Limits...
The crystal structure of D-threonine aldolase from Alcaligenes xylosoxidans provides insight into a metal ion assisted PLP-dependent mechanism.

Uhl MK, Oberdorfer G, Steinkellner G, Riegler-Berket L, Mink D, van Assema F, Schürmann M, Gruber K - PLoS ONE (2015)

Bottom Line: Our results underline the close relationship of DTAs and alanine racemases and allow the identification of a metal binding site close to the PLP-cofactor in the active site of the enzyme which is consistent with the previous observation that divalent cations are essential for DTA activity.The structure of AxDTA is completely different to available structures of LTAs.The enantio-complementarity of DTAs and LTAs can be explained by an approximate mirror symmetry of crucial active site residues relative to the PLP-cofactor.

View Article: PubMed Central - PubMed

Affiliation: Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria.

ABSTRACT
Threonine aldolases catalyze the pyridoxal phosphate (PLP) dependent cleavage of threonine into glycine and acetaldehyde and play a major role in the degradation of this amino acid. In nature, L- as well as D-specific enzymes have been identified, but the exact physiological function of D-threonine aldolases (DTAs) is still largely unknown. Both types of enantio-complementary enzymes have a considerable potential in biocatalysis for the stereospecific synthesis of various β-hydroxy amino acids, which are valuable building blocks for the production of pharmaceuticals. While several structures of L-threonine aldolases (LTAs) have already been determined, no structure of a DTA is available to date. Here, we report on the determination of the crystal structure of the DTA from Alcaligenes xylosoxidans (AxDTA) at 1.5 Å resolution. Our results underline the close relationship of DTAs and alanine racemases and allow the identification of a metal binding site close to the PLP-cofactor in the active site of the enzyme which is consistent with the previous observation that divalent cations are essential for DTA activity. Modeling of AxDTA substrate complexes provides a rationale for this metal dependence and indicates that binding of the β-hydroxy group of the substrate to the metal ion very likely activates this group and facilitates its deprotonation by His193. An equivalent involvement of a metal ion has been implicated in the mechanism of a serine dehydratase, which harbors a metal ion binding site in the vicinity of the PLP cofactor at the same position as in DTA. The structure of AxDTA is completely different to available structures of LTAs. The enantio-complementarity of DTAs and LTAs can be explained by an approximate mirror symmetry of crucial active site residues relative to the PLP-cofactor.

No MeSH data available.


Related in: MedlinePlus

Schematic representation of the structure of AxDTA.(A) Cartoon representation of the AxDTA protomer showing the alanine-racemase-like domain in red and the β-domain in blue. The PLP-cofactor bound to Lys59 is shown in yellow. The manganese ion is depicted as a magenta and the sodium ion as a green sphere. Residues coordinating the Mn- and Na-ion are shown as gray sticks, metal bound water molecules are shown as small red spheres. Metal coordination is indicated by light blue, dashed lines. (B) Cartoon representation of the AxDTA dimer with one protomer shown in darker red/blue (domain coloring as in A) and the other in lighter red/blue.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4401734&req=5

pone.0124056.g002: Schematic representation of the structure of AxDTA.(A) Cartoon representation of the AxDTA protomer showing the alanine-racemase-like domain in red and the β-domain in blue. The PLP-cofactor bound to Lys59 is shown in yellow. The manganese ion is depicted as a magenta and the sodium ion as a green sphere. Residues coordinating the Mn- and Na-ion are shown as gray sticks, metal bound water molecules are shown as small red spheres. Metal coordination is indicated by light blue, dashed lines. (B) Cartoon representation of the AxDTA dimer with one protomer shown in darker red/blue (domain coloring as in A) and the other in lighter red/blue.

Mentions: Each protomer comprises an alanine-racemase-like domain with an eight-stranded α/β-barrel (residues 32–274) together with a β-strand domain consisting of residues from the N-terminus (residues 1–31) and the C-terminus (residue 275–379). This β-domain can be subdivided into two β-stranded motifs composed of a closed, antiparallel 5-stranded β-barrel (residue 275–347) and a 3-stranded β-sheet built up by N- and C-terminal residues (Fig 2A). To classify the β-barrel domain we did a CATH database search employing the CATHEDRAL algorithm [29]. The best hit with an SSAP score of 79.9 and a root-mean-square-deviation (r.m.s.d.) of 3.1 Å belongs to the CATH superfamily 2.40.10.230, annotated as a probable tRNA pseudouridine synthase domain.


