6UIZ

Artificial Iron Proteins: Modelling the Active Sites in Non-Heme Dioxygenases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases.

Miller, K.R.Paretsky, J.D.Follmer, A.H.Heinisch, T.Mittra, K.Gul, S.Kim, I.S.Fuller, F.D.Batyuk, A.Sutherlin, K.D.Brewster, A.S.Bhowmick, A.Sauter, N.K.Kern, J.Yano, J.Green, M.T.Ward, T.R.Borovik, A.S.

(2020) Inorg Chem 59: 6000-6009

  • DOI: https://doi.org/10.1021/acs.inorgchem.9b03791
  • Primary Citation of Related Structures:  
    6UI0, 6UIU, 6UIY, 6UIZ, 6US6

  • PubMed Abstract: 

    An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. We have utilized biotin-streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S 112 E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic Fe II complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S 112 E. Two aqua ligands complete the primary coordination sphere of the Fe II center with both involved in hydrogen bond networks within Sav. The corresponding Fe III protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The Fe III protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.


  • Organizational Affiliation

    Department of Chemistry, 1102 Natural Science II, University of California, Irvine, California 92697, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Streptavidin159Streptomyces avidiniiMutation(s): 3 
UniProt
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22629
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QG4 (Subject of Investigation/LOI)
Query on QG4

Download Ideal Coordinates CCD File 
B [auth A]{N-(2-{bis[(pyridin-2-yl-kappaN)methyl]amino-kappaN}ethyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide}(triaza-1,2-dien-2-ium-1-ide-kappaN~1~)iron(4+)
C24 H33 Fe N9 O2 S
NPUCPLAKXVBABZ-VPTGAVHVSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.75α = 90
b = 57.75β = 90
c = 184.499γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata 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 StatesRO1GM120349

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description