6R76

Crystal structure of trans-3-Hydroxy-L-proline dehydratase from Thermococcus litoralis - open conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

Starting Model: experimental
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This is version 1.2 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

    Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Via Bovio 6, 28100, Novara, Italy; IXTAL srl, Via Bovio 6, 28100, Novara, Italy. Electronic address: davide.ferraris@uniupo.it.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proline racemase
A, C
368Thermococcus litoralis DSM 5473Mutation(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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proline racemase
B, D
368Thermococcus litoralis DSM 5473Mutation(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
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PHD
Query on PHD
B, D
L-PEPTIDE LINKINGC4 H8 N O7 PASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.923α = 90
b = 46.09β = 110.48
c = 143.512γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

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 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description