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: 2.105 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1016/j.str.2015.01.014
  • Primary Citation of Related Structures:  

  • 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 sub ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
A
562Homo sapiensMutation(s): 0 
Gene Names: OGFOD1 (KIAA1612, TPA1)
EC: 1.14.11.-
Find proteins for Q8N543 (Homo sapiens)
Go to Gene View: OGFOD1
Go to UniProtKB:  Q8N543
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

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Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.105 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 64.401α = 90.00
b = 64.401β = 90.00
c = 232.041γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PHASERphasing
DENZOdata reduction
GDAdata collection
PDB_EXTRACTdata extraction
HKL-3000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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