Mechanistic role of each metal ion in Streptomyces dinuclear aminopeptidase: Peptide hydrolysis and 7×1010-fold rate enhancement of phosphodiester hydrolysis

Ercan, Altan; Tay, William M.; Grossman, Steven H.; Ming, Li‐June

doi:10.1016/j.jinorgbio.2009.09.019

Cited by 11 publications

(8 citation statements)

References 89 publications

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“…1D ). Similarly, it was reported for the monomeric Streptomyces dinuclear aminopeptidase that F − ion replaces the hydroxide ion on the catalytic metal, resulting in the enzyme activity inhibition 24 . Thus, the position of the Cl − ion in PfTET3 Gd structure strongly suggest that M2 is the catalytic metal hosting the nucleophilic hydroxide.…”

Section: Discussionmentioning

confidence: 60%

“…It has been proposed that such an environment results in a decreasing of the acidity of the M2 metal 23 allowing the polarization of the nucleophilic water molecule. It was previously reported that F − ions act as a noncompetitive inhibitor by displacing the hydroxide ion from the metal ion 24 . Thus, the Cl − ion can mimic the position of the hydroxide.…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, it has been shown that different metals in the active site of some of these proteases lead to dramatic variations of the enzyme kinetic parameters 40 . While monomeric peptidases have been extensively studied to determine the role of each metal ion in the active site 23 24 41 , there is a lack of information regarding the role of each metal ion in oligomeric peptidases. Here, by means of anomalous X-ray crystallography coupled to enzyme kinetics, we have characterized the respective role of each metal ion in the hyperthermophilic PfTET3 aminopeptidase and determined the molecular basis of Co 2+ activation.…”

Section: Discussionmentioning

confidence: 99%

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Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites

Colombo¹,

Girard²,

Franzetti³

2016

Sci Rep

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TET aminopeptidases are dodecameric particles shared in the three life domains involved in various biological processes, from carbon source provider in archaea to eye-pressure regulation in humans. Each subunit contains a dinuclear metal site (M1 and M2) responsible for the enzyme catalytic activity. However, the role of each metal ion is still uncharacterized. Noteworthy, while mesophilic TETs are activated by Mn2+, hyperthermophilic TETs prefers Co2+. Here, by means of anomalous x-ray crystallography and enzyme kinetics measurements of the TET3 aminopeptidase from the hyperthermophilic organism Pyrococcus furiosus (PfTET3), we show that M2 hosts the catalytic activity of the enzyme, while M1 stabilizes the TET3 quaternary structure and controls the active site flexibility in a temperature dependent manner. A new third metal site (M3) was found in the substrate binding pocket, modulating the PfTET3 substrate preferences. These data show that TET activity is tuned by the molecular interplay among three metal sites.

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Section: Discussionmentioning

confidence: 60%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites

Colombo¹,

Girard²,

Franzetti³

2016

Sci Rep

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“…Many researchers have been working hard for developing the biomimetic models for metalloenzyme with high efficiency and selectivity to achieve friendly environment and high‐economy processes . Over the rapid development of artificial enzyme mimicking, there has been considerable interest in the metal ion, such as Co(III), Cu(II), Zn(II), Ni(II), and lanthanide (Ln) complexes , promoted hydrolysis of phosphate esters, and as potential catalysts for the detoxification of anticholinesterase agents used in chemical warfare since the metal ions play the important role at catalytic active sites in the phosphate ester hydrolysis . The studies show that Ln complexes are generally more kinetically favorable than other transition metal complexes due to special properties of the Ln cation, such as their extremely strong Lewis acidity, the conjunction of higher charge density, coordination number, and rapid ligand exchange rates .…”

Section: Introductionmentioning

confidence: 99%

Construction and Activity of a New Catalytic System in the Hydrolysis of Bis(4‐nitrophenyl) Phosphate Ester

Xie

Wang

et al. 2013

Int J of Chemical Kinetics

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A new catalytic system containing an unsaturated heterocyclic nitrogen ligand and lanthanum(III) was constructed and used as a catalyst in the hydrolysis of bis(4‐nitrophenyl) phosphate ester (BNPP) in this work. The results indicated that this catalytic system showed greater catalytic activity in the hydrolysis of BNPP and better reproducibility and stability than other similar lanthanum(III) systems. The catalytic rate of the BNPP hydrolysis was about 107‐fold faster than that of its spontaneous hydrolysis at the same conditions. Compared with the previous Cu(II) or Ni(II) complex containing the same ligand in the water, the activity of the macrocyclic La(III) complex increases ca. 103‐fold for BNPP catalytic hydrolysis. The experimental data showed that the monohydroxy complex made of the heterocyclic nitrogen ligand and lanthanum(III) is the real active species as a catalyst in BNPP catalytic hydrolysis.

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“…Therefore, the later motif has been commonly utilized in the design of inhibitors for proteases/peptidases . However, Streptomyces griseus aminopeptidase ( Sg AP) is a novel enzyme that exhibits exceptional catalytic promiscuity by hydrolyzing both peptide and phosphoester bonds with remarkable efficiency. , Although an aminopeptidase, it is capable of accelerating the first-order hydrolysis of the phosphodiester bis(4-nitrophenyl) phosphate (BNPP), commonly used model for DNA (Figure ), by 10 10 -fold in comparison to the uncatalyzed reaction. , This is one of the rare examples in which an aminopeptidase hydrolyzes its transition state analogue, a phosphoester, at an enormous rate. In general, members of this family cleave peptide bonds from the N-terminal of their substrates and are classified as “broad” or “narrow” depending on their substrate specificities. , Aminopeptidases such as methionine aminopeptidases (MAP) , and proline aminopeptidases (PAP) are classified as “narrow” for being able to selectively cleave peptide bonds of a specific amino acid, N-terminal Met or Pro, of the substrates.…”

Section: Introductionmentioning

confidence: 99%

Promiscuous Catalytic Activity of a BinuclearMetallohydrolase: Peptide and Phosphoester Hydrolyses

Serafim

Jayasinghe‐Arachchige

Wang

et al. 2022

J. Chem. Inf. Model.

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In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn–Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.

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Mechanistic role of each metal ion in Streptomyces dinuclear aminopeptidase: Peptide hydrolysis and 7×1010-fold rate enhancement of phosphodiester hydrolysis

Cited by 11 publications

References 89 publications

Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites

Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites

Construction and Activity of a New Catalytic System in the Hydrolysis of Bis(4‐nitrophenyl) Phosphate Ester

Promiscuous Catalytic Activity of a BinuclearMetallohydrolase: Peptide and Phosphoester Hydrolyses

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