2ABW | pdb_00002abw

Glutaminase subunit of the plasmodial PLP synthase (Vitamin B6 biosynthesis)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.189 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2ABW

This is version 1.4 of the entry. See complete history

Literature

Vitamin B6 Biosynthesis by the Malaria Parasite Plasmodium falciparum: Biochemical and structural insights

Gengenbacher, M.Fitzpatrick, T.B.Raschle, T.Flicker, K.Sinning, I.Mueller, S.Macheroux, P.Tews, I.Kappes, B.

(2006) J Biological Chem 281: 3633-3641

  • DOI: https://doi.org/10.1074/jbc.M508696200
  • Primary Citation Related Structures: 
    2ABW

  • PubMed Abstract: 

    Vitamin B6 is one of nature's most versatile cofactors. Most organisms synthesize vitamin B6 via a recently discovered pathway employing the proteins Pdx1 and Pdx2. Here we present an in-depth characterization of the respective orthologs from the malaria parasite, Plasmodium falciparum. Expression profiling of Pdx1 and -2 shows that blood-stage parasites indeed possess a functional vitamin B6 de novo biosynthesis. Recombinant Pdx1 and Pdx2 form a complex that functions as a glutamine amidotransferase with Pdx2 as the glutaminase and Pdx1 as pyridoxal-5 '-phosphate synthase domain. Complex formation is required for catalytic activity of either domain. Pdx1 forms a chimeric bi-enzyme with the bacterial YaaE, a Pdx2 ortholog, both in vivo and in vitro, although this chimera does not attain full catalytic activity, emphasizing that species-specific structural features govern the interaction between the protein partners of the PLP synthase complexes in different organisms. To gain insight into the activation mechanism of the parasite bi-enzyme complex, the three-dimensional structure of Pdx2 was determined at 1.62 A. The obstruction of the oxyanion hole indicates that Pdx2 is in a resting state and that activation occurs upon Pdx1-Pdx2 complex formation.


  • Organizational Affiliation
    • Abteilung für Parasitologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 51.51 kDa 
  • Atom Count: 4,130 
  • Modeled Residue Count: 442 
  • Deposited Residue Count: 454 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pdx2 protein
A, B
227Plasmodium falciparumMutation(s): 0 
Gene Names: Pdx2
EC: 2.6 (PDB Primary Data), 4.3.3.6 (UniProt), 3.5.1.2 (UniProt)
UniProt
Find proteins for Q8IIK4 (Plasmodium falciparum (isolate 3D7))
Explore Q8IIK4 
Go to UniProtKB:  Q8IIK4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IIK4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
C [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free:  0.189 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.042α = 90
b = 67.917β = 92.31
c = 70.327γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description