Residual Dipolar Coupling Refinement of Acireductone Dioxygenase from Klebsiella

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 17 

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A refined model for the structure of acireductone dioxygenase from Klebsiella ATCC 8724 incorporating residual dipolar couplings

Pochapsky, T.C.Pochapsky, S.S.Ju, T.Hoefler, C.Liang, J.

(2006) J Biomol NMR 34: 117-127

  • DOI: https://doi.org/10.1007/s10858-005-5735-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Acireductone dioxygenase (ARD) from Klebsiella ATCC 8724 is a metalloenzyme that is capable of catalyzing different reactions with the same substrates (acireductone and O2) depending upon the metal bound in the active site. A model for the solution structure of the paramagnetic Ni2+-containing ARD has been refined using residual dipolar couplings (RDCs) measured in two media. Additional dihedral restraints based on chemical shift (TALOS) were included in the refinement, and backbone structure in the vicinity of the active site was modeled from a crystallographic structure of the mouse homolog of ARD. The incorporation of residual dipolar couplings into the structural refinement alters the relative orientations of several structural features significantly, and improves local secondary structure determination. Comparisons between the solution structures obtained with and without RDCs are made, and structural similarities and differences between mouse and bacterial enzymes are described. Finally, the biological significance of these differences is considered.

  • Organizational Affiliation

    Department of Chemistry, Brandeis University, MS 015, 415 South Street, Waltham, MA 02454-9110, USA. pochapsk@brandeis.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E-2/E-2' protein179Klebsiella oxytocaMutation(s): 0 
Find proteins for Q9ZFE7 (Klebsiella oxytoca)
Explore Q9ZFE7 
Go to UniProtKB:  Q9ZFE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZFE7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NI

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 17 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection