1OBO

W57L flavodoxin from Anabaena


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

How Fmn Binds to Anabaena Apoflavodoxin: A Hydrophobic Encounter at an Open Binding Site

Lostao, A.Daoudi, F.Irun, M.P.Ramon, A.Fernandez-Cabrera, C.Romero, A.Sancho, J.

(2003) J Biol Chem 278: 24053

  • DOI: 10.1074/jbc.M301049200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Molecular recognition begins when two molecules approach and establish interactions of certain strength. The mechanisms of molecular recognition reactions between biological molecules are not well known, and few systems have been analyzed in detail. ...

    Molecular recognition begins when two molecules approach and establish interactions of certain strength. The mechanisms of molecular recognition reactions between biological molecules are not well known, and few systems have been analyzed in detail. We investigate here the reaction between an apoprotein and its physiological cofactor (apoflavodoxin and flavin mononucleotide) that binds reversibly to form a non-covalent complex (flavodoxin) involved in electron transfer reactions. We have analyzed the fast binding reactions between the FMN cofactor (and shorter analogs) and wild type (and nine mutant apoflavodoxins where residues interacting with FMN in the final complex have been replaced). The x-ray structures of two such mutants are reported that show the mutations are well tolerated by the protein. From the calculated microscopic binding rate constants we have performed a Phi analysis of the transition state of complex formation that indicates that the binding starts by interaction of the isoalloxazine-fused rings in FMN with residues of its hydrophobic binding site. In contrast, the phosphate in FMN, known to contribute most to the affinity of the final holoflavodoxin complex, is not bound in the transition state complex. Both the effects of ionic strength and of phosphate concentration on the wild type complex rate constant agree with this scenario. As suggested previously by nmr data, it seems that the isoalloxazine-binding site may be substantially open in solution. Interestingly, although FMN is a charged molecule, electrostatic interactions seem not to play a role in directing the binding, unlike what has been reported for other biological complexes. The binding can thus be best described as a hydrophobic encounter at an open binding site.


    Related Citations: 
    • Closure of a Tyrosine/Tryptophane Aromatic Gate Leeds to a Compact Fold in Apoflavodoxin
      Genzor, C.G., Perales-Alcon, A., Sancho, J., Romero, A.
      (1996) Nat Struct Biol 3: 329

    Organizational Affiliation

    Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias and Biocomputation and Complex Systems Physics Institute, Universidad de Zaragoza 50009-Zaragoza, Madrid, Spain.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FLAVODOXINA, B169Nostoc sp. PCC 7119Mutation(s): 1 
Gene Names: isiB
Find proteins for P0A3E0 (Nostoc sp. (strain ATCC 29151 / PCC 7119))
Explore P0A3E0 
Go to UniProtKB:  P0A3E0
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FMNKd:  6.71999979019165   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.63α = 90
b = 73.1β = 102.58
c = 57.05γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection