Pyridoxine 5'-phosphate synthase (P0A794)

Identification
Name:Pyridoxine 5'-phosphate synthase
Synonyms:
  • PNP synthase
Gene Name:pdxJ
Enzyme Class:
Biological Properties
General Function:Involved in catalytic activity
Specific Function:Catalyzes the complicated 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
Cellular Location:Cytoplasm
SMPDB Pathways:
KEGG Pathways:
KEGG Reactions:
1.03-Amino-2-oxopropyl phosphate+1.0Thumb+1.0Thumb ↔ 1.0Thumb+1.0Thumb+2.0Thumb
1.03-Amino-2-oxopropyl phosphate + 1.01-Deoxy-D-xylulose 5-phosphate + 1.03-Amino-2-oxopropyl phosphate ↔ 1.0Pyridoxine 5'-phosphate + 1.0Phosphate + 2.0Water
ReactionCard
SMPDB Reactions:
1.01-Deoxy-D-xylulose 5-phosphate+1.02-Amino-3-phosphonopropionic acid+1.0Thumb+1.02-Amino-3-phosphonopropionic acid → 1.0Thumb+1.0Thumb+1.0Thumb+2.0Thumb
1.01-Deoxy-D-xylulose 5-phosphate + 1.02-Amino-3-phosphonopropionic acid + 1.01-Deoxy-D-xylulose 5-phosphate + 1.02-Amino-3-phosphonopropionic acid → 1.0Pyridoxine 5'-phosphate + 1.0Phosphate + 1.0Hydrogen ion + 2.0Water
ReactionCard
Complex Reactions:
1.0Thumb+1.0Thumb+1.0Thumb → 1.0Thumb+1.0Thumb+2.0Thumb+1.0Thumb+1.0Thumb+1.0Thumb
1.01-Deoxy-D-xylulose 5-phosphate + 1.0NAD + 1.0O-Phospho-4-hydroxy-L-threonine → 1.0Carbon dioxide + 1.0Hydrogen ion + 2.0Water + 1.0NADH + 1.0Pyridoxine 5'-phosphate + 1.0Phosphate
ReactionCard
Metabolites:
ECMDB IDNameView
ECMDB012131-Deoxy-D-xylulose 5-phosphateMetaboCard
ECMDB237753-Amino-2-oxopropyl phosphateMetaboCard
ECMDB04030Carbon dioxideMetaboCard
ECMDB21225Hydrogen ionMetaboCard
ECMDB21380Inorganic phosphateMetaboCard
ECMDB00902NADMetaboCard
ECMDB01487NADHMetaboCard
ECMDB06802O-Phospho-4-hydroxy-L-threonineMetaboCard
ECMDB01429PhosphateMetaboCard
ECMDB01319Pyridoxine 5'-phosphateMetaboCard
ECMDB00494WaterMetaboCard
GO Classification:
Component
cell part
cytoplasm
intracellular part
Function
catalytic activity
Process
metabolic process
pyridoxine biosynthetic process
pyridoxine metabolic process
small molecule metabolic process
vitamin B6 metabolic process
vitamin metabolic process
water-soluble vitamin metabolic process
Gene Properties
Blattner:b2564
Gene OrientationCounterclockwise
Centisome Percentage:58.17
Left Sequence End2699020
Right Sequence End2699751
Gene Sequence:
>732 bp
ATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAG
ATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTGAAGTGGTGAAC
CGTCGCCTGACGGGCAATAACTTCCATGTTTATCTCAAACCCGATCGGCTGGTGGATCCG
GAAGCCTTTGGCGTACATGGTATTGCCGATGAATTTTTGCTCGATAAGCCCACGTTTGCC
GAAGTAGCCGATGAGTTCATGGACTATATTCGCGGCGCGGAGTTGGTGATCCATAACGCA
GCGTTCGATATCGGCTTTATGGACTACGAGTTTTCGTTGCTTAAGCGCGATATTCCGAAG
ACCAATACTTTCTGTAAGGTCACCGATAGCCTTGCGGTGGCGAGGAAAATGTTTCCCGGT
AAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAACGAACG
CTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGT
GGTCAAACGTCGATGGCTTTTGCGATGGAAGGAGAGACACAACAGCAACAAGGTGAAGCA
ACAATTCAGCGCATTGTACGTCAGGCAAGTAAGTTACGCGTTGTTTTTGCGACAGATGAA
