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Literature summary for 1.5.1.2 extracted from

  • Patel, S.; Seravalli, J.; Liang, X.; Tanner, J.; Becker, D.
    Disease variants of human Delta1-pyrroline-5-carboxylate reductase 2 (PYCR2) (2021), Arch. Biochem. Biophys., 703, 108852 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 1.5.1.2

Cloned(Commentary)

Cloned (Comment) Organism
gene PYR2, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21 (DE3) pLysS Homo sapiens

Protein Variants

Protein Variants Comment Organism
R119C mutation identified in patient with microcephaly and hypomyelination, mutant is catalytically impaired Homo sapiens
R119C a naturally occuring mutation in patients with microcephaly and hypomyelination. The mutant is catalytically impaired, depending on whether NADPH or NADH is used, the catalytic efficiency of the R119C protein variant is 40 or 366 times lower than that of the wild-type enzyme Homo sapiens
R251C mutation identified in patient with microcephaly and hypomyelination, mutant is catalytically impaired and has a pronounced folding defect Homo sapiens
R251C a naturally occuring mutation in patients with microcephaly and hypomyelination. The mutant is catalytically impaired, depending on whether NADPH or NADH is used, the catalytic efficiency of the R119C protein variant is 7 or 26 times lower than that of the wild-type enzyme. The R251C protein variant has a pronounced folding defect. The R251C variant displays the least overall regular alpha-helical character of the PYCR2 proteins, yet the R251C variant also displays strong overall regular beta-strand or beta-sheet character Homo sapiens

Inhibitors

Inhibitors Comment Organism Structure
L-proline at 0-500 microM, the value of KMapp increases whereas Vlim remains fairly unchanged, which is consistent with competitive inhibition Homo sapiens

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information steady-state kinetics of the wild-type enzyme and mutants Homo sapiens
0.03
-
 NADH mutant R119C, pH 7.5, 37°C Homo sapiens
0.034
-
 NADH pH 7.5, 37°C, recombinant mutant R119C, with 1-pyrroline-5-carboxylate Homo sapiens
0.119
-
 NADPH pH 7.5, 37°C, recombinant mutant R251C, with 1-pyrroline-5-carboxylate Homo sapiens
0.12
-
 NADPH mutant R251C, pH 7.5, 37°C Homo sapiens
0.216
-
 NADPH pH 7.5, 37°C, recombinant wild-type enzyme, with 1-pyrroline-5-carboxylate Homo sapiens
0.22
-
 NADPH wild-type, pH 7.5, 37°C Homo sapiens
0.298
-
 NADH pH 7.5, 37°C, recombinant wild-type enzyme, with 1-pyrroline-5-carboxylate Homo sapiens
0.3
-
 NADH wild-type, pH 7.5, 37°C Homo sapiens
0.317
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R119C, with NADH Homo sapiens
0.32
-
 1-pyrroline-5-carboxylate mutant R119C, cosubstrate NADH, pH 7.5, 37°C Homo sapiens
0.33
-
 1-pyrroline-5-carboxylate mutant R119C, cosubstrate NADPH, pH 7.5, 37°C Homo sapiens
0.334
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R119C, with NADPH Homo sapiens
0.537
-
 NADPH pH 7.5, 37°C, recombinant mutant R119C, with 1-pyrroline-5-carboxylate Homo sapiens
0.54
-
 NADPH mutant R119C, pH 7.5, 37°C Homo sapiens
0.949
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant wild-type enzyme, with NADPH Homo sapiens
0.95
-
 NADH mutant R251C, pH 7.5, 37°C Homo sapiens
0.953
-
 NADH pH 7.5, 37°C, recombinant mutant R251C, with 1-pyrroline-5-carboxylate Homo sapiens
0.99
-
 1-pyrroline-5-carboxylate wild-type, cosubstrate NADPH, pH 7.5, 37°C Homo sapiens
1.315
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R251C, with NADH Homo sapiens
1.32
-
 1-pyrroline-5-carboxylate mutant R251C, cosubstrate NADH, pH 7.5, 37°C Homo sapiens
1.499
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R251C, with NADPH Homo sapiens
1.5
-
 1-pyrroline-5-carboxylate mutant R251C, cosubstrate NADPH, pH 7.5, 37°C Homo sapiens
1.509
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant wild-type enzyme, with NADH Homo sapiens
1.51
-
 1-pyrroline-5-carboxylate wild-type, cosubstrate NADH, pH 7.5, 37°C Homo sapiens

Localization

Localization Comment Organism GeneOntology No. Textmining
mitochondrion
-
 Homo sapiens 5739
-

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1-pyrroline-5-carboxylate + NADH + H+ Homo sapiens
-
 L-proline + NAD+
-
 ?
1-pyrroline-5-carboxylate + NADPH + H+ Homo sapiens
-
 L-proline + NADP+
-
 ?

