Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43331.55 
• Atom Count: 2940 
• Residue Count: 371 
• Unique protein chains: 2

5JWP

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

• DOI: 10.2210/pdb5JWP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 2 


• Deposited: 2016-05-12 Released: 2016-11-23 
• Deposition Author(s): Taabazuing, C.Y., Garman, S.C., Eron, S., Knapp, M.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.209 
• R-Value Work: 0.170 

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

• PubMed: 27815979 
• DOI: 10.1016/j.jinorgbio.2016.10.007


• 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 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.

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Organizational Affiliation: 

Department of Chemistry, University of Massachusetts, Amherst, United States. Electronic address: [e-mail].,Department of Chemistry, University of Massachusetts, Amherst, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hypoxia-inducible factor 1-alpha inhibitor	A	352	Homo sapiens	Mutation(s): 1  Gene Names: HIF1AN (FIH1) EC: 1.14.11.30, 1.14.11.n4
Find proteins for Q9NWT6 (Homo sapiens) Go to Gene View: HIF1AN Go to UniProtKB:  Q9NWT6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Hypoxia-inducible factor 1-alpha	B	19	Homo sapiens	Mutation(s): 1  Gene Names: HIF1A (BHLHE78, MOP1, PASD8)
Find proteins for Q16665 (Homo sapiens) Go to Gene View: HIF1A Go to UniProtKB:  Q16665

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
AKG	A	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.209 
• R-Value Work: 0.170 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 86.220	α = 90.00
b = 86.220	β = 90.00
c = 149.903	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-05-12 
• Released Date: 2016-11-23 
• Deposition Author(s): Taabazuing, C.Y., Garman, S.C., Eron, S., Knapp, M.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	T32-GM008515

Revision History 

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