2V5V

W57E Flavodoxin from Anabaena


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Tuning of the Fmn Binding and Oxido-Reduction Properties by Neighboring Side Chains in Anabaena Flavodoxin.

Frago, S.Goni, G.Herguedas, B.Peregrina, J.R.Serrano, A.Perez-Dorado, I.Molina, R.Gomez-Moreno, C.Hermoso, J.A.Martinez-Julvez, M.Mayhew, S.G.Medina, M.

(2007) Arch Biochem Biophys 467: 206

  • DOI: https://doi.org/10.1016/j.abb.2007.08.024
  • Primary Citation of Related Structures:  
    2V5U, 2V5V

  • PubMed Abstract: 

    Contribution of three regions (phosphate-binding, 50's and 90's loops) of Anabaena apoflavodoxin to FMN binding and reduction potential was studied. Thr12 and Glu16 did not influence FMN redox properties, but Thr12 played a role in FMN binding. Replacement of Trp57 with Glu, Lys or Arg moderately shifted E(ox/sq) and E(sq/hq) and altered the energetic of the FMN redox states binding profile. Our data indicate that the side chain of position 57 does not modulate E(ox/sq) by aromatic stacking or solvent exclusion, but rather by influencing the relative strength of the H-bond between the N(5) of the flavin and the Asn58-Ile59 bond. A correlation was observed between the isoalloxazine increase in solvent accessibility and less negative E(sq/hq). Moreover, E(sq/hq) became less negative as positively charged residues were added near to the isoalloxazine. Ile59 and Ile92 were simultaneously mutated to Ala or Glu. These mutations impaired FMN binding, while shifting E(sq/hq) to less negative values and E(ox/sq) to more negative. These effects are discussed on the bases of the X-ray structures of some of the Fld mutants, suggesting that in Anabaena Fld the structural control of both electron transfer steps is much more subtle than in other Flds.


  • Organizational Affiliation

    Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009-Zaragoza, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FLAVODOXIN
A, B
169Nostoc sp. PCC 7119Mutation(s): 2 
UniProt
Find proteins for P0A3E0 (Nostoc sp. (strain ATCC 29151 / PCC 7119))
Explore P0A3E0 
Go to UniProtKB:  P0A3E0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3E0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
FMN Binding MOAD:  2V5V Kd: 4.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.848α = 90
b = 55.576β = 91.17
c = 70.253γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2018-05-30
    Changes: Data collection, Structure summary
  • Version 1.3: 2019-04-10
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description