Organism

Organism UniProt Comment Textmining
Homo sapiens Q96C36
-
-
Homo sapiens Q96C36 isoform PYRC2
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21 (DE3) pLysS by nickel affinity chromatography, dialysis, and ultrafiltration Homo sapiens

Reaction

Reaction Comment Organism Reaction ID
L-proline + NAD(P)+ = 1-pyrroline-5-carboxylate + NAD(P)H + H+ enzyme PYCR2 kinetics suggest a sequential binding mechanism with L-P5C binding before NAD(P)H and NAD(P)+ releasing before L-Pro Homo sapiens
a

Source Tissue

Source Tissue Comment Organism Textmining
epithelium
-
 Homo sapiens
-
esophageal squamous cell carcinoma cell
-
 Homo sapiens
-
skeletal muscle
-
 Homo sapiens
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1-pyrroline-5-carboxylate + NADH
-
 Homo sapiens L-proline + NAD+
-
 ?
1-pyrroline-5-carboxylate + NADH + H+
-
 Homo sapiens L-proline + NAD+
-
 ?
1-pyrroline-5-carboxylate + NADPH
-
 Homo sapiens L-proline + NADP+
-
 ?
1-pyrroline-5-carboxylate + NADPH + H+
-
 Homo sapiens L-proline + NADP+
-
 ?

Synonyms

Synonyms Comment Organism
DELTA1-pyrroline-5-carboxylate reductase 2
-
 Homo sapiens
PYCR2
-
 Homo sapiens

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
 assay at Homo sapiens

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
54 79 PYCR2 wild-type and mutant R119C exhibit fairly sharp unfolding transitions and similar Tm values of 69°C and 67°C, respectively, whereas mutant R251C exhibits a dramatically lower Tm value of 54°C. Incubation of each PYCR2 enzyme with product ligands, L-Pro and NAD+, individually or together has no effect on the observed Tm values Homo sapiens

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.015
-
 NADH mutant R119C, pH 7.5, 37°C Homo sapiens
0.015
-
 NADH pH 7.5, 37°C, recombinant mutant R119C, with 1-pyrroline-5-carboxylate Homo sapiens
0.08
-
 1-pyrroline-5-carboxylate mutant R119C, cosubstrate NADH, pH 7.5, 37°C Homo sapiens
0.08
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R119C, with NADH Homo sapiens
0.13
-
 1-pyrroline-5-carboxylate mutant R119C, cosubstrate NADPH, pH 7.5, 37°C Homo sapiens
0.13
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R119C, with NADPH Homo sapiens
1.5
-
 NADPH mutant R119C, pH 7.5, 37°C Homo sapiens
1.5
-
 NADPH pH 7.5, 37°C, recombinant mutant R119C, with 1-pyrroline-5-carboxylate Homo sapiens
1.8
-
 NADPH mutant R251C, pH 7.5, 37°C Homo sapiens
1.8
-
 NADPH pH 7.5, 37°C, recombinant mutant R251C, with 1-pyrroline-5-carboxylate Homo sapiens
3.1
-
 1-pyrroline-5-carboxylate mutant R251C, cosubstrate NADPH, pH 7.5, 37°C Homo sapiens
3.1
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R251C, with NADPH Homo sapiens
3.2
-
 1-pyrroline-5-carboxylate mutant R251C, cosubstrate NADH, pH 7.5, 37°C Homo sapiens
3.2
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R251C, with NADH Homo sapiens
5.9
-
 NADH mutant R251C, pH 7.5, 37°C Homo sapiens
5.9
-
 NADH pH 7.5, 37°C, recombinant mutant R251C, with 1-pyrroline-5-carboxylate Homo sapiens
24
-
 NADPH wild-type, pH 7.5, 37°C Homo sapiens
24
-
 NADPH pH 7.5, 37°C, recombinant wild-type enzyme, with 1-pyrroline-5-carboxylate Homo sapiens
26
-
 1-pyrroline-5-carboxylate wild-type, cosubstrate NADPH, pH 7.5, 37°C Homo sapiens
26
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant wild-type enzyme, with NADPH Homo sapiens
47.9
-
 NADH wild-type, pH 7.5, 37°C Homo sapiens
47.9
-
 NADH pH 7.5, 37°C, recombinant wild-type enzyme, with 1-pyrroline-5-carboxylate Homo sapiens
61.3
-
 1-pyrroline-5-carboxylate wild-type, cosubstrate NADH, pH 7.5, 37°C Homo sapiens
61.3
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant wild-type enzyme, with NADH Homo sapiens

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
 assay at Homo sapiens

Cofactor

Cofactor Comment Organism Structure
additional information PYCR2 does not show a strong preference for NADH or NADPH Homo sapiens
NAD+
-
 Homo sapiens
NADH
-
 Homo sapiens
NADP+
-
 Homo sapiens
NADPH
-
 Homo sapiens

