1ZPD

PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

High resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis. Implications for substrate activation in pyruvate decarboxylases.

Dobritzsch, D.Konig, S.Schneider, G.Lu, G.

(1998) J Biol Chem 273: 20196-20204

  • DOI: https://doi.org/10.1074/jbc.273.32.20196
  • Primary Citation of Related Structures:  
    1ZPD

  • PubMed Abstract: 

    The crystal structure of tetrameric pyruvate decarboxylase from Zymomonas mobilis has been determined at 1.9 A resolution and refined to a crystallographic R-factor of 16.2% and Rfree of 19.7%. The subunit consists of three domains, all of the alpha/beta type. Two of the subunits form a tight dimer with an extensive interface area. The thiamin diphosphate binding site is located at the subunit-subunit interface, and the cofactor, bound in the V conformation, interacts with residues from the N-terminal domain of one subunit and the C-terminal domain of the second subunit. The 2-fold symmetry generates the second thiamin diphosphate binding site in the dimer. Two of the dimers form a tightly packed tetramer with pseudo 222 symmetry. The interface area between the dimers is much larger in pyruvate decarboxylase from Z. mobilis than in the yeast enzyme, and structural differences in these parts result in a completely different packing of the subunits in the two enzymes. In contrast to other pyruvate decarboxylases, the enzyme from Z. mobilis is not subject to allosteric activation by the substrate. The tight packing of the dimers in the tetramer prevents large rearrangements in the quaternary structure as seen in the yeast enzyme and locks the enzyme in an activated conformation. The architecture of the cofactor binding site and the active site is similar in the two enzymes. However, the x-ray analysis reveals subtle but significant structural differences in the active site that might be responsible for variations in the biochemical properties in these enzymes.


  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet S-17177 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PYRUVATE DECARBOXYLASEA,
B,
C [auth E],
D [auth F]
568Zymomonas mobilisMutation(s): 0 
EC: 4.1.1.1
UniProt
Find proteins for P06672 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4))
Explore P06672 
Go to UniProtKB:  P06672
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06672
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DPX
Query on DPX

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth E],
O [auth F]
MONO-{4-[(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-AMINO]-2-HYDROXY-3-MERCAPTO-PENT-3-ENYL-PHOSPHONO} ESTER
C11 H20 N4 O8 P2 S
XHCFSNVIKLFNIT-WPVMNKCKSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth E],
P [auth F]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth E],
N [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.868α = 102.86
b = 92.168β = 94.59
c = 98.256γ = 112.69
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-02
    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: 2023-08-09
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-05-22
    Changes: Data collection