Inorganic pyrophosphatases of Family <scp>II</scp>—two decades after their discovery

Baykov, Alexander A.; Anashkin, Viktor A.; Salminen, Anu; Lahti, Reijo

doi:10.1002/1873-3468.12877

Cited by 30 publications

(39 citation statements)

References 54 publications

(102 reference statements)

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“…PNP and PCP (both from Sigma-Aldrich) were used as an analogue of the substrate. As a note, Bs-PPase is also able to convert PNP, though its rate is much slower (~10 4 -10 5 times) than that for PPi 4,9 . Mn-Sh-PPase for substrate binding studies were used from the same aliquot as that for the unbound substrate, but the final protein concentrations were reduced to prevent the consumption of substrate analogues.…”

Section: Determination Of Axial Zfs Parameters For S = 2 and Di-mn DImentioning

confidence: 91%

“…Substrate binding effect for Sh-PPase. Family II PPase only weakly converts the substrate analogue PNP to Pi 4,9 . Therefore, for the EPR measurement, enzyme concentration was decreased to ~100 µM to prevent consumption of PNP.…”

Section: Determination Of Axial Zfs Parameters For S = 2 and Di-mn DImentioning

confidence: 99%

“…Metal requirement studies for Bs-PPase have shown that the M2 site is preferred for divalent transition metal ions, such as Mn 2+ or Co 2+ , while other metal binding sites (M3 and M4) favour Mg 2+ ions in catalysis. However, it is still unclear whether the M1 site utilizes a transition metal or Mg 2+ ions 4,8,10 . According to the crystal structure of Bs-PPase, the five-coordination sphere of M2 site is changed to a hexa-coordination by substrate binding.…”

mentioning

confidence: 99%

“…This structural change of the M2 site is considered the main reason for family II PPases requiring transition metal ions for maximum activity. In addition, a nucleophilic water coordinated with three metals (M1, 2 and 4), which is very uncommon in other hydrolysis enzymes 4,5,7,8,11 . This tri-metal coordination might cause higher activity of family II PPase than family I PPase.We previously reported the expression and purification of family II PPase from the psychrophilic Shewanella sp.…”

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confidence: 99%

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X-ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase

Horitani

Kusubayashi

Oshima

et al. 2020

Sci Rep

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inorganic pyrophosphatase (ppase) catalyses the hydrolysis reaction of inorganic pyrophosphate to phosphates. our previous studies showed that manganese (Mn) activated ppase from the psychrophilic bacterium Shewanella sp. AS-11 (Mn-Sh-PPase) has a characteristic temperature dependence of the activity with an optimum at 5 °C. Here we report the X-ray crystallography and electron paramagnetic resonance (epR) spectroscopy structural analyses of Sh-ppase in the absence and presence of substrate analogues. We successfully determined the crystal structure of Mn-Sh-ppase without substrate and Mg-activated Sh-ppase (Mg-Sh-ppase) complexed with substrate analogue (imidodiphosphate; pnp). crystallographic studies revealed a bridged water placed at a distance from the di-Mn centre in Mn-Shppase without substrate. the water came closer to the metal centre when pnp bound. epR analysis of Mn-Sh-ppase without substrate revealed considerably weak exchange coupling, whose magnitude was increased by binding of substrate analogues. the data indicate that the bridged molecule has weak bonds with the di-Mn centre, which suggests a 'loose' structure, whereas it comes closer to di-Mn centre by substrate binding, which suggests a 'well-tuned' structure for catalysis. thus, we propose that Shppase can rearrange the active site and that the 'loose' structure plays an important role in the cold adaptation mechanism.Inorganic pyrophosphatase (PPase) catalyses the hydrolysis reaction of inorganic pyrophosphate (PPi) to two inorganic phosphates (Pi) and plays an essential role for living organisms 1 . Soluble PPase consists of two families, I and II, which have different secondary and tertiary structures. Family I PPases are widespread organisms including bacteria and mammalians 1 , whereas family II PPases are almost exclusively found in bacteria and archaebacteria 2-4 . Both the family I and II PPases require divalent metal ions for their reactivity. All PPases are magnesium ion (Mg 2+ ) dependent enzymes. Family II PPases require divalent transition metals, such as Mn 2+ 3,5 or Co 2+ ions 6 for maximum activity. X-ray structural analyses of family II PPases from Bacillus subtilis (Bs-PPase) and Streptococcus gordonii (Sg-PPase) have been reported 7,8 . They are homodimers and each monomer consists of two domains (N-and C-terminal domains) connected by a flexible hinge region. These two domains are in the 'open' state in the absence of substrate. Substrate binding results in a 'closed' state, with one exception 7 . Two sites (M1 and M2) for transition metal ion have been demonstrated in the active site in the 'open' state of Bs-PPase, while four metal ions (M1 to M4) are found in the crystal structure of Bs-PPase in complex with imidodiphosphate (PNP) 9 . Metal requirement studies for Bs-PPase have shown that the M2 site is preferred for divalent transition metal ions, such as Mn 2+ or Co 2+ , while other metal binding sites (M3 and M4) favour Mg 2+ ions in catalysis. However, it is still unclear whether the M1 site utilizes a transition m...

