1PUT

AN NMR-DERIVED MODEL FOR THE SOLUTION STRUCTURE OF OXIDIZED PUTIDAREDOXIN, A 2FE, 2-S FERREDOXIN FROM PSEUDOMONAS


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 12 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas.

Pochapsky, T.C.Ye, X.M.Ratnaswamy, G.Lyons, T.A.

(1994) Biochemistry 33: 6424-6432

  • Also Cited By: 1YJI, 1YJJ

  • PubMed Abstract: 
  • A model for the solution structure of oxidized putidaredoxin (Pdx), a 106-residue globular protein containing a Fe2S2 cluster, has been determined using homonuclear NMR methods. Pdx is the first of the class of Fe2S2Cys4 ferredoxins which act as elec ...

    A model for the solution structure of oxidized putidaredoxin (Pdx), a 106-residue globular protein containing a Fe2S2 cluster, has been determined using homonuclear NMR methods. Pdx is the first of the class of Fe2S2Cys4 ferredoxins which act as electron-transfer partners for P-450 monooxygenases to be structurally characterized, and no crystal structure has been determined for Pdx or for any closely homologous protein. Pdx is the physiological redox partner of cytochrome P-450cam. A total of 878 NOE distance constraints, 66 phi angular constraints derived from NH-C alpha H coupling constants, and five paramagnetic broadening constraints were used in simulated annealing structural refinements to obtain a family of structures with pairwise rms deviations of 1.14 A for backbone atoms and 1.80 A for all non-hydrogen atoms. Paramagnetic broadening of resonances within a ca. 8-A radius of the metal cluster prevents the use of NMR-derived constraints in this region of the protein; structural constraints used to model the environment of the metal cluster were obtained from site-directed mutagenesis and model compounds and by comparison with known ferredoxin structures. Pdx retains a similar folding topology to other structurally characterized Fe2S2Cys4 ferredoxins but differs from the other ferredoxins in containing a significantly more compact structure in the C-terminal half of the protein.


    Related Citations: 
    • Crystallization and Structure Determination to 2.5-Angstroms Resolution of the Oxidized [2Fe-2S] Ferredoxin Isolated from Anabaena 7120
      Rypniewski, W.R.,Breiter, D.R.,Benning, M.M.,Wesenberg, G.,Oh, B.H.,Markley, J.L.,Rayment, I.,Holden, H.M.
      (1991) Biochemistry 30: 4126
    • 1H NMR Identification of a Beta-Sheet Structure and Description of Folding Topology in Putidaredoxin
      Pochapsky, T.C.,Ye, X.M.
      (1991) Biochemistry 30: 3850
    • Characterization of Hyperfine-Shifted 1H Resonances in Oxidized and Reduced Putidaredoxin, an Fe2S2Ferredoxin from Pseudomonus Putida
      Ratnaswamy, G.,Pochapsky, T.C.
      (1994) Magn.Reson.Chem. 31: S73
    • 1H NMR Sequential Assignments and Identification of Secondary Structural Elements in Oxidized Putidaredoxin, an Electron-Transfer Protein from Pseudomonas
      Ye, X.M.,Pochapsky, T.C.,Pochapsky, S.S.
      (1992) Biochemistry 31: 1961
    • 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

    Department of Chemistry, Brandeis University, Waltham, Massachusetts 02254-9110.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTIDAREDOXIN
A
106Pseudomonas putidaGene Names: camB
Find proteins for P00259 (Pseudomonas putida)
Go to UniProtKB:  P00259
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download SDF File 
Download CCD File 
A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 12 
  • Olderado: 1PUT Olderado
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-09-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other