4BXF

60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Ribosomal oxygenases are structurally conserved from prokaryotes to humans.

Chowdhury, R.Sekirnik, R.Brissett, N.C.Krojer, T.Ho, C.H.Ng, S.S.Clifton, I.J.Ge, W.Kershaw, N.J.Fox, G.C.Muniz, J.R.C.Vollmar, M.Phillips, C.Pilka, E.S.Kavanagh, K.L.von Delft, F.Oppermann, U.McDonough, M.A.Doherty, A.J.Schofield, C.J.

(2014) Nature 510: 422-426

  • DOI: 10.1038/nature13263
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 2-Oxoglutarate (2OG)-dependent oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated chromatin components and in the hydroxylation of transcription factors and splicing factor proteins. Recently, 2OG-d ...

    2-Oxoglutarate (2OG)-dependent oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated chromatin components and in the hydroxylation of transcription factors and splicing factor proteins. Recently, 2OG-dependent oxygenases that catalyse hydroxylation of transfer RNA and ribosomal proteins have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy. The finding that ribosomal oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans raises questions as to their structural and evolutionary relationships. In Escherichia coli, YcfD catalyses arginine hydroxylation in the ribosomal protein L16; in humans, MYC-induced nuclear antigen (MINA53; also known as MINA) and nucleolar protein 66 (NO66) catalyse histidine hydroxylation in the ribosomal proteins RPL27A and RPL8, respectively. The functional assignments of ROXs open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in the residue and protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent oxygenases. ROX structures with and without their substrates support their functional assignments as hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-domain-containing hydroxylases, including the hypoxia-inducible factor asparaginyl hydroxylase FIH and histone N(ε)-methyl lysine demethylases, identifies branch points in 2OG-dependent oxygenase evolution and distinguishes between JmjC-containing hydroxylases and demethylases catalysing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate-oxidizing species reacts. This coordination flexibility has probably contributed to the evolution of the wide range of reactions catalysed by oxygenases.


    Related Citations: 
    • Oxygenase-Catalyzed Ribosome Hydroxylation Occurs in Prokaryotes and Humans.
      Ge, W.,Wolf, A.,Feng, T.,Ho, C.,Sekirnik, R.,Zayer, A.,Granatino, N.,Cockman, M.E.,Loenarz, C.,Loik, N.D.,Hardy, A.P.,Claridge, T.D.W.,Hamed, R.B.,Chowdhury, R.,Gong, L.,Robinson, C.V.,Trudgian, D.C.,Jiang, M.,Mackeen, M.M.,Mccullagh, J.S.,Gordiyenko, Y.,Thalhammer, A.,Yamamoto, A.,Yang, M.,Liu-Yi, P.,Zhang, Z.,Schmidt-Zachmann, M.,Kessler, B.M.,Ratcliffe, P.J.,Preston, G.M.,Coleman, M.L.,Schofield, C.J.
      (2012) Nat.Chem.Biol. 8: 960


    Organizational Affiliation

    The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA
A, B
442Homo sapiensMutation(s): 1 
Gene Names: RIOX2 (MDIG, MINA, MINA53, NO52)
Find proteins for Q8IUF8 (Homo sapiens)
Go to Gene View: RIOX2
Go to UniProtKB:  Q8IUF8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L27A
C, D
19Homo sapiensMutation(s): 1 
Gene Names: RPL27A
Find proteins for P46776 (Homo sapiens)
Go to Gene View: RPL27A
Go to UniProtKB:  P46776
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Download SDF File 
Download CCD File 
A, B
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.340α = 90.00
b = 88.390β = 90.00
c = 167.180γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-05-21
    Type: Database references
  • Version 1.2: 2014-06-25
    Type: Database references
  • Version 1.3: 2018-02-21
    Type: Database references