PDBsum entry 2abw

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Transferase PDB id
Protein chains
216 a.a. *
Waters ×469
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Glutaminase subunit of the plasmodial plp synthase (vitamin biosynthesis)
Structure: Pdx2 protein. Chain: a, b. Synonym: glutaminase. Engineered: yes
Source: Plasmodium falciparum. Malaria parasite p. Falciparum. Organism_taxid: 5833. Gene: pdx2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.62Å     R-factor:   0.153     R-free:   0.189
Authors: M.Gengenbacher,T.B.Fitzpatrick,T.Raschle,K.Flicker,I.Sinning S.Mueller,P.Macheroux,I.Tews,B.Kappes
Key ref:
M.Gengenbacher et al. (2006). Vitamin B6 Biosynthesis by the Malaria Parasite Plasmodium falciparum: BIOCHEMICAL AND STRUCTURAL INSIGHTS. J Biol Chem, 281, 3633-3641. PubMed id: 16339145 DOI: 10.1074/jbc.M508696200
17-Jul-05     Release date:   10-Jan-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q5ND68  (Q5ND68_PLAFA) -  Pdx2 protein
219 a.a.
216 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     pyridoxal phosphate biosynthetic process   2 terms 
  Biochemical function     transferase activity     1 term  


DOI no: 10.1074/jbc.M508696200 J Biol Chem 281:3633-3641 (2006)
PubMed id: 16339145  
Vitamin B6 Biosynthesis by the Malaria Parasite Plasmodium falciparum: BIOCHEMICAL AND STRUCTURAL INSIGHTS.
M.Gengenbacher, T.B.Fitzpatrick, T.Raschle, K.Flicker, I.Sinning, S.Müller, P.Macheroux, I.Tews, B.Kappes.
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.
  Selected figure(s)  
Figure 4.
Structural analysis of Pdx2. A, ribbon representation of the x-ray structure of Pdx2. Amino acids Cys^87, His^196, and Glu^198 make up the catalytic triad. The respective residues are shown in yellow in all panels. Residues involved in the putative interface with the synthase subunit are labeled in green. Differences to the Yaa E ortholog are shown in red. B, stick representation of the active site of Pdx2. The loop carrying the nucleophilic cysteine comprises residues Gly^85, Thr^86, Cys^87, Ala^88, and Gly^89. This loop is shown together with the 2F[o] -F[c] electron density at a level of 1.2σ. The double conformation of Cys^87 is visible. The proposed binding site of the synthase subunit is indicated. C, the proposed oxyanion hole, which forms during catalysis, is obstructed in Pdx2 by the carbonyl of Gly^51. D, the oxyanion hole is formed in the apo-form of CPS (1JDB) by the peptide nitrogens of Gly^241 and Leu^270. E, in the glutamine-bound state of CPS (1A9X), this conformation is maintained. The figure was prepared with PyMOL (53).
Figure 5.
Cross-species interaction between Pdx1 and YaaE. A, growth of the B. subtilis 168 (trpC2) YaaD disruptant complemented with control construct lacking the ribosomal binding site (Pdx1) (1) or the complementation construct (RBS-Pdx1) (2) on minimal plates (TMM) without and with additives (0.05 mm pyridoxal (TMM+pyridoxal) or 2% xylose (TMM+xylose)) in the presence or absence of IPTG. IPTG is required to induce the expression of the endogenous YaaE. B, growth curves of the B. subtilis 168 (trpC2) YaaD disruptant complemented with RBS-Pdx1 (filled symbols: •, ▾, and ▪) or the RBS-lacking Pdx1 control construct (open symbols: ○,▾, and □) in TMM plus IPTG without and with additives (0.05 mm pyridoxal or 2% xylose). •, RBS-Pdx1 in TMM; ○, Pdx1 in TMM; ○, RBS-Pdx1 in TMM plus 0.05 mm pyridoxal;▵, Pdx1 in TMM plus 0.05 mm mm pyridoxal; •, RBS-Pdx1 in TMM -Pdx1 expression was induced by the addition of 2% xylose; □, Pdx1 in TMM plus 2% xylose. C, PLP formation by the Pdx1-YaaE complex in the presence of ribulose 5-phosphate, G3P, and 10 mm Gln: ▴, YaaD-YaaE complex (1:1); •, Pdx1-Pdx2 complex (1:1); •, Pdx1-YaaE (1:5); ○, Pdx1-YaaE (1:1);▵, YaaD; □, Pdx1; ♦, no enzyme.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 3633-3641) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20397182 T.B.Fitzpatrick, C.Moccand, and C.Roux (2010).
