pdxS

pyridoxal-5-phosphate synthase (synthase domain)

locus: BSU_00110

pI: 5.09

mw: 31.46 kDa

protein length: 294 aa

gene length: 885 bp

function: pyridoxal-5-phosphate biosynthesis

product: pyridoxal-5-phosphate synthase (synthase domain)

essential: no

ec: 4.3.3.6

synonyms: yaaD

Genomic Context

categories

• [category|SW 2|Metabolism] → [category|SW 2.6|Additional metabolic pathways] → [category|SW 2.6.2|Biosynthesis of cofactors] → [category|SW 2.6.2.12|Biosynthesis of pyridoxal phosphate]
• [category|SW 3|Information processing] → [category|SW 3.1|Genetics] → [category|SW 3.1.9|Newly identified competence genes]
• [category|SW 6|Groups of genes] → [category|SW 6.4|Phosphoproteins] → [category|SW 6.4.1|Phosphorylation on an Arg residue]
• [category|SW 6|Groups of genes] → [category|SW 6.4|Phosphoproteins] → [category|SW 6.4.8|Phosphorylation on either a Ser, Thr or Tyr residue]

Gene

Coordinates: 19,062 19,946

Phenotypes of a mutant

• auxotrophic for pyridoxal 5'-phosphate [Pubmed|14762015]
• inactivation of ''[gene|651D1E534490276B9BE7BFE7B5819176AE09891E|pdxS]'' reduces sporulation efficiency to 1.2% that of wild type cells [Pubmed|26735940]
• poor growth [pubmed|28189581]
• non-transformable [pubmed|28189581]

The protein

Catalyzed reaction/ biological activity

• Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the [protein|6F96C10759C1C20B3A6B396E3718F0A9281F100A|PdxT] subunit. (according to UniProt)
• aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine --> H⁺ + 3 H₂O + L-glutamate + phosphate + pyridoxal 5'-phosphate (according to UniProt)

Protein family

• PdxS/SNZ family (single member, according to UniProt)

Modification

• phosphorylated on Arg-8 [Pubmed|22517742]
• phosphorylated on STY [Pubmed|16493705], [Pubmed|17726680]

Structure

• [PDB|2NV2] [protein|651D1E534490276B9BE7BFE7B5819176AE09891E|PdxS]-[protein|6F96C10759C1C20B3A6B396E3718F0A9281F100A|PdxT] complex [Pubmed|17159152]
• [PDB|2NV1] [protein|651D1E534490276B9BE7BFE7B5819176AE09891E|PdxS] [Pubmed|17159152]

additional information

• belongs to the 100 [SW|most abundant proteins] [PubMed|15378759]

Expression and Regulation

Operons

• genes: [gene|7C3081BC8D416127A881627EB56C0628359111CF|dacA]-[gene|651D1E534490276B9BE7BFE7B5819176AE09891E|pdxS]-[gene|6F96C10759C1C20B3A6B396E3718F0A9281F100A|pdxT]-[gene|82B92D2FB8DB88689D3A8B77FAD2F63FCCA04C7E|serS]
  description: [Pubmed|22383849]

  regulation

  • the leader mRNA is processed upstream of [gene|7C3081BC8D416127A881627EB56C0628359111CF|dacA] by [protein|872CCB5A49C9000BD95E4B0472556D5F60F7D7A4|RNase Y], this requires the [protein|EE52DFA35B935E551871D079A9BE877DB2001A3B|YmcA]-[protein|6C9A092F38739A3759793EF8B496569CD02C2E3F|YlbF]-[protein|EBD15C174A03B7FCDFFE4C5DB5D86E93F1B9CAC4|YaaT] complex [Pubmed|29794222]

  Additional information

  • [protein|638D6D2FCCA2A167EFED05CB4E60C2D78D5319AE|PhoP]∼P binds to the promoter region, but regulation has not been explored [pubmed|25666134]

• genes: [gene|651D1E534490276B9BE7BFE7B5819176AE09891E|pdxS]-[gene|6F96C10759C1C20B3A6B396E3718F0A9281F100A|pdxT]
  description: [Pubmed|22383849]

  regulatory mechanism

  • [protein|2C54FE2ADC82FF414D732018C90649D477A925AD|Spo0A]: repression, [Pubmed|14651647], in [regulon|2C54FE2ADC82FF414D732018C90649D477A925AD|Spo0A regulon]

  regulation

  • negatively controlled by [SW|Spo0A] [Pubmed|14651647]

• genes: [gene|651D1E534490276B9BE7BFE7B5819176AE09891E|pdxS]-[gene|6F96C10759C1C20B3A6B396E3718F0A9281F100A|pdxT]-[gene|82B92D2FB8DB88689D3A8B77FAD2F63FCCA04C7E|serS]
  description: [Pubmed|22383849]

Biological materials

Mutant

• BKE00110 ([gene|651D1E534490276B9BE7BFE7B5819176AE09891E|pdxS]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE00110 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATTTCTTGGTCCCCCTAAT, downstream forward: _UP4_TAAGAACATAGGAGCGCTGC
• BKK00110 ([gene|651D1E534490276B9BE7BFE7B5819176AE09891E|pdxS]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK00110 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATTTCTTGGTCCCCCTAAT, downstream forward: _UP4_TAAGAACATAGGAGCGCTGC
• BV604 (([gene|651D1E534490276B9BE7BFE7B5819176AE09891E|pdxS]-[gene|6F96C10759C1C20B3A6B396E3718F0A9281F100A|pdxT])::tet), available in [SW|Fabian Commichau]'s lab, [Pubmed|24972371]
• BP1100 (([gene|651D1E534490276B9BE7BFE7B5819176AE09891E|pdxS]-[gene|6F96C10759C1C20B3A6B396E3718F0A9281F100A|pdxT])::tet trp⁺), available in [SW|Jörg Stülke]'s and [SW|Fabian Commichau]'s labs

Expression vector

• pBP766: IPTG inducible expression, purification in E. coli with cleaveable N-terminal His-tag, in petSUMOadapt, available in [SW|Fabian Commichau]'s and [SW|Jörg Stülke]'s labs
• pBP772: expression of ''pdxST''-Strep by [SW|pGP382] in ''B. subtilis'' suitable for [SW|SPINE], available in [SW|Jörg Stülke]'s and [SW|Fabian Commichau]'s labs
• pBP774: IPTG inducible expression and purification of ''pdxST'' in ''E. coli'' with C-terminal Strep-tag, in [SW|pGP574], available in [SW|Jörg Stülke]'s and [SW|Fabian Commichau]'s labs
• pBP775: constitutive expression of ''pdxS'' by [SW|pBQ200] in ''B. subtilis''

References

• 15911615,14762015,25473090,14651647,17726680,16493705,16030023,19152323,17159152,22517742,15378759,25568319,26490441,16233205,28189581