1YJI

RDC-refined Solution NMR structure of reduced putidaredoxin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 11 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Redox-dependent structural differences in putidaredoxin derived from homologous structure refinement via residual dipolar couplings.

Jain, N.U.Tjioe, E.Savidor, A.Boulie, J.

(2005) Biochemistry 44: 9067-9078

  • DOI: 10.1021/bi050152c
  • Primary Citation of Related Structures:  
    1YJI, 1YJJ

  • PubMed Abstract: 
  • Structural differences in the [2Fe-2S] ferredoxin, putidaredoxin (Pdx), from the camphor hydroxylation pathway of Pseudomonas putida have been investigated as a function of oxidation state of the iron cluster. Pdx is involved in biological electron transfer to cytochrome P450(cam) (CYP101) ...

    Structural differences in the [2Fe-2S] ferredoxin, putidaredoxin (Pdx), from the camphor hydroxylation pathway of Pseudomonas putida have been investigated as a function of oxidation state of the iron cluster. Pdx is involved in biological electron transfer to cytochrome P450(cam) (CYP101). Redox-dependent differences have been observed previously for Pdx in terms of binding affinities to CYP101, NMR spectral differences, and dynamic properties. To further characterize these differences, structure refinement of both oxidized and reduced Pdx has been carried out using a hybrid approach utilizing paramagnetic distance restraints and NMR orientational restraints in the form of backbone (15)N residual dipolar couplings. Use of these new restraints has improved the structure of oxidized Pdx considerably over the earlier solution NMR structure without RDC restraints, with the new structure now much closer in overall fold to the recently published X-ray crystal structures. We now observe better defined relative orientations of the major secondary structure elements as also of the conformation of the metal binding loop region. Extension of this approach to structure calculation of reduced Pdx has identified structural differences that are primarily localized for residues in the C-terminal interaction domain consisting of the functionally important residue Trp 106 and regions near the metal binding loop in Pdx. These redox-dependent structural differences in Pdx correlate to dynamic changes observed before and may be linked to differences in binding and electron transfer properties between oxidized and reduced Pdx.


    Related Citations: 
    • A refined model for the solution structure of oxidized putidaredoxin
      Pochapsky, T.C., Jain, N.U., Kuti, M., Lyons, T.A., Heymont, J.
      (1999) Biochemistry 38: 4681
    • New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, ADX(4-108)
      MULLER, A., MULLER, J.J., MULLER, Y.A., UHLMANN, H., BERNHARDT, R., HEINEMANN, U.
      (1998) Structure 6: 269
    • An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2Fe-2S Ferredoxin from pseudomonas
      POCHAPSKY, T.C., YE, X.M., RATNASWAMY, G., LYONS, T.A.
      (1994) Biochemistry 33: 6424
    • Redox-Dependent 1H NMR spectral features and tertiary structural constraints on the C-terminal region of putidaredoxin
      POCHAPSKY, T.C., Ratnaswamy, G., Patera, A.
      (1994) Biochemistry 33: 6433

    Organizational Affiliation

    Biochemistry, Cellular and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee 37996-0840, USA. njain@utk.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PutidaredoxinA106Pseudomonas putidaMutation(s): 0 
Gene Names: camB
UniProt
Find proteins for P00259 (Pseudomonas putida)
Explore P00259 
Go to UniProtKB:  P00259
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download Ideal Coordinates CCD File 
B [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 11 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 1YJI Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance