1MVL

PPC decarboxylase mutant C175S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Plant PPC Decarboxylase AtHAL3a Complexed with an Ene-thiol Reaction Intermediate

Steinbacher, S.Hernandez-Acosta, P.Bieseler, B.Blaesse, M.Huber, R.Culianez-Macia, F.A.Kupke, T.

(2003) J.Mol.Biol. 327: 193-202

  • Primary Citation of Related Structures:  1MVN

  • PubMed Abstract: 
  • The Arabidopsis thaliana protein AtHAL3a decarboxylates 4'-phosphopantothenoylcysteine to 4'-phosphopantetheine, a step in coenzyme A biosynthesis. Surprisingly, this decarboxylation reaction is carried out as an FMN-dependent redox reaction. In the ...

    The Arabidopsis thaliana protein AtHAL3a decarboxylates 4'-phosphopantothenoylcysteine to 4'-phosphopantetheine, a step in coenzyme A biosynthesis. Surprisingly, this decarboxylation reaction is carried out as an FMN-dependent redox reaction. In the first half-reaction, the side-chain of the cysteine residue of 4'-phosphopantothenoylcysteine is oxidised and the thioaldehyde intermediate decarboxylates spontaneously to the 4'-phosphopantothenoyl-aminoethenethiol intermediate. In the second half-reaction this compound is reduced to 4'-phosphopantetheine and the FMNH(2) cofactor is re-oxidised. The active site mutant C175S is unable to perform this reductive half-reaction. Here, we present the crystal structure of the AtHAL3a mutant C175S in complex with the reaction intermediate pantothenoyl-aminoethenethiol and FMNH(2). The geometry of binding suggests that reduction of the C(alpha)=C(beta) double bond of the intermediate can be performed by direct hydride-transfer from N5 of FMNH(2) to C(beta) of the aminoethenethiol-moiety supported by a protonation of C(alpha) by Cys175. The binding mode of the substrate is very similar to that previously observed for a pentapeptide to the homologous enzyme EpiD that introduces the aminoethenethiol-moiety as final reaction product at the C terminus of peptidyl-cysteine residues. This finding further supports our view that these homologous enzymes form a protein family of homo-oligomeric flavin-containing cysteine decarboxylases, which we have termed HFCD family.


    Related Citations: 
    • Arabidopsis thaliana AtHal3: a flavoprotein related to salt and osmotic tolerance and plant growth
      Espinosa-Ruiz, A.,Belles, J.M.,Serrano, R.,Culianez-Macia, F.A.
      (1999) Plant J. 20: 529
    • Molecular characterization of the Arabidopsis thaliana flavoprotein AtHAL3a reveals the general reaction mechanism of 4'-phosphopantothenoylcysteine decarboxylases
      Hernandez-Acosta, P.,Schmid, D.G.,Jung, G.,Culianez-Macia, F.A.,Kupke, T.
      (2002) J.Biol.Chem. 277: 20490
    • Arabidopsis thaliana flavoprotein AtHAL3a catalyzes the decarboxylation of 4'-phosphopantothenoylcysteine to 4'-phosphopantetheine, a key step in coenzyme A biosynthesis
      Kupke, T.,Hernandez-Acosta, P.,Steinbacher, S.,Culianez-Macia, F.A.
      (2001) J.Biol.Chem. 276: 19190
    • The X-ray structure of the FMN-binding protein AtHal3 provides the structural basis for the activity of a regulatory subunit involved in signal transduction
      Albert, A.,Martinez-Ripoll, M.,Espinosa-Ruiz, A.,Yenush, L.,Culianez-Macia, F.A.,Serrano, R.
      (2000) Structure 8: 961


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung für Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany. steinbac@biochem.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PPC decarboxylase AtHAL3a
A
209Arabidopsis thalianaGene Names: HAL3A (COAC1)
EC: 4.1.1.36
Find proteins for Q9SWE5 (Arabidopsis thaliana)
Go to UniProtKB:  Q9SWE5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 111.790α = 90.00
b = 111.790β = 90.00
c = 32.996γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance