5JWP

Crystal structure of human FIH D201E variant in complex with Zn, alpha-ketoglutarate, and HIF1 alpha peptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

The facial triad in the alpha-ketoglutarate dependent oxygenase FIH: A role for sterics in linking substrate binding to O2 activation.

Hangasky, J.A.Taabazuing, C.Y.Martin, C.B.Eron, S.J.Knapp, M.J.

(2016) J Inorg Biochem 166: 26-33

  • DOI: 10.1016/j.jinorgbio.2016.10.007
  • Primary Citation of Related Structures:  
    5JWP

  • PubMed Abstract: 
  • The factor inhibiting hypoxia inducible factor-1α (FIH) is a nonheme Fe(II)/αKG oxygenase using a 2-His-1-Asp facial triad. FIH activates O 2 via oxidative decarboxylation of α-ketoglutarate (αKG) to generate an enzyme-based oxidant which ...

    The factor inhibiting hypoxia inducible factor-1α (FIH) is a nonheme Fe(II)/αKG oxygenase using a 2-His-1-Asp facial triad. FIH activates O 2 via oxidative decarboxylation of α-ketoglutarate (αKG) to generate an enzyme-based oxidant which hydroxylates the Asn 803 residue within the C-terminal transactivation domain (CTAD) of HIF-1α. Tight coupling of these two sequential reactions requires a structural linkage between the Fe(II) and the substrate binding site to ensure that O 2 activation occurs after substrate binds. We tested the hypothesis that the facial triad carboxylate (Asp 201 ) of FIH linked substrate binding and O 2 binding sites. Asp 201 variants of FIH were constructed and thoroughly characterized in vitro using steady-state kinetics, crystallography, autohydroxylation, and coupling measurements. Our studies revealed each variant activated O 2 with a catalytic efficiency similar to that of wild-type (WT) FIH (k cat aK M(O 2 )=0.17μM -1 min -1 ), but led to defects in the coupling of O 2 activation to substrate hydroxylation. Steady-state kinetics showed similar catalytic efficiencies for hydroxylation by WT-FIH (k cat /K M(CTAD) =0.42μM -1 min -1 ) and D201G (k cat /K M(CTAD) =0.34μM -1 min -1 ); hydroxylation by D201E was greatly impaired, while hydroxylation by D201A was undetectable. Analysis of the crystal structure of the D201E variant revealed steric crowding near the diffusible ligand site supporting a role for sterics from the facial triad carboxylate in the O 2 binding order. Our data support a model in which the facial triad carboxylate Asp 201 provides both steric and polar contacts to favor O 2 access to the Fe(II) only after substrate binds, leading to coupled turnover in FIH and other αKG oxygenases.


    Organizational Affiliation

    Department of Chemistry, University of Massachusetts, Amherst, United States. Electronic address: mknapp@chem.umass.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypoxia-inducible factor 1-alpha inhibitorA352Homo sapiensMutation(s): 1 
Gene Names: HIF1ANFIH1
EC: 1.14.11.30 (PDB Primary Data), 1.14.11 (PDB Primary Data)
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:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hypoxia-inducible factor 1-alphaB19Homo sapiensMutation(s): 1 
Gene Names: HIF1ABHLHE78MOP1PASD8
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: 2.10 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.22α = 90
b = 86.22β = 90
c = 149.903γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM008515

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 2.0: 2017-09-27
    Changes: Author supporting evidence, Database references, Polymer sequence
  • Version 2.1: 2019-12-25
    Changes: Author supporting evidence