_EC 4.3.3.6 Pyridoxal 5'-phosphate synthase (glutamine hydrolyzing). 23 PDB entries  
EC 4.-.-.- Lyases. [3,828 PDB entries]
EC 4.3.-.- Carbon-nitrogen lyases. [278 PDB entries]
EC 4.3.3.- Amine-lyases. [101 PDB entries]
EC 4.3.3.6 Pyridoxal 5'-phosphate synthase (glutamine hydrolyzing). [23 PDB entries]    
1q7r

Reaction: D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H(2)O + phosphate.
 


D-ribose 5-phosphate
+
D-glyceraldehyde 3-phosphate
+
L-glutamine
=
pyridoxal 5'-phosphate
+
L-glutamate
+ 3 × H(2)O
+
phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

Comments: The ammonia is provided by the glutaminase subunit and channeled to the active site of the lyase subunit by a 100 A tunnel. The enzyme can also use ribulose 5-phosphate and dihydroxyacetone phosphate. The enzyme complex is found in aerobic bacteria, archeae, fungi and plants.
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There are 23 PDB entries in enzyme class E.C.4.3.3.6

  PDB code Protein
1q7r
X-ray crystallographic analysis of a predicted amidotransferase from b. Stearothermophilus at 1.9 a resolution
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Chain: A (202 residues) CATH domain: 3.40.50.880
1r9g
Three-dimensional structure of yaae from bacillus subtilis
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: yaae, bsu00120. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (196 residues) CATH domain: 3.40.50.880
1znn
Structure of the synthase subunit of plp synthase
Source: Geobacillus stearothermophilus. Organism_taxid: 1422
Chains: A, B, C, D, E, F (245 residues) CATH domain: Unassigned
2abw
Glutaminase subunit of the plasmodial plp synthase (vitamin biosynthesis)
Source: Plasmodium falciparum. Malaria parasite p. Falciparum. Organism_taxid: 5833. Gene: pdx2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (216 residues) CATH domain: 3.40.50.880
2iss
Structure of the plp synthase holoenzyme from thermotoga mar
Source: Thermotoga maritima. Organism_taxid: 2336. Strain: dsm3109. Gene: pdxs. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: pdxt.
Chains: A, B, C, D, E, F (281 residues)
2nv0
Structure of the glutaminase subunit pdx2 (yaae) of plp synt bacillus subtilis
Source: Bacillus subtilis. Organism_taxid: 1423. Strain: strain 168. Gene: pdxt. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (191 residues) CATH domain: 3.40.50.880
2nv1
Structure of the synthase subunit pdx1 (yaad) of plp synthas bacillus subtilis
Source: Bacillus subtilis. Organism_taxid: 1423. Strain: strain 168. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D, E, F (259 residues)
2nv2
Structure of the plp synthase complex pdx1/2 (yaad/e) from b subtilis
Source: Bacillus subtilis. Organism_taxid: 1423. Strain: strain 168. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X (268 residues)
2ywd
Crystal structure of glutamine amidotransferase
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: pdxt. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (189 residues) CATH domain: 3.40.50.880
2ywj
Crystal structure of uncharacterized conserved protein from methanocaldococcus jannaschii
Source: Methanocaldococcus jannaschii. Organism_taxid: 243232. Strain: dsm 2661. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (185 residues) CATH domain: 3.40.50.880
2yzr
Crystal structure of pyridoxine biosynthesis protein from methanocaldococcus jannaschii
Source: Methanocaldococcus jannaschii. Organism_taxid: 243232. Strain: dsm 2661. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C (307 residues) CATH domain: Unassigned
2zbt
Crystal structure of pyridoxine biosynthesis protein from th thermophilus hb8
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: pdxs. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Chains: A, B, C, D (276 residues)
3fem
Structure of the synthase subunit pdx1.1 (snz1) of plp synth saccharomyces cerevisiae
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: snz1, snz1p, ym6543.03, ymr096w. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D, E, F (281 residues) CATH domain: Unassigned
3o05
Crystal structure of yeast pyridoxal 5-phosphate synthase sn complxed with substrate plp
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: snz1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C (261 residues) CATH domain: Unassigned
3o06
Crystal structure of yeast pyridoxal 5-phosphate synthase sn
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: snz1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C (258 residues) CATH domain: Unassigned
3o07
Crystal structure of yeast pyridoxal 5-phosphate synthase sn complexed with substrate g3p
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: snz1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C (259 residues) CATH domain: Unassigned
4ads
Crystal structure of plasmodial plp synthase complex
Source: Plasmodium berghei. Organism_taxid: 5821. Strain: nk65. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: ril. Plasmodium falciparum. Malaria parasite. Organism_taxid: 36329.
Chains: G, H, I, J, K, L (217 residues) CATH domain: 3.40.50.880
4fiq
Crystal structure of pyridoxal biosynthesis lyase pdxs from horikoshii
Source: Pyrococcus horikoshii. Organism_taxid: 70601. Strain: atcc 700860 / dsm 12428 / jcm 9974 / nbrc 100139 / gene: pdxs, ph1355. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D, E, F (315 residues) CATH domain: Unassigned
4fir
Crystal structure of pyridoxal biosynthesis lyase pdxs from
Source: Pyrococcus horikoshii. Organism_taxid: 70601. Strain: atcc 700860 / dsm 12428 / jcm 9974 / nbrc 100139 / gene: pdxs, ph1355. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D, E, F (333 residues) CATH domain: Unassigned
4jdy
Crystal structure of rv2606c
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: pdxs, rv2606c, mt2681, mtcy1a10.27. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C (264 residues) CATH domain: Unassigned
4wxy
Plps (inactive glutaminase mutant) co-crystallized with glut r5p.
Source: Geobacillus kaustophilus. Organism_taxid: 235909. Strain: hta426. Gene: pdxs, gk0011. Expressed in: escherichia coli. Expression_system_taxid: 469008. Gene: pdxt, gk0012.
Chains: A, C, E, G, I, K, B, D, F, H, J, L (288 residues)
4wxz
Pdxs (g. Stearothermophilus) co-crystallized with r5p
Source: Geobacillus kaustophilus. Organism_taxid: 235909. Strain: hta426. Gene: pdxs, gk0011. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Chains: A, B, C, D, E, F (244 residues)
4wy0
Pdxs (g. Stearothermophilus) co-crystallized with r5p in the of ammonia.
Source: Geobacillus kaustophilus (strain hta42 organism_taxid: 235909. Strain: hta426. Gene: pdxs, gk0011. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Chains: A, B, C, D, E, F, G, H, I, J, K, L (248 residues)