Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 87.27 kDa 
• Atom Count: 6087 
• Residue Count: 743 
• Unique protein chains: 1

4CCL

X-Ray structure of E. coli ycfD

• DOI: 10.2210/pdb4CCL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-10-23 Released: 2014-04-30 
• Deposition Author(s): McDonough, M.A., Ho, C.H., Kershaw, N.J., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.249 
• R-Value Work: 0.198 
• R-Value Observed: 0.202 

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

• PubMed: 24814345 
• DOI: 10.1038/nature13263
• Primary Citation of Related Structures:  
  4CCL, 4CCM, 4CCN, 4CCO, 4CCJ, 4CCK, 4CSW, 4CUG, 2XDV, 4LIT


• 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-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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L16 ARGININE HYDROXYLASE	A, B	373	Escherichia coli	Mutation(s): 0  EC: 1.14.11 (PDB Primary Data), 1.14.11.47 (UniProt)
Find proteins for P27431 (Escherichia coli (strain K12)) Explore P27431  Go to UniProtKB:  P27431

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	A, B	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.249 
• R-Value Work: 0.198 
• R-Value Observed: 0.202 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.693	α = 90
b = 120.693	β = 90
c = 133.498	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-23 
• Released Date: 2014-04-30 
Deposition Author(s): McDonough, M.A., Ho, C.H., Kershaw, N.J., Schofield, C.J.

Revision History 

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2014-05-14
  Changes: Database references
• Version 1.2: 2014-05-21
  Changes: Database references
• Version 1.3: 2014-06-25
  Changes: Database references
• Version 1.4: 2018-02-21
  Changes: Database references
• Version 1.5: 2019-10-16
  Changes: Data collection, Derived calculations, Other
• Version 1.6: 2020-06-03
  Changes: Derived calculations