pyridoxine 5'-phosphate synthase catalyzes the ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate
Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of ...
2-255
5.54e-117
Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the biosynthesis of vitamin B6. PNP synthase, a homooctameric enzyme, catalyzes the final step in PNP biosynthesis, the condensation of 1-amino-acetone 3-phosphate and 1-deoxy-D-xylulose 5-phosphate. PNP synthase adopts a TIM barrel topology, intersubunit contacts are mediated by three ''extra'' helices, generating a tetramer of symmetric dimers with shared active sites; the open state has been proposed to accept substrates and to release products, while most of the catalytic events are likely to occur in the closed state; a hydrophilic channel running through the center of the barrel was identified as the essential structural feature that enables PNP synthase to release water molecules produced during the reaction from the closed, solvent-shielded active site.
Pssm-ID: 237977 Cd Length: 234 Bit Score: 334.08 E-value: 5.54e-117
Pyridoxal phosphate biosynthesis protein PdxJ; Members of this family belong to the PdxJ ...
2-255
8.31e-117
Pyridoxal phosphate biosynthesis protein PdxJ; Members of this family belong to the PdxJ family that catalyzes the condensation of 1-deoxy-d-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxine 5'-phosphate (PNP). This reaction is involved in de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate.
Pssm-ID: 461034 Cd Length: 234 Bit Score: 333.57 E-value: 8.31e-117
Pyridoxine 5'-phosphate synthase PdxJ [Coenzyme transport and metabolism]; Pyridoxine 5 ...
1-255
3.86e-115
Pyridoxine 5'-phosphate synthase PdxJ [Coenzyme transport and metabolism]; Pyridoxine 5'-phosphate synthase PdxJ is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis
Pssm-ID: 440615 Cd Length: 235 Bit Score: 329.30 E-value: 3.86e-115
pyridoxine 5'-phosphate synthase; PdxJ is required in the biosynthesis of pyridoxine (vitamin ...
2-255
7.26e-85
pyridoxine 5'-phosphate synthase; PdxJ is required in the biosynthesis of pyridoxine (vitamin B6), a precursor to the enzyme cofactor pyridoxal phosphate. ECOCYC describes the predicted reaction equation as 1-amino-propan-2-one-3-phosphate + deoxyxylulose-5-phosphate = pyridoxine-5'-phosphate. The product of that reaction is oxidized by PdxH to pyridoxal 5'-phosphate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine]
Pssm-ID: 188064 Cd Length: 236 Bit Score: 252.78 E-value: 7.26e-85
Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of ...
2-255
5.54e-117
Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the biosynthesis of vitamin B6. PNP synthase, a homooctameric enzyme, catalyzes the final step in PNP biosynthesis, the condensation of 1-amino-acetone 3-phosphate and 1-deoxy-D-xylulose 5-phosphate. PNP synthase adopts a TIM barrel topology, intersubunit contacts are mediated by three ''extra'' helices, generating a tetramer of symmetric dimers with shared active sites; the open state has been proposed to accept substrates and to release products, while most of the catalytic events are likely to occur in the closed state; a hydrophilic channel running through the center of the barrel was identified as the essential structural feature that enables PNP synthase to release water molecules produced during the reaction from the closed, solvent-shielded active site.
Pssm-ID: 237977 Cd Length: 234 Bit Score: 334.08 E-value: 5.54e-117
Pyridoxal phosphate biosynthesis protein PdxJ; Members of this family belong to the PdxJ ...
2-255
8.31e-117
Pyridoxal phosphate biosynthesis protein PdxJ; Members of this family belong to the PdxJ family that catalyzes the condensation of 1-deoxy-d-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxine 5'-phosphate (PNP). This reaction is involved in de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate.
Pssm-ID: 461034 Cd Length: 234 Bit Score: 333.57 E-value: 8.31e-117
Pyridoxine 5'-phosphate synthase PdxJ [Coenzyme transport and metabolism]; Pyridoxine 5 ...
1-255
3.86e-115
Pyridoxine 5'-phosphate synthase PdxJ [Coenzyme transport and metabolism]; Pyridoxine 5'-phosphate synthase PdxJ is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis
Pssm-ID: 440615 Cd Length: 235 Bit Score: 329.30 E-value: 3.86e-115
pyridoxine 5'-phosphate synthase; PdxJ is required in the biosynthesis of pyridoxine (vitamin ...
2-255
7.26e-85
pyridoxine 5'-phosphate synthase; PdxJ is required in the biosynthesis of pyridoxine (vitamin B6), a precursor to the enzyme cofactor pyridoxal phosphate. ECOCYC describes the predicted reaction equation as 1-amino-propan-2-one-3-phosphate + deoxyxylulose-5-phosphate = pyridoxine-5'-phosphate. The product of that reaction is oxidized by PdxH to pyridoxal 5'-phosphate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine]
Pssm-ID: 188064 Cd Length: 236 Bit Score: 252.78 E-value: 7.26e-85
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
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if a domain or superfamily has been annotated with functional sites (conserved features),
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The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
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To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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