2ZGD | pdb_00002zgd

Asn-hydroxylation stabilises the ankyrin repeat domain fold

• PDB DOI: https://doi.org/10.2210/pdb2ZGD/pdb

• Classification: DE NOVO PROTEIN
• Mutation(s): No 


• Deposited: 2008-01-21 Released: 2008-02-05 
• Deposition Author(s): McDonough, M.A., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.178 (DCC) 

Starting Model: experimental

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

• PubMed: 19081931 
• DOI: https://doi.org/10.1039/b815271c
• Primary Citation Related Structures: 
  2ZGD, 2ZGG


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.29 kDa 
• Atom Count: 782 
• Modeled Residue Count: 97 
• Deposited Residue Count: 110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3 repeat synthetic ankyrin	A	110	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL	G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AHB	A	L-PEPTIDE LINKING	C4 H8 N2 O4		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.178 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.887	α = 90
b = 48.887	β = 90
c = 67.088	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): McDonough, M.A., Schofield, C.J.

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description