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Information on EC 2.6.1.52 - phosphoserine transaminase and Organism(s) Arabidopsis thaliana
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2.6.1.52 phosphoserine transaminaseIUBMB Comments
A pyridoxal 5'-phosphate protein. This enzyme catalyses the second step in the phosphorylated pathway of serine biosynthesis [1,3] and the third step in pyridoxal 5'-phosphate biosynthesis in the bacterium Escherichia coli . Pyridoxal 5'-phosphate is the cofactor for both activities and therefore seems to be involved in its own biosynthesis . Non-phosphorylated forms of serine and threonine are not substrates . The archaeal enzyme has a relaxed specificity and can act on L-cysteate and L-alanine as alternative substrates to O-phospho-L-serine .
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The taxonomic range for the selected organisms is: Arabidopsis thaliana
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
psat, phosphoserine aminotransferase, phosphoserine aminotransferase 1, ehpsat, 3-phosphoserine aminotransferase, psat2, l-phosphoserine aminotransferase, bmpsat, psat beta, psat alpha, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3-phosphoserine aminotransferase
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hydroxypyruvic phosphate-glutamic transaminase
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L-phosphoserine aminotransferase
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phosphohydroxypyruvate transaminase
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phosphohydroxypyruvic-glutamic transaminase
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phosphoserine aminotransferase
PSAT
phosphoserine aminotransferase
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PSAT
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
O-phospho-L-serine + 2-oxoglutarate = 3-phosphooxypyruvate + L-glutamate
bimolecular ping-pong mechanism, the transamination reaction catalyzed by PSAT consists of two reversible half-reactions, detailed overview
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
amino group transfer
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PATHWAY SOURCE
PATHWAYS
KEGG
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-, -, -
SYSTEMATIC NAME
IUBMB Comments
O-phospho-L-serine:2-oxoglutarate aminotransferase
A pyridoxal 5'-phosphate protein. This enzyme catalyses the second step in the phosphorylated pathway of serine biosynthesis [1,3] and the third step in pyridoxal 5'-phosphate biosynthesis in the bacterium Escherichia coli [3]. Pyridoxal 5'-phosphate is the cofactor for both activities and therefore seems to be involved in its own biosynthesis [4]. Non-phosphorylated forms of serine and threonine are not substrates [4]. The archaeal enzyme has a relaxed specificity and can act on L-cysteate and L-alanine as alternative substrates to O-phospho-L-serine [7].
CAS REGISTRY NUMBER
COMMENTARY
9030-90-4
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
L-glutamate + 3-phosphohydroxypyruvate
O-phospho-L-serine + 2-oxoglutarate
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r
L-glutamate + 3-phosphohydroxypyruvate
O-phospho-L-serine + 2-oxoglutarate
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r
O-phospho-L-serine + 2-oxoglutarate
3-phosphooxypyruvate + L-glutamate
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r
O-phospho-L-serine + 2-oxoglutarate
3-phosphooxypyruvate + L-glutamate
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r
additional information
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the transamination reaction catalyzed by PSAT consists of two reversible half-reactions, overview. Substrate binding requires a conformational change of AtPSAT1
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additional information
?
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the transamination reaction catalyzed by PSAT consists of two reversible half-reactions, overview. Substrate binding requires a conformational change of AtPSAT1
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
L-glutamate + 3-phosphohydroxypyruvate
O-phospho-L-serine + 2-oxoglutarate
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-
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r
O-phospho-L-serine + 2-oxoglutarate
3-phosphooxypyruvate + L-glutamate
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-
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r
O-phospho-L-serine + 2-oxoglutarate
3-phosphooxypyruvate + L-glutamate
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r
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
PLP, dependent on, the PLP prosthetic group creates a Schiff base (internal aldimine) between C4' and Nzeta of K265, PLP bound in the active site forms an internal aldimine with residue K265, the residue placed in the coil between beta9 and beta10
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
additional information
PSAT1 is the most expressed isoform and the expression of both genes is higher in root than in shoot tissue. In 10-days-old plants the activity of both PSAT gene promoters is high in the shoot apical meristem (SAM), the root apical meristem (RAM), in the vasculature of the hypocotyl and in the vasculature of roots, whereas the PSAT1 promoter is additionally active in the vasculature tissue of cotyledons and young leaves. Specific expression pattern of PSAT genes, overview
