4NHX

Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with N-oxalylglycine (NOG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Structure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases.

Horita, S.Scotti, J.S.Thinnes, C.Mottaghi-Taromsari, Y.S.Thalhammer, A.Ge, W.Aik, W.Loenarz, C.Schofield, C.J.McDonough, M.A.

(2015) Structure 23: 639-652

  • DOI: https://doi.org/10.1016/j.str.2015.01.014
  • Primary Citation of Related Structures:  
    4NHK, 4NHL, 4NHM, 4NHX, 4NHY

  • PubMed Abstract: 

    Post-translational ribosomal protein hydroxylation is catalyzed by 2-oxoglutarate (2OG) and ferrous iron dependent oxygenases, and occurs in prokaryotes and eukaryotes. OGFOD1 catalyzes trans-3 prolyl hydroxylation at Pro62 of the small ribosomal subunit protein uS12 (RPS23) and is conserved from yeasts to humans. We describe crystal structures of the human uS12 prolyl 3-hydroxylase (OGFOD1) and its homolog from Saccharomyces cerevisiae (Tpa1p): OGFOD1 in complex with the broad-spectrum 2OG oxygenase inhibitors; N-oxalylglycine (NOG) and pyridine-2,4-dicarboxylate (2,4-PDCA) to 2.1 and 2.6 Å resolution, respectively; and Tpa1p in complex with NOG, 2,4-PDCA, and 1-chloro-4-hydroxyisoquinoline-3-carbonylglycine (a more selective prolyl hydroxylase inhibitor) to 2.8, 1.9, and 1.9 Å resolution, respectively. Comparison of uS12 hydroxylase structures with those of other prolyl hydroxylases, including the human hypoxia-inducible factor (HIF) prolyl hydroxylases (PHDs), reveals differences between the prolyl 3- and prolyl 4-hydroxylase active sites, which can be exploited for developing selective inhibitors of the different subfamilies.


  • Organizational Affiliation

    Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK; Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1562Homo sapiensMutation(s): 0 
Gene Names: OGFOD1KIAA1612TPA1
EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N543 (Homo sapiens)
Explore Q8N543 
Go to UniProtKB:  Q8N543
PHAROS:  Q8N543
GTEx:  ENSG00000087263 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N543
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.401α = 90
b = 64.401β = 90
c = 232.041γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
GDAdata collection
HKL-3000data scaling
PHASERphasing
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references
  • Version 1.2: 2015-04-29
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description