6CD3

Crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase I142A from Cupriavidus metallidurans in complex with 3-HAA

  • Classification: OXIDOREDUCTASE
  • Organism(s): Cupriavidus metallidurans
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2018-02-07 Released: 2018-06-06 
  • Deposition Author(s): Yang, Y., Liu, F., Liu, A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.198 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1074/jbc.RA118.002698
  • Primary Citation of Related Structures:  
    6BVP, 6BVQ, 6BVR, 6BVS, 6CD3, 6D60, 6D61, 6D62

  • 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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-hydroxyanthranilate 3,4-dioxygenase195Cupriavidus metalliduransMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1LCS4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.198 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.41α = 90
b = 58.41β = 90
c = 230.814γ = 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 General Medical Sciences (NIH/NIGMS)United StatesR01GM108988
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)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: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description