6D62

Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142P from Cupriavidus metallidurans in complex with 3-HAA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Adapting to oxygen: 3-Hydroxyanthrinilate 3,4-dioxygenase employs loop dynamics to accommodate two substrates with disparate polarities.

Yang, Y.Liu, F.Liu, A.

(2018) J Biol Chem 293: 10415-10424

  • DOI: 10.1074/jbc.RA118.002698
  • Primary Citation of Related Structures:  
    6D61, 6D60, 6D62, 6BVS, 6BVR, 6BVQ, 6BVP, 6CD3

  • PubMed Abstract: 
  • 3-Hydroxyanthranilate 3,4-dioxygenase (HAO) is an iron-dependent protein that activates O 2 and inserts both oxygen atoms into 3-hydroxyanthranilate (3-HAA). An intriguing question is how HAO can rapidly bind O 2 , even though local O 2 concentrations and diffusion rates are relatively low ...

    3-Hydroxyanthranilate 3,4-dioxygenase (HAO) is an iron-dependent protein that activates O 2 and inserts both oxygen atoms into 3-hydroxyanthranilate (3-HAA). An intriguing question is how HAO can rapidly bind O 2 , even though local O 2 concentrations and diffusion rates are relatively low. Here, a close inspection of the HAO structures revealed that substrate- and inhibitor-bound structures exhibit a closed conformation with three hydrophobic loop regions moving toward the catalytic iron center, whereas the ligand-free structure is open. We hypothesized that these loop movements enhance O 2 binding to the binary complex of HAO and 3-HAA. We found that the carboxyl end of 3-HAA triggers changes in two loop regions and that the third loop movement appears to be driven by an H-bond interaction between Asn 27 and Ile 142 Mutational analyses revealed that N27A, I142A, and I142P variants cannot form a closed conformation, and steady-state kinetic assays indicated that these variants have a substantially higher K m for O 2 than WT HAO. This observation suggested enhanced hydrophobicity at the iron center resulting from the concerted loop movements after the binding of the primary substrate, which is hydrophilic. Given that O 2 is nonpolar, the increased hydrophobicity at the iron center of the binary complex appears to be essential for rapid O 2 binding and activation, explaining the reason for the 3-HAA-induced loop movements. Because substrate binding-induced open-to-closed conformational changes are common, the results reported here may help further our understanding of how oxygen is enriched in nonheme iron-dependent dioxygenases.


    Organizational Affiliation

    From the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249 and Feradical@utsa.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-hydroxyanthranilate 3,4-dioxygenaseA195Cupriavidus metallidurans CH34Mutation(s): 1 
Gene Names: nbaCRmet_5193
EC: 1.13.11.6
UniProt
Find proteins for Q1LCS4 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Explore Q1LCS4 
Go to UniProtKB:  Q1LCS4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3HA (Subject of Investigation/LOI)
Query on 3HA

Download Ideal Coordinates CCD File 
D [auth A]3-HYDROXYANTHRANILIC ACID
C7 H7 N O3
WJXSWCUQABXPFS-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
E [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.881α = 90
b = 58.881β = 90
c = 232.305γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United StatesR01GM108988
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United StatesR21MH10798
National Science Foundation (NSF, United States)United StatesCHE-1623856

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence