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

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Structure of Thermococcus litoralis Delta1-pyrroline-2-carboxylate reductase in complex with NADH and L-proline.

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

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

  • DOI: https://doi.org/10.1107/S2059798320004866
  • Primary Citation of Related Structures:  

  • 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 1 -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.

  • Organizational Affiliation

    Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DELTA1-pyrroline-2-carboxylate reductase
A, B
349Thermococcus litoralis DSM 5473Mutation(s): 0 
Find proteins for H3ZMH3 (Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C))
Explore H3ZMH3 
Go to UniProtKB:  H3ZMH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH3ZMH3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.688α = 90
b = 51.509β = 115.906
c = 92.29γ = 90
Software Package:
Software NamePurpose
EDNAdata collection
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description