6R77

Crystal structure of trans-3-Hydroxy-L-proline dehydratase in complex with substrate - closed conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

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This is version 2.1 of the entry. See complete history


Literature

Structure of Thermococcus litoralis trans-3-hydroxy-l-proline dehydratase in the free and substrate-complexed form.

Ferraris, D.M.Miggiano, R.Watanabe, S.Rizzi, M.

(2019) Biochem Biophys Res Commun 516: 189-195

  • DOI: https://doi.org/10.1016/j.bbrc.2019.06.021
  • Primary Citation of Related Structures:  
    6R76, 6R77

  • PubMed Abstract: 

    Hydroxyprolines (Hyp) are non-standard amino acids derived from the post-translational modification of proteins by prolyl hydroxylase enzymes. Some plants and bacteria produce Hyp, and the isomers trans-3-Hydroxy-l-proline (T3LHyp) and trans-4-Hydroxy-l-proline (T4LHyp) are major components of mammalian collagen. While T4LHyp is metabolised following distinct degradative pathways in mammals and bacteria, T3LHyp metabolic pathway is conserved in bacteria, plants and mammals, and involves a T3LHyp dehydratase (T3LHypD) in the first degradation step. We report here the crystal structure of T3LHypD from the archaea Thermococcus litoralis in the free and substrate-complexed form. The model shows an "open" and a "closed" conformation depending on the presence (or absence) of the substrate in the catalytic site and allows the mapping of the residues involved in ligand recognition. Moreover, the structure highlights the presence of a water molecule interacting with the hydroxy group of the substrate and potentially involved in catalysis. The structure here reported is the first of its family to be elucidated, and represents a valid model for rationalising the substrate specificity and catalysis of T3LHyp dehydratases.


  • Organizational Affiliation

    Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Center for Marine Environmental Studies (CMES), Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proline racemase
A, B
368Thermococcus litoralisMutation(s): 0 
Gene Names: OCC_00387
UniProt
Find proteins for H3ZMH8 (Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C))
Explore H3ZMH8 
Go to UniProtKB:  H3ZMH8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH3ZMH8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.415α = 90
b = 106.547β = 90
c = 149.456γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Refinement description
  • Version 2.1: 2024-01-24
    Changes: Refinement description