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Literature summary extracted from

  • Ferrario, E.; Miggiano, R.; Rizzi, M.; Ferraris, D.M.
    Structure of Thermococcus litoralis DELTA1-pyrroline-2-carboxylate reductase in complex with NADH and L-proline (2020), Acta Crystallogr. Sect. D, 76, 496-505 .
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.5.1.B5 purified enzyme in complex with NADH and L-proline, X-ray diffraction structure determination and analysis Thermococcus litoralis

Protein Variants

EC Number Protein Variants Comment Organism
1.5.1.B5 N168A site-directed mutagenesis Thermococcus litoralis
1.5.1.B5 R43A site-directed mutagenesis Thermococcus litoralis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.5.1.B5 L-proline + NAD+ Thermococcus litoralis
-
 DELTA1-pyrroline-2-carboxylate + NADH + H+
-
 r
1.5.1.B5 L-proline + NAD+ Thermococcus litoralis JCM 8560
-
 DELTA1-pyrroline-2-carboxylate + NADH + H+
-
 r
1.5.1.B5 L-proline + NAD+ Thermococcus litoralis DSM 5473
-
 DELTA1-pyrroline-2-carboxylate + NADH + H+
-
 r
1.5.1.B5 L-proline + NAD+ Thermococcus litoralis ATCC 51850
-
 DELTA1-pyrroline-2-carboxylate + NADH + H+
-
 r
1.5.1.B5 L-proline + NAD+ Thermococcus litoralis NS-C
-
 DELTA1-pyrroline-2-carboxylate + NADH + H+
-
 r

Organism

EC Number Organism UniProt Comment Textmining
1.5.1.B5 Thermococcus litoralis
-
-
-
1.5.1.B5 Thermococcus litoralis ATCC 51850
-
-
-
1.5.1.B5 Thermococcus litoralis DSM 5473
-
-
-
1.5.1.B5 Thermococcus litoralis JCM 8560
-
-
-
1.5.1.B5 Thermococcus litoralis NS-C
-
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
1.5.1.B5 L-proline + NAD+ = DELTA1-pyrroline-2-carboxylate + NADH + H+ catalytic mechanism, overview. The hydride ion is transferred from the C4 atom of NADH to the C2 atom of Pyr2C, causing electron transfer to the vicinal N atom of Pyr2C, which is now capable of accepting the proton donated by the guanidine group of Arg43. The product L-proline forms a hydrogen bond to the carbonyl O atom of Val301, which stabilizes formation of the product prior to its release. Lys71 and Arg114 are highly conserved and are involved in substrate binding through their interaction with the substrate carboxyl group. But the NH2 group of the guanidine of Arg43 engages in a hydrogen bond to the close carbonyl O atom of Val301 and to the distant N atom of the substrate, the putative proton acceptor of the catalytic reaction Thermococcus litoralis
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.5.1.B5 L-proline + NAD+
-
 Thermococcus litoralis DELTA1-pyrroline-2-carboxylate + NADH + H+
-
 r
1.5.1.B5 L-proline + NAD+
-
 Thermococcus litoralis JCM 8560 DELTA1-pyrroline-2-carboxylate + NADH + H+
-
 r
1.5.1.B5 L-proline + NAD+
-
 Thermococcus litoralis DSM 5473 DELTA1-pyrroline-2-carboxylate + NADH + H+
-
 r
1.5.1.B5 L-proline + NAD+
-
 Thermococcus litoralis ATCC 51850 DELTA1-pyrroline-2-carboxylate + NADH + H+
-
 r
1.5.1.B5 L-proline + NAD+
-
 Thermococcus litoralis NS-C DELTA1-pyrroline-2-carboxylate + NADH + H+
-
 r

Subunits

EC Number Subunits Comment Organism
1.5.1.B5 dimer an alpha-helix (residues 106-126) is linking the dimerization domain to the Rossmann-fold NADH-binding domain Thermococcus litoralis

Synonyms

EC Number Synonyms Comment Organism
1.5.1.B5 DELTA-pyrroline-2-carboxylate reductase
-
 Thermococcus litoralis
1.5.1.B5 NADH-dependent Pyr2C reductase
-
 Thermococcus litoralis
1.5.1.B5 Pyr2C reductase
-
 Thermococcus litoralis
1.5.1.B5 tlPyr2C
-
 Thermococcus litoralis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.5.1.B5 6 10 broad optimum of wild-type enzyme and mutant N168A Thermococcus litoralis
1.5.1.B5 7
-
 optimum of mutant R43A Thermococcus litoralis

pH Range

EC Number pH Minimum pH Maximum Comment Organism
1.5.1.B5 6 10 the mutant R43A shows highest activity at pH 7.0, moderate to higher activity at pH 8.0 and pH 6.0, but lower activity at pH 10.0. The wild-type enzyme shows contantly high activity at pH 6.0-10.0 Thermococcus litoralis

Cofactor

EC Number Cofactor Comment Organism Structure
1.5.1.B5 additional information the preference of tlPyr2C for NADH instead of NADPH can be rationalized by analysing the residues of tlPyr2C that bind to the 2'-hydroxyl group of NADH and comparing them with the residues of tlPyr2C orthologues that bind to the phosphate group of NADPH. Determination and analysis of the NADH binding structure and interaction network of tlPyr2C, structure comparisons, detailed overview. A role of Asn168 in the selectivity for NADH versus NADPH is suggested Thermococcus litoralis
1.5.1.B5 NAD+
-
 Thermococcus litoralis
1.5.1.B5 NADH
-
 Thermococcus litoralis

General Information

EC Number General Information Comment Organism
1.5.1.B5 metabolism the enzyme performs the second step of the trans-3-hydroxy-L-proline (T3LHyp) degradation pathway Thermococcus litoralis
1.5.1.B5 physiological function approximately 40% of L-proline in collagen are post-translationally converted by proline hydroxylases into the isomers trans-4-hydroxy-L-proline (T4LHyp) and trans-3-hydroxy-L-proline (T3LHyp). The isomers trans-3-hydroxy-L-proline (T3LHyp) and trans-4-hydroxy-L-proline (T4LHyp) are major components of mammalian collagen. T4LHyp follows two distinct degradation pathways in bacteria and mammals, while T3LHyp is metabolized by a two-step metabolic pathway that is conserved in bacteria and mammals, which involves a T3LHyp dehydratase and a DELTA1-pyrroline-2-carboxylate (Pyr2C) reductase Thermococcus litoralis