 protein with 1010 non-hydrogen protein atoms and 232 water molecules, has been determined ab initio using the program SnB at an ultrahigh resolution of 0.8 Å. The lack of catalytic activity appears to be related to the presence of Phe 102 , which prevents the access of substrate to the active site. The substitution of tryptophan for leucine at residue 10 interferes with dimer formation and may be responsible for the additional loss of hemolytic activity. The ultrahigh resolution of the experimental diffraction data permits alternative conformations to be modeled for disordered residues, many hydrogen atoms to be located, the protonation of the N⑀2 atom in the catalytic residue His 48 to be observed experimentally, and the density of the bonding electrons to be analyzed in detail.

show abstract

Structural Basis of Perturbed pKa Values of Catalytic Groups in Enzyme Active Sites

Cited by 485 publications

References 80 publications

Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases

Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases

Computational Study of the pK_aValues of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B

The Crystal Structure of a Novel, Inactive, Lysine 49 PLA2 from Agkistrodon acutus Venom

Contact Info

Product

Resources

About

Structural Basis of Perturbed pKa Values of Catalytic Groups in Enzyme Active Sites

Cited by 485 publications

References 80 publications

Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases

Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases

Computational Study of the pKaValues of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B

The Crystal Structure of a Novel, Inactive, Lysine 49 PLA2 from Agkistrodon acutus Venom

Contact Info

Product

Resources

About

Computational Study of the pK_aValues of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B