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
additional information
-
 additional information product(s) inhibition kinetics are analyzed by global fitting of the data to different inhibition models Homo sapiens
0.145
-
 L-proline pH 7.5, 37°C, recombinant wild-type enzyme, competitive inhibition Homo sapiens

Expression

Organism Comment Expression
Homo sapiens in a mass spectrometry-based screening of metabolites in tissue sections from 256 esophageal squamous cell carcinoma (ESCC) patients, a significant upregulation of L-proline metabolism is found in the cancer region compared to the normal epithelium and muscle regions. Immunohistochemistry staining of the ESCC tissue sections identifies PYCR2 as the most enriched metabolic enzyme in the cancer region, consistent with increased L-proline found in the same tissue region up

General Information

General Information Comment Organism
malfunction homozygous mutations in human PYCR2 lead to postnatal microcephaly and hypomyelination, including hypomyelinating leukodystrophy type 10. PYCR2 mutations are detected in patients with lethal microcephaly, loss of PYCR2 is proposed to impair mitochondria function and disrupt oxidative balance, namely NAD(P)+ levels. The R251C variant displays the least overall regular alpha-helical character of the PYCR2 proteins, yet the R251C variant also displays strong overall regular beta-strand or beta-sheet character Homo sapiens
metabolism sequential binding mechanism with 1-pyrroline-5-carboxylate binding before NAD(P)H and NAD(P)+ releasing before L-Pro Homo sapiens
metabolism the enzyme is involved in the proline metabolism in the mitochondrion, overview Homo sapiens
physiological function pyrroline-5-carboxylate reductase (PYCR in humans) catalyzes the final step of L-proline biosynthesis by catalyzing the reduction of L-DELTA1-pyrroline-5-carboxylate (L-P5C) to L-proline using NAD(P)H as the hydride donor. In humans, three isoforms PYCR1c, and PYCR3 are known. Isozyme PYCR3 is a cytosolic enzyme whereas PYCR1 and PYCR2 are identified as mitochondrial isozymes. PYCR2 not only drives cellular supply of L-proline but it is also important for redox cycling of NAD(P)H/NAD(P)+ Homo sapiens

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.25
-
 1-pyrroline-5-carboxylate mutant R119C, cosubstrate NADH, pH 7.5, 37°C Homo sapiens
0.25
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R119C, with NADH Homo sapiens
0.39
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R119C, with NADPH Homo sapiens
0.4
-
 1-pyrroline-5-carboxylate mutant R119C, cosubstrate NADPH, pH 7.5, 37°C Homo sapiens
0.44
-
 NADH mutant R119C, pH 7.5, 37°C Homo sapiens
0.441
-
 NADH pH 7.5, 37°C, recombinant mutant R119C, with 1-pyrroline-5-carboxylate Homo sapiens
2.07
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R251C, with NADPH Homo sapiens
2.1
-
 1-pyrroline-5-carboxylate mutant R251C, cosubstrate NADPH, pH 7.5, 37°C Homo sapiens
2.4
-
 1-pyrroline-5-carboxylate mutant R251C, cosubstrate NADH, pH 7.5, 37°C Homo sapiens
2.43
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant mutant R251C, with NADH Homo sapiens
2.793
-
 NADPH pH 7.5, 37°C, recombinant mutant R119C, with 1-pyrroline-5-carboxylate Homo sapiens
2.8
-
 NADPH mutant R119C, pH 7.5, 37°C Homo sapiens
6.19
-
 NADH pH 7.5, 37°C, recombinant mutant R251C, with 1-pyrroline-5-carboxylate Homo sapiens
6.2
-
 NADH mutant R251C, pH 7.5, 37°C Homo sapiens
15
-
 NADPH mutant R251C, pH 7.5, 37°C Homo sapiens
15.13
-
 NADPH pH 7.5, 37°C, recombinant mutant R251C, with 1-pyrroline-5-carboxylate Homo sapiens
26
-
 1-pyrroline-5-carboxylate wild-type, cosubstrate NADPH, pH 7.5, 37°C Homo sapiens
27.4
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant wild-type enzyme, with NADPH Homo sapiens
40.62
-
 1-pyrroline-5-carboxylate pH 7.5, 37°C, recombinant wild-type enzyme, with NADH Homo sapiens
41
-
 1-pyrroline-5-carboxylate wild-type, cosubstrate NADH, pH 7.5, 37°C Homo sapiens
111
-
 NADPH wild-type, pH 7.5, 37°C Homo sapiens
111.11
-
 NADPH pH 7.5, 37°C, recombinant wild-type enzyme, with 1-pyrroline-5-carboxylate Homo sapiens
160.74
-
 NADH pH 7.5, 37°C, recombinant wild-type enzyme, with 1-pyrroline-5-carboxylate Homo sapiens
161
-
 NADH wild-type, pH 7.5, 37°C Homo sapiens