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Section: Determination Of Axial Zfs Parameters For S = 2 and Di-mn DImentioning

confidence: 91%

Section: Determination Of Axial Zfs Parameters For S = 2 and Di-mn DImentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

X-ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase

Horitani

Kusubayashi

Oshima

et al. 2020

Sci Rep

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“…Family II PPases have a more variable domain organization and are divided into two subfamilies. In the "canonical" subfamily, which has been well characterized both structurally and mechanistically [6], each subunit of 33-34 kDa is formed by two catalytic domains, DHH and DHHA2, connected by a flexible linker, and the active site is located between the domains [7,8] (Fig. 1A).…”

Section: Introductionmentioning

confidence: 99%

The Tetrameric Structure of Nucleotide-regulated Pyrophosphatase and Its Modulation by Deletion Mutagenesis and Ligand Binding

Anashkin

Salminen

Орлов

et al. 2020

Preprint

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A quarter of prokaryotic Family II inorganic pyrophosphatases (PPases) contain a regulatory insert comprised of two cystathionine β-synthase (CBS) domains and one DRTGG domain in addition to the two catalytic domains that form canonical Family II PPases. The CBS domain-containing PPases (CBS-PPases) are allosterically activated or inhibited by adenine nucleotides that cooperatively bind to the CBS domains. Here we use chemical cross-linking and analytical ultracentrifugation to show that CBS-PPases from Desulfitobacterium hafniense and four other bacterial species are active as 200-250-kDa homotetramers, which seems unprecedented among the four PPase families. The tetrameric structure is stabilized by Co 2+ , the essential cofactor, pyrophosphate, the substrate, and adenine nucleotides, including diadenosine tetraphosphate. The deletion variants of dhPPase containing only catalytic or regulatory domains are dimeric. Co 2+ depletion by incubation with EDTA converts CBS-PPase into inactive tetrameric and dimeric forms. Dissociation of tetrameric CBS-PPase and its catalytic part by dilution renders them inactive. The structure of CBS-PPase tetramer was modelled from the structures of dimeric catalytic and regulatory parts. These findings signify the role of the unique oligomeric structure of CBS-PPase in its multifaced regulation.

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Crystallographic and modeling study of the human inorganic pyrophosphatase 1: A potential anti‐cancer drug target

Niu

Zhu

et al. 2021

Proteins

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Inorganic pyrophosphatases (PPases) catalyze the hydrolysis of pyrophosphate to phosphates. PPases play essential roles in growth and development, and are found in all kingdoms of life. Human possess two PPases, PPA1 and PPA2. PPA1 is present in all tissues, acting largely as a housekeeping enzyme. Besides pyrophosphate hydrolysis, PPA1 can also directly dephosphorylate phosphorylated c-Jun N-terminal kinases 1 (JNK1). Upregulated expression of PPA1 has been linked to many human malignant tumors. PPA1 knockdown induces apoptosis and decreases proliferation. PPA1 is emerging as a potential prognostic biomarker and target for anti-cancer drug development. In spite of the biological and physiopathological importance of PPA1, there is no detailed study on the structure and catalytic mechanisms of mammalian origin PPases. Here we report the crystal structure of human PPA1 at a resolution of 2.4 Å.We also carried out modeling studies of PPA1 in complex with JNK1 derived phosphor-peptides. The monomeric protein fold of PPA1 is similar to those found in other family I PPases. PPA1 forms a dimeric structure that should be conserved in animal and fungal PPases. Analysis of the PPA1 structure and comparison with available structures of PPases from lower organisms suggest that PPA1 has a largely preorganized and relatively rigid active site for pyrophosphate hydrolysis. Results from the modeling study indicate the active site of PPA1 has the potential to accommodate double-phosphorylated peptides from JNK1. In short, results from the study provides new insights into the mechanisms of human PPA1 and basis for structurebased anti-cancer drug developments using PPA1 as the target.

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Inorganic pyrophosphatases of Family II—two decades after their discovery

Cited by 30 publications

References 54 publications

X-ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase

X-ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase

The Tetrameric Structure of Nucleotide-regulated Pyrophosphatase and Its Modulation by Deletion Mutagenesis and Ligand Binding

Crystallographic and modeling study of the human inorganic pyrophosphatase 1: A potential anti‐cancer drug target

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