5JWP | pdb_00005jwp

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 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5JWP

This is version 2.2 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: https://doi.org/10.1016/j.jinorgbio.2016.10.007
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 43.33 kDa 
  • Atom Count: 3,114 
  • Modeled Residue Count: 355 
  • Deposited Residue Count: 371 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypoxia-inducible factor 1-alpha inhibitor352Homo sapiensMutation(s): 1 
Gene Names: HIF1ANFIH1
EC: 1.14.11.30 (PDB Primary Data), 1.14.11 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT6 (Homo sapiens)
Explore Q9NWT6 
Go to UniProtKB:  Q9NWT6
PHAROS:  Q9NWT6
GTEx:  ENSG00000166135 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWT6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypoxia-inducible factor 1-alpha19Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16665 (Homo sapiens)
Explore Q16665 
Go to UniProtKB:  Q16665
PHAROS:  Q16665
GTEx:  ENSG00000100644 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16665
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKG

Query on AKG



Download:Ideal Coordinates CCD File
C [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth 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 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
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

View Full Validation Report



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  (Full details and data files)

  • 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
  • Version 2.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description