additional information
PSAT1 is the most expressed isoform and the expression of both genes is higher in root than in shoot tissue. In 10-days-old plants the activity of both PSAT gene promoters is high in the shoot apical meristem (SAM), the root apical meristem (RAM), in the vasculature of the hypocotyl and in the vasculature of roots, whereas the PSAT1 promoter is additionally active in the vasculature tissue of cotyledons and young leaves. Specific expression pattern of PSAT genes, overview
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
isozyme PSAT1 has a truncated 71-residue-long chloroplast targeting signal peptide
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
a growth phenotype is observed for PSAT1-silenced plants due to serine deficiency
metabolism
physiological function
phosphoserine aminotransferase1 is part of the phosphorylated pathways for serine biosynthesis and essential for light and sugar-dependent growth promotion
additional information
evolution
phosphoserine aminotransferases belong to the class IV of aminotransferases with the alpha-type fold. In general, this class of enzymes is characterized by the presence of two domains with mixed alpha/beta fold
evolution
the Arabidopsis genome contains three genes for the PGDH (At4g34200/PGDH1, At1g17745/ PGDH2, and At3g19480/ PGDH3), two genes for the PSAT (At4g35630/PSAT1, and At2g17630/PSAT2) and one gene for the PSP (At1g18640). The PSAT1 gene is the most expressed isoform in Arabidopsis thaliana
metabolism
phosphoserine aminotransferase (PSAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of 3-phosphohydroxypyruvate (3-PHP) to 3-phosphoserine (PSer) in an L-glutamate (Glu)-linked reversible transamination reaction. This process in plants takes place in plastids. It is a part of the phosphorylated pathway of serine biosynthesis, one of three routes recognized in plant organisms that yield serine. In this three-step biotransformation, 3-phosphoglycerate (3-PGA) delivered from plastidial glycolysis and Calvin cycle is oxidized by 3-PGA dehydrogenase. Then, 3-PHP is subjected to transamination with Glu to yield PSer and 2-oxoglutarate (AKG). In the last step of the pathway, serine is produced by the action of phosphoserine phosphatase
metabolism
the serine biosynthesis pathway consists of three sequential reactions that are catalyzed by 3-phosphoglycerate dehydrogenase (PGDH), 3-phosphoserine aminotransferase (PSAT), and 3-phosphoserine phosphatase (PSP) enzymes, all localized in the plastids. Serine biosynthesis pathways in plants, overview
additional information
conformational changes of the protein during the catalytic event concern (i) the neighborhood of K265 when the amino group is transferred to the cofactor to form PMP and (ii) movement of the gate-keeping loop (residues 391-401) upon binding of of 3-phosphohydroxypyruvate to 3-phosphoserine. The latter conformational change of the loop may likely be one of key elements that regulate catalytic activity of PSATs. The conserved catalytic lysine, which directly follows a hydrophobic beta-strand, is localized closer to the C-terminus than the Gly-rich region. PSATs have an aspartate residue which hydrogen bonds the pyridoxal ring N1 atom and precedes the Schiff base lysine by 20-50 amino acids. The complex structure with pyridoxamine shows the enzyme primes for a covalent binding of 3-phosphohydroxypyruvate. The complex structure with phopshoserine reveals the geminal diamine intermediate state
additional information
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conformational changes of the protein during the catalytic event concern (i) the neighborhood of K265 when the amino group is transferred to the cofactor to form PMP and (ii) movement of the gate-keeping loop (residues 391-401) upon binding of of 3-phosphohydroxypyruvate to 3-phosphoserine. The latter conformational change of the loop may likely be one of key elements that regulate catalytic activity of PSATs. The conserved catalytic lysine, which directly follows a hydrophobic beta-strand, is localized closer to the C-terminus than the Gly-rich region. PSATs have an aspartate residue which hydrogen bonds the pyridoxal ring N1 atom and precedes the Schiff base lysine by 20-50 amino acids. The complex structure with pyridoxamine shows the enzyme primes for a covalent binding of 3-phosphohydroxypyruvate. The complex structure with phopshoserine reveals the geminal diamine intermediate state
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). SERB1_ARATH
430
0
47359
Swiss-Prot
Chloroplast (Reliability: 1)
SERB2_ARATH
422
0
46634
Swiss-Prot
Chloroplast (Reliability: 1)
A0A178UW75_ARATH
430
0
47331
TrEMBL
Chloroplast (Reliability: 1)
B9DHW8_ARATH
184
0
20409
TrEMBL
other Location (Reliability: 2)
A0A5S9WYV3_ARATH
422
0
46633
TrEMBL
Chloroplast (Reliability: 1)
A0A654ETP0_ARATH
422
0
46689
TrEMBL
Chloroplast (Reliability: 1)
A0A178VNF1_ARATH
422
0
46742
TrEMBL
Chloroplast (Reliability: 1)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