Vitamin B6 biosynthesis: charting the mechanistic landscape.
  Chembiochem, 11, 1185-1193.  
20815826 T.Dick, U.Manjunatha, B.Kappes, and M.Gengenbacher (2010).
Vitamin B6 biosynthesis is essential for survival and virulence of Mycobacterium tuberculosis.
  Mol Microbiol, 78, 980-988.  
19306104 H.Chen, and L.Xiong (2009).
The short-rooted vitamin B(6)-deficient mutant pdx1 has impaired local auxin biosynthesis.
  Planta, 229, 1303-1310.  
19656333 H.Chen, and L.Xiong (2009).
Enhancement of vitamin B(6) levels in seeds through metabolic engineering.
  Plant Biotechnol J, 7, 673-681.  
19197387 I.B.Müller, F.Wu, B.Bergmann, J.Knöckel, R.D.Walter, H.Gehring, and C.Wrenger (2009).
Poisoning pyridoxal 5-phosphate-dependent enzymes: a new strategy to target the malaria parasite Plasmodium falciparum.
  PLoS ONE, 4, e4406.  
19674326 K.Benabdellah, C.Azcón-Aguilar, A.Valderas, D.Speziga, T.B.Fitzpatrick, and N.Ferrol (2009).
GintPDX1 encodes a protein involved in vitamin B6 biosynthesis that is up-regulated by oxidative stress in the arbuscular mycorrhizal fungus Glomus intraradices.
  New Phytol, 184, 682-693.  
19074821 T.Raschle, D.Speziga, W.Kress, C.Moccand, P.Gehrig, N.Amrhein, E.Weber-Ban, and T.B.Fitzpatrick (2009).
Intersubunit cross-talk in pyridoxal 5'-phosphate synthase, coordinated by the C terminus of the synthase subunit.
  J Biol Chem, 284, 7706-7718.  
18350152 I.B.Müller, J.Knöckel, M.R.Groves, R.Jordanova, S.E.Ealick, R.D.Walter, and C.Wrenger (2008).
The assembly of the plasmodial PLP synthase complex follows a defined course.
  PLoS ONE, 3, e1815.  
17898895 D.E.Scott, A.Ciulli, and C.Abell (2007).
Coenzyme biosynthesis: enzyme mechanism, structure and inhibition.
  Nat Prod Rep, 24, 1009-1026.  
17898894 M.E.Webb, A.Marquet, R.R.Mendel, F.Rébeillé, and A.G.Smith (2007).
Elucidating biosynthetic pathways for vitamins and cofactors.
  Nat Prod Rep, 24, 988.  
17875391 P.Gayathri, H.Balaram, and M.R.Murthy (2007).
Structural biology of plasmodial proteins.
  Curr Opin Struct Biol, 17, 744-754.  
17276140 S.Müller, and B.Kappes (2007).
Vitamin and cofactor biosynthesis pathways in Plasmodium and other apicomplexan parasites.
  Trends Parasitol, 23, 112-121.  
17951049 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Conformational changes in ammonia-channeling glutamine amidotransferases.
  Curr Opin Struct Biol, 17, 653-664.  
17144654 F.Zein, Y.Zhang, Y.N.Kang, K.Burns, T.P.Begley, and S.E.Ealick (2006).
Structural insights into the mechanism of the PLP synthase holoenzyme from Thermotoga maritima.
  Biochemistry, 45, 14609-14620.
PDB code: 2iss
17132104 M.L.Eschbach, I.B.Müller, T.W.Gilberger, R.D.Walter, and C.Wrenger (2006).
The human malaria parasite Plasmodium falciparum expresses an atypical N-terminally extended pyrophosphokinase with specificity for thiamine.
  Biol Chem, 387, 1583-1591.  
17159152 M.Strohmeier, T.Raschle, J.Mazurkiewicz, K.Rippe, I.Sinning, T.B.Fitzpatrick, and I.Tews (2006).
Structure of a bacterial pyridoxal 5'-phosphate synthase complex.
  Proc Natl Acad Sci U S A, 103, 19284-19289.
PDB codes: 2nv0 2nv1 2nv2
17227548 O.Titiz, M.Tambasco-Studart, E.Warzych, K.Apel, N.Amrhein, C.Laloi, and T.B.Fitzpatrick (2006).
PDX1 is essential for vitamin B6 biosynthesis, development and stress tolerance in Arabidopsis.
  Plant J, 48, 933-946.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.