GAGATTGCAGCTCATGAAGCCCGTCTCGATCTGGTGCAGAAGAAAGGCGGAAGTTGCCTC
TGGCGAGCATAA
Protein Properties
Pfam Domain Function:
Protein Residues:243
Protein Molecular Weight:26384
Protein Theoretical pI:6
PDB File:1M5W
Signaling Regions:
  • None
Transmembrane Regions:
  • None
Protein Sequence:
>Pyridoxine 5'-phosphate synthase
MAELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRI
LRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDAC
KRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAAT
FAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLE
ARG
References
External Links:
ResourceLink
Uniprot ID:P0A794
Uniprot Name:PDXJ_ECOLI
GenBank Gene ID:AP009048
Genebank Protein ID:4902952
PDB ID:1M5W
Ecogene ID:EG10693
Ecocyc:EG10693
ColiBase:b2564
Kegg Gene:b2564
EchoBASE ID:EB0687
CCDB:PDXJ_ECOLI
BacMap:16130489
General Reference:
  • Blattner, F. R., Plunkett, G. 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., Shao, Y. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277:1453-1462. Pubmed: 9278503
  • Franco, M. G., Laber, B., Huber, R., Clausen, T. (2001). "Structural basis for the function of pyridoxine 5'-phosphate synthase." Structure 9:245-253. Pubmed: 11286891
  • Garrido Franco, M., Huber, R., Schmidt, F. S., Laber, B., Clausen, T. (2000). "Crystallization and preliminary X-ray crystallographic analysis of PdxJ, the pyridoxine 5'-phosphate synthesizing enzyme." Acta Crystallogr D Biol Crystallogr 56:1045-1048. Pubmed: 10944349
  • Garrido-Franco, M. (2003). "Pyridoxine 5'-phosphate synthase: de novo synthesis of vitamin B6 and beyond." Biochim Biophys Acta 1647:92-97. Pubmed: 12686115
  • Garrido-Franco, M., Laber, B., Huber, R., Clausen, T. (2002). "Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis." J Mol Biol 321:601-612. Pubmed: 12206776
  • Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2:2006.0007. Pubmed: 16738553
  • Laber, B., Maurer, W., Scharf, S., Stepusin, K., Schmidt, F. S. (1999). "Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein." FEBS Lett 449:45-48. Pubmed: 10225425
  • Lam, H. M., Tancula, E., Dempsey, W. B., Winkler, M. E. (1992). "Suppression of insertions in the complex pdxJ operon of Escherichia coli K-12 by lon and other mutations." J Bacteriol 174:1554-1567. Pubmed: 1537800
  • Man, T. K., Zhao, G., Winkler, M. E. (1996). "Isolation of a pdxJ point mutation that bypasses the requirement for the PdxH oxidase in pyridoxal 5' -phosphate coenzyme biosynthesis in Escherichia coli K-12." J Bacteriol 178:2445-2449. Pubmed: 8636054
  • Takiff, H. E., Baker, T., Copeland, T., Chen, S. M., Court, D. L. (1992). "Locating essential Escherichia coli genes by using mini-Tn10 transposons: the pdxJ operon." J Bacteriol 174:1544-1553. Pubmed: 1537799
  • Yeh, J. I., Du, S., Pohl, E., Cane, D. E. (2002). "Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate." Biochemistry 41:11649-11657. Pubmed: 12269807