the crystal asymmetric unit with four subunits represents two functional AtPSAT1 dimers. The subunit of AtPSAT1 consists of two domains with mixed alpha/beta topology. This is a typical fold of class IV of the alpha-type aminotransferases with a much larger N-terminal catalytic domain and a smaller C-terminal domain. Hydrophobic core of the N-terminal domain is constituted by a seven-stranded beta-sheet with one anti-parallel strand. Subunit structure model, overview
additional information
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the crystal asymmetric unit with four subunits represents two functional AtPSAT1 dimers. The subunit of AtPSAT1 consists of two domains with mixed alpha/beta topology. This is a typical fold of class IV of the alpha-type aminotransferases with a much larger N-terminal catalytic domain and a smaller C-terminal domain. Hydrophobic core of the N-terminal domain is constituted by a seven-stranded beta-sheet with one anti-parallel strand. Subunit structure model, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
three crystal structures of isozyme AtPSAT1 are captured at different stages of the reaction: (i) internal aldimine state with PLP covalently bound to the catalytic K265, (ii) holoenzyme in complex with pyridoxamine-50-phosphate (PMP) after transfer of the amino group from glutamate and (iii) the geminal diamine intermediate state wherein the cofactor is covalently bound to both, K265 and PSer. These snapshots over the course of the reaction present the detailed architecture of AtPSAT1. Purified detagged recombinant enzyme in complex with cofactor PLP or pyridoxamine or product phosphoserine, sitting drop method, mixing of 15 mg/ml protein and 1 mM ligand (PLP, PMP) or 50 mM ligand (PSer) in 25 mM HEPES, pH 7.4, 100 mM KCl, 50 mM NaCl, and 1 mM TCEP with crystallization solution containing 0.2 M lithium sulfate, 17% PEG 3350, and 0.1 M Tris at pH 8.5 for ATPSAT1-PLP, with 0.2 M lithium sulfate, 17% PEG 3350, and 0.1 M Tris at pH 8.5, and 10 mM glutamate for AtPSAT1-PMP, and with 19% PEG 3350 and 0.1 M Tris at pH 8.5 for AtPSAT1-PSer, xadX-ray diffraction structure determination and analysis at 1.57-1.70 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
PSAT1-silenced lines (ts-psat1.1 and ts-psat1.2) are generated for functional characterization using a microRNA-based approach. Overexpression of the artificial PSAT1-silencing construct in Arabidopsis thaliana leads to a significant reduction of PSAT1 expression, which subsequently results in a strong inhibition of growth. The expression of the PSAT2 gene is unaltered in PSAT1-silenced plants, phenotype, overview
additional information
PSAT1-silenced lines (ts-psat1.1 and ts-psat1.2) are generated for functional characterization using a microRNA-based approach. Overexpression of the artificial PSAT1-silencing construct in Arabidopsis thaliana leads to a significant reduction of PSAT1 expression, which subsequently results in a strong inhibition of growth. The expression of the PSAT2 gene is unaltered in PSAT1-silenced plants, phenotype, overview
additional information
PSAT1-silenced lines (ts-psat1.1 and ts-psat1.2) are generated for functional characterization using a microRNA-based approach. The expression of the PSAT2 gene is unaltered in PSAT1-silenced plants, phenotype, overview
additional information
PSAT1-silenced lines (ts-psat1.1 and ts-psat1.2) are generated for functional characterization using a microRNA-based approach. The expression of the PSAT2 gene is unaltered in PSAT1-silenced plants, phenotype, overview
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged from Escherichia coli strain BL21 Gold by nickel affinity chromatography, tag cleavage through TEV protease, dialysis, gel filtration and ultrafiltration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
cDNA encoding PSAT, single gene mapped on the lower arm of chromosome 4, overexpressed in Escherichia coli AD494 and BL21
gene PSAT1, recombinant expression of His6-tagged in Escherichia coli strain BL21 Gold
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ho, C.L.; Noji, M.; Saito, M.; Yamazaki, M.; Saito, K.
Molecular characterization of plastidic phosphoserine aminotransferase in serine biosynthesis from Arabidopsis
Plant J.
16
443-452
1998
Spinacia oleracea, Arabidopsis thaliana (Q96255), Arabidopsis thaliana
Ali, V.; Nozaki, T.
Biochemical and functional characterization of phosphoserine aminotransferase from Entamoeba histolytica, which possesses both phosphorylated and non-phosphorylated serine metabolic pathways
Mol. Biochem. Parasitol.
145
71-83
2006
Arabidopsis thaliana, Entamoeba histolytica (Q60I38), Entamoeba histolytica
Wulfert, S.; Krueger, S.
Phosphoserine aminotransferase1 is part of the phosphorylated pathways for serine biosynthesis and essential for light and sugar-dependent growth promotion
Front. Plant Sci.
871
1712
2018
Arabidopsis thaliana (Q96255), Arabidopsis thaliana (Q9SHP0)
Sekula, B.; Ruszkowski, M.; Dauter, Z.
Structural analysis of phosphoserine aminotransferase (isoform 1) from Arabidopsis thaliana - the enzyme involved in the phosphorylated pathway of serine biosynthesis
Front. Plant Sci.
9
876
2018
Arabidopsis thaliana (Q96255), Arabidopsis thaliana
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