MetaCyc Polypeptide: glutaminase

Gene: At5G60540 Accession Number: AT5G60540 (MetaCyc)

Synonyms: PDX2

Species: Arabidopsis thaliana col

Component of: pyridoxal 5'-phosphate synthase (extended summary available)

Unification Links: ArrayExpress:Q8LAD0, Mint:MINT-8063085, PhylomeDB:Q8LAD0, Pride:Q8LAD0, Protein Model Portal:Q8LAD0, SMR:Q8LAD0, String:3702.AT5G60540.1, TAIR:At5G60540, UniProt:Q8LAD0

Relationship Links: InterPro:IN-FAMILY:IPR002161, InterPro:IN-FAMILY:IPR021196, InterPro:IN-FAMILY:IPR029062, Pfam:IN-FAMILY:PF01174, Prosite:IN-FAMILY:PS01236, Prosite:IN-FAMILY:PS51130

Gene-Reaction Schematic

Gene-Reaction Schematic

Created 22-Jul-2010 by Zhang P, TAIR

Subunit of: pyridoxal 5'-phosphate synthase

Species: Arabidopsis thaliana col

Subunit composition of pyridoxal 5'-phosphate synthase = [At5G60540][At2g38230]
         glutaminase = At5G60540
         pyridoxal 5'-phosphate synthase = At2g38230

Pyridoxal 5'-phosphate (PLP) synthase is a protein complex composed of two subunits, PDX1 and PDX2. The PDX2 subunit functions as a glutaminase that deaminates glutamine to producing glutamate and ammonia. The ammonia is channeled to the active site of the PLP synthase subunit PDX1 [TambascoStudart07] (reviewed in [Mooney10, Fitzpatrick07]).

In Arabidopsis, there are three homologous genes encoding PDX1, PDX1.1, 1.2 and 1.3, and one gene encoding PDX2. In a yeast complementation experiment, PDX1.1 and PDX1.3 were able to restore the yeast PDX1 mutant. In addition, the Arabidopsis PDX2 was also able to complement the yeast PDX2 mutant [TambascoStudart05].

Enzyme activities of PDX1.1 and PDX1.3 were proved in an in vitro assay of the recombinant proteins [TambascoStudart05, TambascoStudart07]. The activities observed were very similar with PDX1.1 and PDX1.3. Both proteins were able to accept either ribose 5-phosphate or ribulose 5-phosphate as the pentose sugar, and either glyceraldehyde 3-phosphate or dihydroxyacetone phosphate as the triose sugar, together with ammonia to form PLP. Whereas no preference was found for the triose, both proteins preferred ribose 5-phosphate to ribulose 5-phosphate [TambascoStudart07]. On the other hand, PDX1.2 was not active in the assay. Together with the genetic complementation data, PDX1.2 is not a functional PDX1.

The glutaminase activity of PDX2 was also proven in an in vitro assay [TambascoStudart07]. Comparing to PDX2 of other organisms (i.e. B. subtilis and P. falciparum), the Arabidopsis PDX2 had a substantially lower Kcat whereas its Km for glutamine was in the same range of those reported from the microorganisms. In microorganisms, 12 PDX1 subunits assemble with 12 PDX2 subunits to form a highly conserved cogwheel-like structure. Although it is unknown how precisely the Arabidopsis PDX complex assembles, it was shown that optimum enzyme activity was achieved when PDX1 and PDX2 were in a 1:1 molar ratio [TambascoStudart07].

Created 22-Jul-2010 by Zhang P, TAIR

Enzymatic reaction of: pyridoxal 5'-phosphate synthase

Inferred from experiment

Synonyms: pyridoxal phosphate synthase

EC Number:

keto-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine → pyridoxal 5'-phosphate + L-glutamate + phosphate + 3 H2O + H+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates for keto-D-ribose 5-phosphate: D-ribulose 5-phosphate [TambascoStudart05]
Alternative Substrates for D-glyceraldehyde 3-phosphate: glycerone phosphate [TambascoStudart05]

In Pathways: superpathway of L-citrulline metabolism, pyridoxal 5'-phosphate biosynthesis II

Kinetic Parameters:
Substrate Km (μM) Citations
L-glutamine 1920.0 [TambascoStudart07]


Fitzpatrick07: Fitzpatrick TB, Amrhein N, Kappes B, Macheroux P, Tews I, Raschle T (2007). "Two independent routes of de novo vitamin B6 biosynthesis: not that different after all." Biochem J 407(1);1-13. PMID: 17822383

Mooney10: Mooney S, Hellmann H (2010). "Vitamin B6: Killing two birds with one stone?." Phytochemistry 71(5-6);495-501. PMID: 20089286

TambascoStudart05: Tambasco-Studart M, Titiz O, Raschle T, Forster G, Amrhein N, Fitzpatrick TB (2005). "Vitamin B6 biosynthesis in higher plants." Proc Natl Acad Sci U S A 102(38);13687-92. PMID: 16157873

TambascoStudart07: Tambasco-Studart M, Tews I, Amrhein N, Fitzpatrick TB (2007). "Functional analysis of PDX2 from Arabidopsis, a glutaminase involved in vitamin B6 biosynthesis." Plant Physiol 144(2);915-25. PMID: 17468224

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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