Proline 3-hydroxylase (type II) -apo form

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

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This is version 1.4 of the entry. See complete history


Structure of proline 3-hydroxylase. Evolution of the family of 2-oxoglutarate dependent oxygenases.

Clifton, I.J.Hsueh, L.C.Baldwin, J.E.Harlos, K.Schofield, C.J.

(2001) Eur J Biochem 268: 6625-6636

  • DOI: https://doi.org/10.1046/j.0014-2956.2001.02617.x
  • Primary Citation of Related Structures:  
    1E5R, 1E5S

  • PubMed Abstract: 

    Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative reactions in a range of metabolic processes including the hydroxylation of proline and lysine residues during the post-translational modification of collagen. 2-OG oxygenases commonly require ascorbate for full activity. In the vitamin C deficient disease, scurvy, reduced activity of 2-OG oxygenases results in impaired formation of collagen. Here we report the crystal structure of bacterial proline 3-hydroxylase from Streptomyces sp., an enzyme which hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. Structures were obtained for the enzyme in the absence of iron (to 2.3A resolution, R=20.2%, Rfree=25.3%) and that complexed to iron (II) (to 2.4A resolution, R=19.8%, Rfree=22.6%). The structure contains conserved motifs present in other 2-OG oxygenases including a 'jelly roll' beta strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. The structure differs significantly from many other 2-OG oxygenases in possessing a discrete C-terminal helical domain. Analysis of the structure suggests a model for proline binding and a mechanism for uncoupling of proline and 2-OG turnover.

  • Organizational Affiliation

    The Dyson Perrins Laboratory and the Oxford Centre for Molecular Sciences, Oxford, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
290Streptomyces sp. TH1Mutation(s): 0 
Find proteins for O09345 (Streptomyces sp)
Explore O09345 
Go to UniProtKB:  O09345
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO09345
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.54α = 90
b = 72.54β = 90
c = 223.92γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-02
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references