Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 43.33 kDa 
• Atom Count: 3114 
• Residue Count: 355 
• 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): Yes 


• 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 (NIH/NIGMS)

---

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 

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
• 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 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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxia-inducible factor 1-alpha inhibitor	A	352	Homo sapiens	Mutation(s): 1  Gene Names: HIF1AN, FIH1 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 GTEx  ENSG00000166135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxia-inducible factor 1-alpha	B	19	Homo sapiens	Mutation(s): 1  Gene Names: HIF1A, BHLHE78, MOP1, PASD8
Find proteins for Q16665 (Homo sapiens) Explore Q16665  Go to UniProtKB:  Q16665
NIH Common Fund Data Resources
PHAROS  Q16665 GTEx  ENSG00000100644

Small Molecules

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

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 = 86.22	α = 90
b = 86.22	β = 90
c = 149.903	γ = 90

Software Package:

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

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.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32-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