1AKT

G61N OXIDIZED FLAVODOXIN MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Modulation of the redox potentials of FMN in Desulfovibrio vulgaris flavodoxin: thermodynamic properties and crystal structures of glycine-61 mutants.

O'Farrell, P.A.Walsh, M.A.McCarthy, A.A.Higgins, T.M.Voordouw, G.Mayhew, S.G.

(1998) Biochemistry 37: 8405-8416

  • DOI: 10.1021/bi973193k
  • Primary Citation of Related Structures:  
    1AKR, 1AKT, 1AKW, 1AZL

  • PubMed Abstract: 
  • Mutants of the electron-transfer protein flavodoxin from Desulfovibrio vulgaris were made by site-directed mutagenesis to investigate the role of glycine-61 in stabilizing the semiquinone of FMN by the protein and in controlling the flavin redox potentials ...

    Mutants of the electron-transfer protein flavodoxin from Desulfovibrio vulgaris were made by site-directed mutagenesis to investigate the role of glycine-61 in stabilizing the semiquinone of FMN by the protein and in controlling the flavin redox potentials. The spectroscopic properties, oxidation-reduction potentials, and flavin-binding properties of the mutant proteins, G61A/N/V and L, were compared with those of wild-type flavodoxin. The affinities of all of the mutant apoproteins for FMN and riboflavin were less than that of the wild-type apoprotein, and the redox potentials of the two 1-electron steps in the reduction of the complex with FMN were also affected by the mutations. Values for the dissociation constants of the complexes of the apoprotein with the semiquinone and hydroquinone forms of FMN were calculated from the redox potentials and the dissociation constant of the oxidized complex and used to derive the free energies of binding of the FMN in its three oxidation states. These showed that the semiquinone is destabilized in all of the mutants, and that the extent of destabilization tends to increase with increasing bulkiness of the side chain at residue 61. It is concluded that the hydrogen bond between the carbonyl of glycine-61 and N(5)H of FMN semiquinone in wild-type flavodoxin is either absent or severely impaired in the mutants. X-ray crystal structure analysis of the oxidized forms of the four mutant proteins shows that the protein loop that contains residue 61 is moved away from the flavin by 5-6 A. The hydrogen bond formed between the backbone nitrogen of aspartate-62 and O(4) of the dimethylisoalloxazine of the flavin in wild-type flavodoxin is absent in the mutants. Reliable structural information was not obtained for the reduced forms of the mutant proteins, but if the mutants change conformation when the flavin is reduced to the semiquinone, to facilitate hydrogen bonding between N(5)H and the carbonyl of residue 61, then the change must be different from that known to occur in wild-type flavodoxin.


    Related Citations: 
    • X-Ray Crystallographic Studies on the Flavin Binding Site of Flavodoxin from Desulfovibrio Vulgaris
      Mccarthy, A.
      () To be published --: --
    • Comparison of the Crystal Structures of a Flavodoxin in its Three Oxidation States at Cryogenic Temperatures
      Watt, W., Tulinsky, A., Swenson, R.P., Watenpaugh, K.D.
      (1991) J Mol Biol 218: 195
    • Cloning,Nucleotide Sequence,and Expression of the Flavodoxin Gene from Desulfovibrio Vulgaris (Hildenborough)
      Krey, G.D., Vanin, E.F., Swenson, R.P.
      (1988) J Biol Chem 263: 15436
    • Cloning and Sequencing of the Gene Encoding Flavodoxin from Desulfovibrio Vulgaris Hildenborough
      Curley, G.P., Voordouw, G.
      (1988) FEMS Microbiol Lett 49: 295
    • Structure of the Oxidized Form of a Flavodoxin at 2.5-Angstrom Resolution:Resolution of the Phase Ambiguity by Anomalous Scattering
      Watenpaugh, K.D., Sieker, L.C., Jensen, L.H., Legall, J., Dubourdieu, M.
      (1972) Proc Natl Acad Sci U S A 69: 3185

    Organizational Affiliation

    Department of Biochemistry, University College Dublin, Ireland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FLAVODOXINA147Desulfovibrio vulgaris str. HildenboroughMutation(s): 1 
Gene Names: DVU_2680
UniProt
Find proteins for P00323 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P00323 
Go to UniProtKB:  P00323
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00323
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FMN Binding MOAD:  1AKT Kd: 3.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.14α = 90
b = 87.58β = 90
c = 34.99γ = 90
Software Package:
Software NamePurpose
AMoREphasing
PROLSQrefinement
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2021-11-03
    Changes: Database references, Derived calculations