2ILM

Factor Inhibiting HIF-1 Alpha D201A Mutant in Complex with FE(II), Alpha-Ketoglutarate and HIF-1 Alpha 35mer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

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:  
    3D8C, 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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypoxia-inducible factor 1 alpha inhibitorA349Homo sapiensMutation(s): 1 
Gene Names: HIF1ANFIH1
EC: 1.14.11.16 (PDB Primary Data), 1.14.11.30 (UniProt), 1.14.11 (UniProt)
Find proteins for Q9NWT6 (Homo sapiens)
Explore Q9NWT6 
Go to UniProtKB:  Q9NWT6
NIH Common Fund Data Resources
PHAROS  Q9NWT6
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hypoxia-inducible factor 1 alphaS41N/AMutation(s): 0 
Find proteins for Q16665 (Homo sapiens)
Explore Q16665 
Go to UniProtKB:  Q16665
NIH Common Fund Data Resources
PHAROS  Q16665
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.531α = 90
b = 86.531β = 90
c = 147.64γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance