2ZGG

Asn-hydroxylation stabilises the ankyrin repeat domain fold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Asparagine beta-hydroxylation stabilizes the ankyrin repeat domain fold

Kelly, L.McDonough, M.A.Coleman, M.L.Ratcliffe, P.J.Schofield, C.J.

(2009) Mol Biosyst 5: 52-58

  • DOI: 10.1039/b815271c
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ankyrin repeats (ARs) are one of the most common structural motifs among eukaryotic proteins. Recent analyses have shown that factor inhibiting hypoxia-inducible factor (FIH) catalyses the hydroxylation of highly conserved Asn-residues within ankyrin ...

    Ankyrin repeats (ARs) are one of the most common structural motifs among eukaryotic proteins. Recent analyses have shown that factor inhibiting hypoxia-inducible factor (FIH) catalyses the hydroxylation of highly conserved Asn-residues within ankyrin repeat domains (ARDs). However, the effect of Asn-hydroxylation on ARD structure is unknown. Supporting the proposal that FIH-mediated ARD hydroxylation is ubiquitous we report that consensus ARD proteins are FIH substrates both in vitro and in vivo. X-ray diffraction analyses revealed that hydroxylation does not alter the archetypical ARD conformation in the crystalline state. However, other biophysical analyses revealed that hydroxylation significantly stabilizes the ARD fold in solution. We propose that intracellular protein hydroxylation is much more common than previously thought and that one of its roles is stabilization of localized regions of ARD folds.


    Related Citations: 
    • Posttranslational hydroxylation of ankyrin repeats in IkappaB proteins by the hypoxia-inducible factor (HIF) asparaginyl hydroxylase, factor inhibiting HIF (FIH)
      Cockman, M.E.,Lancaster, D.E.,Stolze, I.P.,Hewitson, K.S.,McDonough, M.A.,Coleman, M.L.,Coles, C.H.,Yu, X.,Hay, R.T.,Ley, S.C.,Pugh, C.W.,Oldham, N.J.,Masson, N.,Schofield, C.J.,Ratcliffe, P.J.
      (2006) Proc.Natl.Acad.Sci.Usa 103: 14767
    • Asparaginyl hydroxylation of the Notch ankyrin repeat domain by factor inhibiting hypoxia-inducible factor
      Coleman, M.L.,McDonough, M.A.,Hewitson, K.S.,Coles, C.,Mecinovic, J.,Edelmann, M.,Cook, K.M.,Cockman, M.E.,Lancaster, D.E.,Kessler, B.M.,Oldham, N.J.,Ratcliffe, P.J.,Schofield, C.J.
      (2007) J.Biol.Chem. 282: 24027


    Organizational Affiliation

    The Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UKOX1 3TA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3 repeat synthetic ankyrin
A
92N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.212 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 48.959α = 90.00
b = 48.959β = 90.00
c = 79.042γ = 120.00
Software Package:
Software NamePurpose
DNAdata collection
DENZOdata reduction
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description