1MVL

PPC decarboxylase mutant C175S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


This is version 1.3 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

  • DOI: 10.1016/s0022-2836(03)00092-5
  • Primary Citation of Related Structures:  
    1MVL, 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 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 ...

    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 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
    • 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 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
    • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PPC decarboxylase AtHAL3aA209Arabidopsis thalianaMutation(s): 1 
Gene Names: HAL3ACOAC1At3g18030MBG14.2
EC: 4.1.1.36
UniProt
Find proteins for Q9SWE5 (Arabidopsis thaliana)
Explore Q9SWE5 
Go to UniProtKB:  Q9SWE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SWE5
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 Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.79α = 90
b = 111.79β = 90
c = 32.996γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations