1FVX

CLOSTRIDIUM BEIJERINCKII FLAVODOXIN MUTANT: G57N OXIDIZED


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Control of oxidation-reduction potentials in flavodoxin from Clostridium beijerinckii: the role of conformation changes.

Ludwig, M.L.Pattridge, K.A.Metzger, A.L.Dixon, M.M.Eren, M.Feng, Y.Swenson, R.P.

(1997) Biochemistry 36: 1259-1280

  • DOI: 10.1021/bi962180o
  • Primary Citation of Related Structures:  
    3NLL, 4NLL, 4NUL, 5ULL, 6NUL, 1FLN, 1FLD, 1FLA, 5NLL, 5NUL

  • PubMed Abstract: 
  • X-ray analyses of wild-type and mutant flavodoxins from Clostridium beijerinckii show that the conformation of the peptide Gly57-Asp58, in a bend near the isoalloxazine ring of FMN, is correlated with the oxidation state of the FMN prosthetic group. ...

    X-ray analyses of wild-type and mutant flavodoxins from Clostridium beijerinckii show that the conformation of the peptide Gly57-Asp58, in a bend near the isoalloxazine ring of FMN, is correlated with the oxidation state of the FMN prosthetic group. The Gly-Asp peptide may adopt any of three conformations: trans O-up, in which the carbonyl oxygen of Gly57 (O57) points toward the flavin ring; trans O-down, in which O57 points away from the flavin; and cis O-down. Interconversions among these conformers that are linked to oxidation-reduction of the flavin can modulate the redox potentials of bound FMN. In the semiquinone and reduced forms of the protein, the Gly57-Asp58 peptide adopts the trans O-up conformation and accepts a hydrogen bond from the flavin N5H [Smith, W. W., Burnett, R. M., Darling, G. D., & Ludwig, M. L. (1977) J. Mol. Biol. 117, 195-225; Ludwig, M. L., & Luschinsky, C. L. (1992) in Chemistry and Biochemistry of Flavoenzymes III (Müller, F., Ed.) pp 427-466, CRC Press, Boca Raton, FL]. Analyses reported in this paper confirm that, in crystals of wild-type oxidized C. beijerinckii flavodoxin, the Gly57-Asp58 peptide adopts the O-down orientation and isomerizes to the cis conformation. This cis form is preferentially stabilized in the crystals by intermolecular hydrogen bonding to Asn137. Structures for the mutant Asn137Ala indicate that a mixture of all three conformers, mostly O-down, exists in oxidized C. beijerinckii flavodoxin in the absence of intermolecular hydrogen bonds. Redox potentials have been manipulated by substitutions that alter the conformational energies of the bend at 56M-G-D-E. The mutation Asp58Pro was constructed to study a case where energies for cis-trans conversion would be different from that of wild type. Intermolecular interactions with Asn137 are precluded in the crystal, yet Gly57-Pro58 is cis, and O-down, when the flavin is oxidized. Reduction of the flavin induces rearrangement to the trans O-up conformation. Redox potential shifts reflect the altered energies associated with the peptide rearrangement; E(ox/sq) decreases by approximately 60 mV (1.3 kcal/mol). Further, the results of mutation of Gly57 agree with predictions that a side chain at residue 57 should make addition of the first electron more difficult, by raising the energy of the O-up conformer that forms when the flavin is reduced to its semiquinone state. The ox/sq potentials in the mutants Gly57Ala, Gly57Asn, and Gly57Asp are all decreased by approximately 60 mV (1.3 kcal/mol). Introduction of the beta-branched threonine side chain at position 57 has much larger effects on the conformations and potentials. The Thr57-Asp58 peptide adopts a trans O-down conformation when the flavin is oxidized; upon reduction to the semiquinone, the 57-58 peptide rotates to a trans O-up conformation resembling that found in the wild-type protein. Changes in FMN-protein interactions and in conformational equilibria in G57T combine to decrease the redox potential for the ox/sq equilibrium by 180 mV (+4.0 kcal/mol) and to increase the sq/hq potential by 80 mV (-1.7 kcal/mol). A thermodynamic scheme is introduced as a framework for rationalizing the properties of wild-type flavodoxin and the effects of the mutations.


    Related Citations: 
    • Cis-Trans Isomerization of the 57-58 Peptide in Crystalline Flavodoxins from C. Beijerinckii
      Ludwig, M.L., Dixon, M.M., Pattridge, K.A., Swenson, R.P.
      (1994) Flavins And Flavoproteins 1993 : Proceedings Of The Eleventh International Symposium, Nagoya (japan) July 27-31, 1993 --: 363
    • Structure and Redox Properties of Clostridial Flavodoxin
      Ludwig, M.L., Luschinsky, C.L.
      (1992) Chemistry And Biochemistry Of Flavoenzymes 3: 427
    • Structural Characterization of Site Mutants of Clostridial Flavodoxin
      Ludwig, M.L., Pattridge, K.A., Eren, M., Swenson, R.P.
      (1991) Flavins And Flavoproteins 1990 : Proceedings Of The Tenth International Symposium, Como, Italy, July 15-20, 1990 --: 423
    • Structure and Oxidation-Reduction Behavior of 1-Deaza-Fmn Flavodoxins: Modulation of Redox Potentials in Flavodoxins
      Ludwig, M.L., Schopfer, L.M., Metzger, A.L., Pattridge, K.A., Massey, V.
      (1990) Biochemistry 29: 10364
    • Structure of the Semiquinone Form of Flavodoxin from Clostridium Mp. Extension of 1.8 A Resolution and Some Comparisons with the Oxidized State
      Smith, W.W., Burnett, R.M., Darling, G.D., Ludwig, M.L.
      (1977) J Mol Biol 117: 195
    • The Structure of Clostridium Mp Flavodoxin as a Function of Oxidation State, Some Comparisons of the Fmn-Binding Sites in Oxidized, Semiquinone and Reduced Forms
      Ludwig, M.L., Burnett, R.M., Darling, G.D., Jordan, S.R., Kendall, D.S., Smith, W.W.
      (1976) Flavins And Flavoproteins --: 393
    • The Structure of the Oxidized Form of Clostridial Flavodoxin at 1.9-A Resolution
      Burnett, R.M., Darling, G.D., Kendall, D.S., Lequesne, M.E., Mayhew, S.G., Smith, W.W., Ludwig, M.L.
      (1974) J Biol Chem 249: 4383
    • Structure of the Radical Form of Clostridial Flavodoxin: A New Molecular Model
      Andersen, R.D., Apgar, P.A., Burnett, R.M., Darling, G.D., Lequesne, M.E., Mayhew, S.G., Ludwig, M.L.
      (1972) Proc Natl Acad Sci U S A 69: 3189
    • The Structure of a Clostridial Flavodoxin. I. Crystallographic Characterization of the Oxidized and Semiquinone Forms
      Ludwig, M.L., Andersen, R.D., Mayhew, S.G., Massey, V.
      (1969) J Biol Chem 244: 6047

    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor 48109-1055, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FLAVODOXINA138Clostridium beijerinckiiMutation(s): 1 
Find proteins for P00322 (Clostridium beijerinckii)
Explore P00322 
Go to UniProtKB:  P00322
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.52α = 90
b = 61.52β = 90
c = 70.77γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-03-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance