3D8C

Factor inhibiting HIF-1 alpha D201G mutant in complex with ZN(II), alpha-ketoglutarate and HIF-1 alpha 19mer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Evidence that two enzyme-derived histidine ligands are sufficient for iron binding and catalysis by factor inhibiting HIF (FIH).

Hewitson, K.S.Holmes, S.L.Ehrismann, D.Hardy, A.P.Chowdhury, R.Schofield, C.J.McDonough, M.A.

(2008) J.Biol.Chem. 283: 25971-25978

  • DOI: 10.1074/jbc.M804999200
  • Primary Citation of Related Structures:  2ILM

  • PubMed Abstract: 
  • A 2-His-1-carboxylate triad of iron binding residues is present in many non-heme iron oxygenases including the Fe(II) and 2-oxoglutarate (2OG)-dependent dioxygenases. Three variants (D201A, D201E, and D201G) of the iron binding Asp-201 residue of an ...

    A 2-His-1-carboxylate triad of iron binding residues is present in many non-heme iron oxygenases including the Fe(II) and 2-oxoglutarate (2OG)-dependent dioxygenases. Three variants (D201A, D201E, and D201G) of the iron binding Asp-201 residue of an asparaginyl hydroxylase, factor inhibiting HIF (FIH), were made and analyzed. FIH-D201A and FIH-D201E did not catalyze asparaginyl hydroxylation, but in the presence of a reducing agent, they displayed enhanced 2OG turnover when compared with wild-type FIH. Turnover of 2OG by FIH-D201A was significantly stimulated by the addition of HIF-1alpha(786-826) peptide. Like FIH-D201A and D201E, the D201G variant enhanced 2OG turnover but rather unexpectedly catalyzed asparaginyl hydroxylation. Crystal structures of the FIH-D201A and D201G variants in complex with Fe(II)/Zn(II), 2OG, and HIF-1alpha(786-826/788-806) implied that only two FIH-based residues (His-199 and His-279) are required for metal binding. The results indicate that variation of 2OG-dependent dioxygenase iron-ligating residues as a means of functional assignment should be treated with caution. The results are of mechanistic interest in the light of recent biochemical and structural analyses of non-heme iron and 2OG-dependent halogenases that are similar to the FIH-D201A/G variants in that they use only two His-residues to ligate iron.


    Related Citations: 
    • Selective Inhibition of Factor Inhibiting Hypoxia Inducible Factor
      Mcdonough, M.A.,Mcneill, L.A.,Tilliet, M.,Papamicael, C.A.,Chen, Q.Y.,Banerji, B.,Hewitson, K.S.,Schofield, C.J.
      (2005) J.Am.Chem.Soc. 127: 7680
    • Structure of Factor-Inhibiting Hypoxia-Inducible Factor (Hif) Reveals Mechanism of Oxidative Modification of Hif-1 Alpha
      Elkins, J.M.,Hewitson, K.S.,Mcneill, L.A.,Seibel, J.F.,Schlemminger, I.,Pugh, C.W.,Ratcliffe, P.J.,Schofield, C.J.
      (2003) J.Biol.Chem. 278: 1802


    Organizational Affiliation

    Chemistry Research Laboratory, The Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypoxia-inducible factor 1 alpha inhibitor
A
349Homo sapiensGene Names: HIF1AN (FIH1)
EC: 1.14.11.n4, 1.14.11.30
Find proteins for Q9NWT6 (Homo sapiens)
Go to Gene View: HIF1AN
Go to UniProtKB:  Q9NWT6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
B
19N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
AKG
Query on AKG

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Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.218 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 86.427α = 90.00
b = 86.427β = 90.00
c = 148.065γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
SCALEPACKdata scaling
PXGENdata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance