2FZ5

Solution structure of two-electron reduced Megasphaera elsdenii flavodoxin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 3000 
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tertiary structure of two-electron reduced Megasphaera elsdenii flavodoxin and some implications, as determined by two-dimensional 1H NMR and restrained molecular dynamics

van Mierlo, C.P.M.Lijnzaad, P.Vervoort, J.Mueller, F.Berendsen, H.J.de Vlieg, J.

(1990) Eur.J.Biochem. 194: 185-198


  • PubMed Abstract: 
  • The tertiary structure of the non-crystallizable two-electron-reduced Megasphaera elsdenii flavodoxin (15 kDa, 137 amino acid residues) has been determined using nuclear Overhauser enhancement restraints extracted from two-dimensional 1H-NMR spectra. ...

    The tertiary structure of the non-crystallizable two-electron-reduced Megasphaera elsdenii flavodoxin (15 kDa, 137 amino acid residues) has been determined using nuclear Overhauser enhancement restraints extracted from two-dimensional 1H-NMR spectra. A tertiary structure satisfying the experimental restraints very well (maximum NOE violation of 66 pm) was obtained with use of restrained molecular dynamics, using 509 distance restraints (including one non-NOE) on a starting structure modeled from the crystal structure of one-electron-reduced Clostridium MP flavodoxin. The protein consists of a central parallel beta-sheet surrounded on both sides by two alpha-helices. The flavin is positioned at the periphery of the molecule. The tertiary structure of the protein is highly defined with the exception of the flavin. The latter is expected to result from performing the restrained molecular dynamics simulation without water molecules and without proper charges on the flavin. The flavin, including the phosphate, the ribityl side chain and the isoalloxazine ring, is solvent accessible under the experimental conditions used and evidenced by a two-dimensional amide exchange experiment. This accessibility is expected to be important in the redox potential regulation of the semiquinone/hydroquinone couple of the protein. The amide exchange against deuterons and several typical line shapes in the two-dimensional NMR spectra are consistent with the structure generated. The structure is discussed in detail.


    Related Citations: 
    • A two-dimensional 1H NMR study on Megasphaera elsdenii flavodoxin in the reduced state: sequential assignments
      van Mierlo, C.P.M.,Vervoort, J.,Mueller, F.,Bacher, A.
      (1990) Eur.J.Biochem. 187: 521
    • A two-dimensional 1H NMR study on Megasphaera elsdenii flavodoxin in the oxidized state and some comparisons with the two-electron reduced state
      van Mierlo, C.P.M.,van der Sanden, B.P.,van Woensel, P.,Mueller, F.,Vervoort, J.
      (1990) Eur.J.Biochem. 194: 199
    • Secondary and tertiary structure characteristics of Megasphaera elsdenii flavodoxin in the reduced state as determined by two-dimensional 1H NMR
      van Mierlo, C.P.M.,Mueller, F.,Vervoort, J.
      (1990) Eur.J.Biochem. 189: 589


    Organizational Affiliation

    Department of Biochemistry, Agricultural University, Wageningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flavodoxin
A
137Megasphaera elsdeniiMutation(s): 0 
Find proteins for P00321 (Megasphaera elsdenii)
Go to UniProtKB:  P00321
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FNR
Query on FNR

Download SDF File 
Download CCD File 
A
1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE
C17 H23 N4 O9 P
YTNIXZGTHTVJBW-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 3000 
  • Conformers Submitted: 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance