Structure of the dodecamer of the aminopeptidase APDkam598 from the archaeon<i>Desulfurococcus kamchatkensis</i>

Petrova, T.; Slutskaya, E. S.; Boyko, K.М.; Sokolova, Olga S.; Rakitina, Tatiana V.; Korzhenevskiy, D.A.; Gorbacheva, M.A.; Bezsudnova, Ekaterina Yu.; Popov, Vladimir O.

doi:10.1107/s2053230x15000783

Cited by 8 publications

(13 citation statements)

References 31 publications

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“…The M18 family is widely distributed in all domains of life (14) while the M42 family is unique to prokaryotes (23). Several structures of archaeal M42 aminopeptidases have been studied (13,15,17,18,(24)(25)(26) but only one structure has been reported for bacteria (27). Franzetti et al (2002) described the first TET-aminopeptidase structure of the Haloarcula marismortui M42 aminopeptidase, consisting of twelve subunits adopting a tetrahedron-shaped quaternary structure (25).…”

Section: Introductionmentioning

confidence: 99%

How metal cofactors drive dimer–dodecamer transition of the M42 aminopeptidase TmPep1050 of Thermotoga maritima

Dutoit

Gompel

Brandt³

et al. 2019

Journal of Biological Chemistry

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The M42 aminopeptidases are dinuclear aminopeptidases displaying a peculiar tetrahedral-shaped structure with twelve subunits. Their quaternary structure results from the selfassembly of six dimers controlled by their divalent metal ion cofactors. The oligomeric state transition remains debated despite the structural characterization of several archaeal M42 aminopeptidases. The main bottleneck is the lack of dimer structures, hindering the understanding of structural changes occurring during the oligomerization process. We present the first dimer structure of an M42 aminopeptidase, TmPep1050 of Thermotoga maritima, along with the dodecamer structure. The comparison of both structures allows to describe how the metal ion cofactors modulate the active site fold and, subsequently, affect the interaction interface between dimers. A mutational study shows that the M1 site strictly controls dodecamer formation. The dodecamer structure of TmPep1050 also reveals that a part of the dimerization domain delimits the catalytic pocket and could participate in substrate binding.

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Section: Introductionmentioning

confidence: 99%

How metal cofactors drive dimer–dodecamer transition of the M42 aminopeptidase TmPep1050 of Thermotoga maritima

Dutoit

Gompel

Brandt³

et al. 2019

Journal of Biological Chemistry

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“…In general, Trp residues do not often occur on the protein surface (Samanta et al 2000). Among 13,672 sequences from the IMG Database (Markowitz et al 2014) that have more than 30 % identity with the APDkam589 sequence, only 15 sequences contain six Trp residues, the same as in APDkam589 (Petrova et al 2015). All Trp residues of APDkam589 are located on the surface of the monomer and the dimer; and all Trp residues, except one (Trp49), are on the external surface of the APDkam589 molecule (Fig.…”

Section: Resultsmentioning

confidence: 97%

“…In the crystal, the symmetryrelated monomers of APDkam589 form a compact, tetrahedrally shaped, 12-subunit structure. Independently, single-particle electron microscopy analysis revealed that the APDkam589 molecule exists as a tetrahedral dodecamer in solution (Petrova et al 2015).…”

Section: Structure Of the Apdkam589 Moleculementioning

confidence: 99%

“…The X-ray crystal structure of APDkam589 was determined at 3.0-Å resolution (Petrova et al 2015). Atomic coordinates and structure factors were deposited in the Protein Data Bank (code 4WWV).…”

Section: Structure Of the Apdkam589 Moleculementioning

confidence: 99%

“…However, it remained unclear which conformational changes at the secondary and tertiary structure levels contribute to the structural changes that occur in APDkam589 upon its thermal inactivation. The structure of APDkam589 was determined by X-ray diffraction and single-particle electron microscopy analysis (Petrova et al 2015). It was shown that the APDkam589 molecule, in both crystal and solution, is a compact 12-subunit complex.…”

Section: Introductionmentioning

confidence: 99%

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Heat-induced conformational changes of TET peptidase from crenarchaeon Desulfurococcus kamchatkensis

et al. 2015

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The effects of heating on the structure and stability of multimeric TET aminopeptidase (APDkam589) were studied by differential scanning calorimetry, tryptophan fluorescence quenching, and dynamic light scattering. Thermally induced structural changes in APDkam589 were found to occur in two phases: local conformational changes, which occur below 70 °C and are not associated with thermal denaturation of the protein, and global structural changes (above 70 °C) induced by irreversible thermal unfolding of the protein accompanied by its spontaneous aggregation. These results may explain the bell-shaped temperature dependence with a maximum at ~70 °C previously observed for enzymatic activity of APDkam589. Interestingly, the thermal unfolding of APDkam589 at about 81.2 °C is accompanied by a so-called blue-shift of about 10 nm-a shift of the Trp fluorescence spectrum toward shorter wavelength. From this point of view, APDkam589 is quite different from most proteins, which are characterized by a long wavelength shift of the spectrum ("red-shift") upon denaturation. The blue-shift of the Trp fluorescence spectrum reflects the changes in the environment of Trp residues, which becomes more hydrophobic upon denaturation. The molecular structure of APDkam589 was determined by X-ray diffraction. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. Therefore, the blue-shift of the Trp fluorescence spectrum can be explained, at least partly, by aggregation of APDkam589, which occurs simultaneously with its thermal denaturation and probably makes the environment of these Trp residues more hydrophobic.

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M42 aminopeptidase catalytic site: the structural and functional role of a strictly conserved aspartate residue

Dutoit

Brandt²,

Gompel

et al. 2020

Proteins

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The M42 aminopeptidases are a family of dinuclear aminopeptidases widely distributed in 16 Prokaryotes. They are potentially associated to the proteasome, achieving complete peptide 17 destruction. Their most peculiar characteristic is their quaternary structure, a tetrahedron-18 shaped particle made of twelve subunits. The catalytic site of M42 aminopeptidases is defined 19 by seven conserved residues. Five of them are involved in metal ion binding which is important 20 to maintain both the activity and the oligomeric state. The sixth conserved residue, a glutamate, 21 is the catalytic base deprotonating the water molecule during peptide bond hydrolysis. The 22 seventh residue is an aspartate whose function remains poorly understood. This aspartate 23 residue, however, must have a critical role as it is strictly conserved in all MH clan enzymes. 24 It forms some kind of catalytic triad with the histidine residue and the metal ion of the M2

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Structure of the dodecamer of the aminopeptidase APDkam598 from the archaeonDesulfurococcus kamchatkensis

Cited by 8 publications

References 31 publications

How metal cofactors drive dimer–dodecamer transition of the M42 aminopeptidase TmPep1050 of Thermotoga maritima

How metal cofactors drive dimer–dodecamer transition of the M42 aminopeptidase TmPep1050 of Thermotoga maritima

Heat-induced conformational changes of TET peptidase from crenarchaeon Desulfurococcus kamchatkensis

M42 aminopeptidase catalytic site: the structural and functional role of a strictly conserved aspartate residue

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