1E5R

Proline 3-hydroxylase (type II) -apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • Primary Citation of Related Structures:  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 com ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROLINE OXIDASE
A, B
290Streptomyces spEC: 1.14.11.28
Find proteins for O09345 (Streptomyces sp)
Go to UniProtKB:  O09345
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.225 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.540α = 90.00
b = 72.540β = 90.00
c = 223.920γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
SHARPphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance