VOOZH about

URL: https://pubmed.ncbi.nlm.nih.gov/15608117/

⇱ Enzyme adaptation to alkaline pH: atomic resolution (1.08 A) structure of phosphoserine aminotransferase from Bacillus alcalophilus - PubMed

Clipboard, Search History, and several other advanced features are temporarily unavailable.
Skip to main page content
👁 Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

👁 Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Abstract

The crystal structure of the vitamin B(6)-dependent enzyme phosphoserine aminotransferase from the obligatory alkaliphile Bacillus alcalophilus has been determined at 1.08 A resolution. The model was refined to an R-factor of 11.7% (R(free) = 13.9%). The enzyme displays a narrow pH optimum of enzymatic activity at pH 9.0. The final structure was compared to the previously reported structure of the mesophilic phosphoserine aminotransferase from Escherichia coli and to that of phosphoserine aminotransferase from a facultative alkaliphile, Bacillus circulans subsp. alkalophilus. All three enzymes are homodimers with each monomer comprising a two-domain architecture. Despite the high structural similarity, the alkaliphilic representatives possess a set of distinctive structural features. Two residues directly interacting with pyridoxal-5'-phosphate are replaced, and an additional hydrogen bond to the O3' atom of the cofactor is present in alkaliphilic phosphoserine aminotransferases. The number of hydrogen bonds and hydrophobic interactions at the dimer interface is increased. Hydrophobic interactions between the two domains in the monomers are enhanced. Moreover, the number of negatively charged amino acid residues increases on the solvent-accessible molecular surface and fewer hydrophobic residues are exposed to the solvent. Further, the total amount of ion pairs and ion networks is significantly reduced in the Bacillus enzymes, while the total number of hydrogen bonds is increased. The mesophilic enzyme from Escherichia coli contains two additional beta-strands in a surface loop with a third beta-strand being shorter in the structure. The identified structural features are proposed to be possible factors implicated in the alkaline adaptation of phosphoserine aminotransferase.

PubMed Disclaimer

Figures

👁 Figure 1.
Figure 1.
The pH-dependence of BALC PSAT enzymatic activity. The value of Vmax for the reaction of phosphoserine synthesis was measured at different pH in 0.1 M HEPES (triangles) or CHES (circles).
👁 Figure 2.
Figure 2.
Ribbon diagram of the BALC PSAT monomer. The α-helices are shown in light gray and the β-strands in dark gray. Secondary structure elements and N and C termini are labeled. The dashed line depicts the boundary between the small and the large domain. The side chain of the active site residue Lys196 and the PLP molecule are shown in ball-and-stick representation. The figure was produced using MOLSCRIPT (Kraulis 1991) and Raster3D (Merritt and Murphy 1994).
👁 Figure 3.
Figure 3.
Ribbon representation of the BALC PSAT dimer. The two monomers are depicted in yellow and in blue, respectively. Ligands included in the final model (PLP, PEG, HEPES, glycerol) are shown in ball-and-sticks. Mg2+ ions are shown as gray spheres and Cl− ions as pink spheres. (A) View along the twofold noncrystallographic axis. The active site clefts are shown with arrows. (B) BALC PSAT dimer after 90° rotation. The twofold axis in this orientation is vertical and lying within the plane of the figure. The figure was produced using MOLSCRIPT (Kraulis 1991) and Raster3D (Merritt and Murphy 1994).
👁 Figure 4.
Figure 4.
Key interactions of PLP in the active site of BALC PSAT. PLP molecule and the side chain of Lys196 are presented in bold. Hydrogen bonds are shown as dotted lines and their length is indicated. Residues marked with an asterisk originate from the opposite subunit. The figure was produced using ISIS/Draw (MDL, Inc.).
👁 Figure 5.
Figure 5.
Definition of torsion angle for the internal aldimine bond and atom names in pyridoxal-5′-phosphate. The figure was produced using ISIS/Draw (MDL, Inc.).
👁 Figure 6.
Figure 6.
Structural alignment of PSAT from B. alcalophilus (BALC), B. circulans (BCIR), and E. coli (ECOLI). Identical residues are shown in red boxes. The residues are numbered as in the BALC PSAT model. Secondary structure elements for BALC, BCIR, and ECOLI PSAT are presented in blue, red, and green, respectively; helices (α), strands (β), and 310 helices (η) are labeled for BALC PSAT. Active site residues are labeled with triangles. The figure was produced using ESPript (Gouet et al. 1999).
👁 Figure 7.
Figure 7.
Stereo diagrams of superimposed Cα traces of PSAT monomers. (A) BALC (black) and ECOLI PSAT (gray). (B) BALC (black) and BCIR PSAT (gray). Every 20th position in BALC PSAT is labeled. The figure was produced using BOBSCRIPT (Esnouf 1997).
👁 Figure 8.
Figure 8.
Content of amino acid residues on the molecular surface of PSAT dimers. Black bars represent negatively charged residues (Asp and Glu); white bars, positively charged residues (Arg and Lys); dark gray bars, polar uncharged residues (Asn, Gln, His, Ser, and Thr); light gray bars, hydrophobic residues (Ala, Gly, Ile, Leu, Phe, Pro, and Val).
👁 Figure 9.
Figure 9.
Differences in the active site of BALC (black), BCIR (dashed) and ECOLI (gray) PSAT. Eighteen active site residues were superimposed. Only part of them is shown for clarity of presentation. The residues are labeled for BALC PSAT and ECOLI PSAT (in parentheses) if the residue type is different. The figure was produced using MOLSCRIPT (Kraulis 1991) and Raster3D (Merritt and Murphy 1994).

References

    1. Alexander, F.W., Sandmeier, E., Mehta, P.K., and Christen, P. 1994. Evolutionary relationships among pyridoxal-5′-phosphate-dependent enzymes: Regiospecificα, β and γ families. Eur. J. Biochem. 219 953–960. - PubMed
    1. Baek, J.Y., Jun, D.Y., Taub, D., and Kim, Y.H. 2003. Characterization of human phosphoserine aminotransferase involved in the phosphorylated pathway of L-serine biosynthesis. Biochem. J. 373 191–200. - PMC - PubMed
    1. Basurko, M.J., Marche, M., Darriet, M., and Cassaigne, A. 1999. Phosphoserine aminotransferase, the second step-catalyzing enzyme for serine biosynthesis. IUBMB Life 48 525–529. - PubMed
    1. Brünger, A.T. 1997. Free R value: Cross-validation in crystallography. Methods Enzymol. 277 366–396. - PubMed
    1. Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. 1998. Crystallography & NMR system: A new software suite for macro-molecular structure determination. Acta Crystallogr. Sect. D Biol. Crystallogr. 54 905–921. - PubMed

Publication types

MeSH terms

Substances

Associated data

LinkOut - more resources

Full text links
👁 Wiley full text link
Wiley Free PMC article
Cite
Send To

NCBI Literature Resources

MeSH PMC Bookshelf Disclaimer

The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.