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Gene Review:

UTI89_C3974 - phosphoglycerate dehydrogenase

Escherichia coli UTI89

Ho, C.L. et al., Ali, V. et al., Grant, G.A. et al., Dubrow, R. et al., Tobey, K.L. et al., et al.

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Disease relevance of UTI89_C3974

The crystal structure of the phosphoglycerate dehydrogenase from Escherichia coli is unique among dehydrogenases [1].
EhPGDH showed high homology to PGDH from bacteroides and another enteric protozoan ciliate, Entodinium caudatum [2].

High impact information on UTI89_C3974

They reveal that PGDH displays half-of-the-sites activity with respect to its active sites and that the two sites that are active at any particular time lie in subunits on either side of the nucleotide binding domain interface [3].
D-3-Phosphoglycerate dehydrogenase (PGDH) from Escherichia coli is allosterically inhibited by L-serine, the end product of its metabolic pathway [4].
3-Phosphoglycerate dehydrogenase (PGDH), the first enzyme that is involved in the phosphorylated pathway of Ser biosynthesis, is responsible for the oxidation of 3-phosphoglycerate to phosphohydroxypyruvate [5].
Southern hybridization analysis and restriction fragment length polymorphism mapping indicated that PGDH is a single-copy gene that is mapped to the upper arm of chromosome 1 [5].
These consist of a group of cationic residues (Arg-240, Arg-60, Arg-62, Lys-39, and Lys-141') that potentially form an electrostatic environment for the binding of the negatively charged substrate, as well as the only tryptophan residue found in PGDH and which fits into a hydrophobic pocket immediately adjacent to the active site histidine residue [4].

Chemical compound and disease context of UTI89_C3974

The level of phosphoglycerate dehydrogenase, the first enzyme in the biosynthetic pathway to serine and glycine, has been studied in Escherichia coli grown under different conditions [6].
Escherichia coli 3-phosphoglycerate dehydrogenase (PGDH) catalyzes the first step in serine biosynthesis, and is allosterically inhibited by serine [7].

Biological context of UTI89_C3974

Comparison of the amino acid sequence of phosphoglycerate dehydrogenase with other NAD-dependent oxidoreductases reveals less than 20% homology, although conservation of certain specific residues in the coenzyme binding domain appears to be evident [8].
Sequence analysis of cDNA and a genomic clone revealed that the PGDH gene is composed of three exons, encoding a 623-amino acid polypeptide (66, 453 Da) [5].
Stopped flow spectrophotometry was used to investigate the kinetics of the transition of the phosphoglycerate dehydrogenase (3-phosphoglycerate: NAD oxidoreductase, EC 1.1.1.95) reaction from the active to the inhibited rate upon the addition of the physiological inhibitor serine [9].
The derived amino acid sequence from this open reading frame is 26% identical and 50% similar to the amino acid sequence of the E. coli enzyme phosphoglycerate dehydrogenase, which catalyzes a similar reaction and functions in a related pathway [10].
Kinetic parameters of EhPGDH were similar to those of mammalian PGDH, for example the preference of NADH cofactor, substrate specificities and salt-reversible substrate inhibition [2].

Associations of UTI89_C3974 with chemical compounds

Regulation of serine biosynthesis in Arabidopsis. Crucial role of plastidic 3-phosphoglycerate dehydrogenase in non-photosynthetic tissues [5].
The reduction of enzyme-bound DPN constitutes a half-reaction of phosphoglycerate dehydrogenase and has been investigated fluorometrically [11].
A putative phosphoglycerate dehydrogenase (PGDH), which catalyzes the oxidation of d-phosphoglycerate to 3-phosphohydroxypyruvate in the so-called phosphorylated serine metabolic pathway, from the enteric protozoan parasite Entamoeba histolytica was characterized [2].

Analytical, diagnostic and therapeutic context of UTI89_C3974

Here we report the first molecular cloning and characterization of PGDH from Arabidopsis thaliana [5].
In this study, the active site of PGDH has been studied by site-directed mutagenesis to assess the role of certain residues in substrate binding and catalysis [4].
An active conformation of phosphoglycerate dehydrogenase (PGDH) from Escherichia coli has been obtained using X-ray crystallography [12].
In contrast to PGDH from bacteria, plants and mammals, the EhPGDH protein is present as a homodimer as demonstrated by gel filtration chromatography [2].

References

The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Schuller, D.J., Grant, G.A., Banaszak, L.J. Nat. Struct. Biol. (1995) [Pubmed]
Molecular and biochemical characterization of D-phosphoglycerate dehydrogenase from Entamoeba histolytica. A unique enteric protozoan parasite that possesses both phosphorylated and nonphosphorylated serine metabolic pathways. Ali, V., Hashimoto, T., Shigeta, Y., Nozaki, T. Eur. J. Biochem. (2004) [Pubmed]
Quantitative relationships of site to site interaction in Escherichia coli D-3-phosphoglycerate dehydrogenase revealed by asymmetric hybrid tetramers. Grant, G.A., Xu, X.L., Hu, Z. J. Biol. Chem. (2004) [Pubmed]
The contribution of adjacent subunits to the active sites of D-3-phosphoglycerate dehydrogenase. Grant, G.A., Kim, S.J., Xu, X.L., Hu, Z. J. Biol. Chem. (1999) [Pubmed]
Regulation of serine biosynthesis in Arabidopsis. Crucial role of plastidic 3-phosphoglycerate dehydrogenase in non-photosynthetic tissues. Ho, C.L., Noji, M., Saito, M., Saito, K. J. Biol. Chem. (1999) [Pubmed]
Regulation of phosphoglycerate dehydrogenase levels and effect on serine synthesis in Escherichia coli K-12. McKitrick, J.C., Pizer, L.I. J. Bacteriol. (1980) [Pubmed]
De-regulation of D-3-phosphoglycerate dehydrogenase by domain removal. Bell, J.K., Pease, P.J., Bell, J.E., Grant, G.A., Banaszak, L.J. Eur. J. Biochem. (2002) [Pubmed]
The nucleotide sequence of the serA gene of Escherichia coli and the amino acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenase. Tobey, K.L., Grant, G.A. J. Biol. Chem. (1986) [Pubmed]
Transient kinetic studies on the allosteric transition of phosphoglycerate dehydrogenase. Dubrow, R., Pizer, L.I. J. Biol. Chem. (1977) [Pubmed]
Isolation, characterization and sequence analysis of a full-length cDNA clone encoding NADH-dependent hydroxypyruvate reductase from cucumber. Greenler, J.M., Sloan, J.S., Schwartz, B.W., Becker, W.M. Plant Mol. Biol. (1989) [Pubmed]
The mechanism of end product inhibition of serine biosynthesis. V. Mechanism of serim inhibition of phosphoglycerate dehydrogenases. Winicov, I. J. Biol. Chem. (1975) [Pubmed]
Vmax regulation through domain and subunit changes. The active form of phosphoglycerate dehydrogenase. Thompson, J.R., Bell, J.K., Bratt, J., Grant, G.A., Banaszak, L.J. Biochemistry (2005) [Pubmed]

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