PDBsum entry 6t3e

Oxidoreductase

PDB id: 6t3e

Contents

Protein chains

323 a.a.

Ligands

PRO ×2

NAI ×2

Waters ×19

PDB id:

6t3e

Name:

Oxidoreductase

Title:

Structure of thermococcus litoralis delta(1)-pyrroline-2-carboxylate reductase in complex with nadh and l-proline

Structure:

Delta1-pyrroline-2-carboxylate reductase. Chain: a, b. Engineered: yes

Source:

Thermococcus litoralis dsm 5473. Organism_taxid: 523849. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.60Å R-factor: 0.191 R-free: 0.242

Authors:

D.M.Ferraris,R.Miggiano,E.Ferrario,M.Rizzi

Key ref:

E.Ferrario et al. (2020). Structure of Thermococcus litoralis Δ¹-pyrroline-2-carboxylate reductase in complex with NADH and L-proline. Acta Crystallogr D Struct Biol, 76, 496-505. PubMed id: 32355045 DOI: 10.1107/S2059798320004866

Date:

10-Oct-19 Release date: 13-May-20

Protein chains

H3ZMH3  (H3ZMH3_THELN) -  Ornithine cyclodeaminase family protein from Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C)

Seq: 220 a.a.

Struc: 323 a.a.*

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.5.1.21 - 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH).
• Reaction:
  1. L-pipecolate + NADP⁺ = Delta₁-piperideine-2-carboxylate + NADPH + H⁺
  2. L-proline + NADP⁺ = 1-pyrroline-2-carboxylate + NADPH + H⁺

L-pipecolate (Bound ligand (Het Group name = PRO) matches with 88.89% similarity) + NADP(+) (Bound ligand (Het Group name = NAI) matches with 91.67% similarity) = Delta(1)-piperideine-2-carboxylate + NADPH + H(+)

L-proline (Bound ligand (Het Group name = PRO) corresponds exactly) + NADP(+) (Bound ligand (Het Group name = NAI) matches with 91.67% similarity) = 1-pyrroline-2-carboxylate + NADPH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S2059798320004866

Acta Crystallogr D Struct Biol 76:496-505 (2020)

PubMed id: 32355045

Structure of Thermococcus litoralis Δ¹-pyrroline-2-carboxylate reductase in complex with NADH and L-proline.

E.Ferrario, R.Miggiano, M.Rizzi, D.M.Ferraris.

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 Δ¹-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.