The crystal structure of D-threonine aldolase from Alcaligenes xylosoxidans provides insight into a metal ion assisted PLP-dependent mechanism.

Uhl MK, Oberdorfer G, Steinkellner G, Riegler-Berket L, Mink D, van Assema F, Schürmann M, Gruber K - PLoS ONE (2015)

Schematic representation of the structure of AxDTA.(A) Cartoon representation of the AxDTA protomer showing the alanine-racemase-like domain in red and the β-domain in blue. The PLP-cofactor bound to Lys59 is shown in yellow. The manganese ion is depicted as a magenta and the sodium ion as a green sphere. Residues coordinating the Mn- and Na-ion are shown as gray sticks, metal bound water molecules are shown as small red spheres. Metal coordination is indicated by light blue, dashed lines. (B) Cartoon representation of the AxDTA dimer with one protomer shown in darker red/blue (domain coloring as in A) and the other in lighter red/blue.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401734&req=5

pone.0124056.g002: Schematic representation of the structure of AxDTA.(A) Cartoon representation of the AxDTA protomer showing the alanine-racemase-like domain in red and the β-domain in blue. The PLP-cofactor bound to Lys59 is shown in yellow. The manganese ion is depicted as a magenta and the sodium ion as a green sphere. Residues coordinating the Mn- and Na-ion are shown as gray sticks, metal bound water molecules are shown as small red spheres. Metal coordination is indicated by light blue, dashed lines. (B) Cartoon representation of the AxDTA dimer with one protomer shown in darker red/blue (domain coloring as in A) and the other in lighter red/blue.
Mentions: Each protomer comprises an alanine-racemase-like domain with an eight-stranded α/β-barrel (residues 32–274) together with a β-strand domain consisting of residues from the N-terminus (residues 1–31) and the C-terminus (residue 275–379). This β-domain can be subdivided into two β-stranded motifs composed of a closed, antiparallel 5-stranded β-barrel (residue 275–347) and a 3-stranded β-sheet built up by N- and C-terminal residues (Fig 2A). To classify the β-barrel domain we did a CATH database search employing the CATHEDRAL algorithm [29]. The best hit with an SSAP score of 79.9 and a root-mean-square-deviation (r.m.s.d.) of 3.1 Å belongs to the CATH superfamily 2.40.10.230, annotated as a probable tRNA pseudouridine synthase domain.

Bottom Line: Our results underline the close relationship of DTAs and alanine racemases and allow the identification of a metal binding site close to the PLP-cofactor in the active site of the enzyme which is consistent with the previous observation that divalent cations are essential for DTA activity.The structure of AxDTA is completely different to available structures of LTAs.The enantio-complementarity of DTAs and LTAs can be explained by an approximate mirror symmetry of crucial active site residues relative to the PLP-cofactor.

View Article: PubMed Central - PubMed

Affiliation: Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria.

ABSTRACT
Threonine aldolases catalyze the pyridoxal phosphate (PLP) dependent cleavage of threonine into glycine and acetaldehyde and play a major role in the degradation of this amino acid. In nature, L- as well as D-specific enzymes have been identified, but the exact physiological function of D-threonine aldolases (DTAs) is still largely unknown. Both types of enantio-complementary enzymes have a considerable potential in biocatalysis for the stereospecific synthesis of various β-hydroxy amino acids, which are valuable building blocks for the production of pharmaceuticals. While several structures of L-threonine aldolases (LTAs) have already been determined, no structure of a DTA is available to date. Here, we report on the determination of the crystal structure of the DTA from Alcaligenes xylosoxidans (AxDTA) at 1.5 Å resolution. Our results underline the close relationship of DTAs and alanine racemases and allow the identification of a metal binding site close to the PLP-cofactor in the active site of the enzyme which is consistent with the previous observation that divalent cations are essential for DTA activity. Modeling of AxDTA substrate complexes provides a rationale for this metal dependence and indicates that binding of the β-hydroxy group of the substrate to the metal ion very likely activates this group and facilitates its deprotonation by His193. An equivalent involvement of a metal ion has been implicated in the mechanism of a serine dehydratase, which harbors a metal ion binding site in the vicinity of the PLP cofactor at the same position as in DTA. The structure of AxDTA is completely different to available structures of LTAs. The enantio-complementarity of DTAs and LTAs can be explained by an approximate mirror symmetry of crucial active site residues relative to the PLP-cofactor.

No MeSH data available.


Related in: MedlinePlus