6T3E

Structure of Thermococcus litoralis Delta(1)-pyrroline-2-carboxylate reductase in complex with NADH and L-proline

Summary for 6T3E

• Entry DOI: 10.2210/pdb6t3e/pdb
• Descriptor: DELTA1-pyrroline-2-carboxylate reductase, PROLINE, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: reductase, l-hydroxyproline metabolism, delta(1)-pyrroline-2-carboxylate, thermococcus litoralis, oxidoreductase
• Biological source: Thermococcus litoralis DSM 5473
• Total number of polymer chains: 2
• Total formula weight: 78105.24

Authors

Ferraris, D.M.,Miggiano, R.,Ferrario, E.,Rizzi, M. (deposition date: 2019-10-10, release date: 2020-05-13, Last modification date: 2024-01-24)

Primary citation

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.
Acta Crystallogr D Struct Biol, 76:496-505, 2020

PubMed Abstract: L-Hydroxyproline (L-Hyp) is a nonstandard amino acid that is present in certain proteins, in some antibiotics and in the cell-wall components of plants. L-Hyp is the product of the post-translational modification of protein prolines by prolyl hydroxylase enzymes, and 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 Δ-pyrroline-2-carboxylate (Pyr2C) reductase. In order to shed light on the structure and catalysis of the enzyme involved in the second step of the T3LHyp degradation pathway, the crystal structure of Pyr2C reductase from the archaeon Thermococcus litoralis DSM 5473 complexed with NADH and L-proline is presented. The model allows the mapping of the residues involved in cofactor and product binding and represents a valid model for rationalizing the catalysis of Pyr2C reductases.

PubMed: 32355045
DOI: 10.1107/S2059798320004866

Experimental method

X-RAY DIFFRACTION (2.6 Å)