speD [2019-10-30 10:28:04]

S-adenosylmethionine decarboxylase, required for biofilm formation

locus: BSU_29010

pI: 4.77

mw: 13.96 kDa

protein length: 126 aa

gene length: 381 bp

function: spermidine, polyamine biosynthesis

product: S-adenosylmethionine decarboxylase

essential: no

ec: 4.1.1.50

synonyms: ytcF

Genomic Context

categories

• [category|SW 2|Metabolism] → [category|SW 2.6|Additional metabolic pathways] → [category|SW 2.6.6|Miscellaneous metabolic pathways] → [category|SW 2.6.6.6|Metabolism of polyamines]
• [category|SW 4|Lifestyles] → [category|SW 4.1|Exponential and early post-exponential lifestyles] → [category|SW 4.1.2|Biofilm formation]
• [category|SW 4|Lifestyles] → [category|SW 4.1|Exponential and early post-exponential lifestyles] → [category|SW 4.1.2|Biofilm formation] → [category|SW 4.1.2.5|Other proteins required for biofilm formation]

Gene

Coordinates: 2,966,413 → 2,966,793

Phenotypes of a mutant

• no [SW|biofilm formation] [Pubmed|24529384]

The protein

Catalyzed reaction/ biological activity

• H⁺ + S-adenosyl-L-methionine --> CO₂ + S-adenosyl 3-(methylsulfanyl)propylamine (according to UniProt)

Protein family

• prokaryotic AdoMetDC family (single member, according to UniProt)

Structure

• [PDB|1VR7] (from ''Thermotoga maritima'', 47% identity, 72% similarity)

Expression and Regulation

Operons

• genes: [gene|C1B89BD3DD27CD566018558D3A7845FB451056F0|gapB]-[gene|CDD5C7B1CE58352D29BB86BCC2C3685D1D8898ED|speD]
  description: [Pubmed|15720552]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|15720552], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]

  regulatory mechanism

  • [protein|2234D81F8F9B92EAF1CF6F73BEC92D4DE54E2636|CcpN]: repression, [Pubmed|15720552], in [regulon|2234D81F8F9B92EAF1CF6F73BEC92D4DE54E2636|CcpN regulon]

  regulation

  • ''[protein|search|gapB]'': repressed in the presence of glucose ([protein|search|CcpN]) [Pubmed|15720552]

  additional information

  • '[protein|search|speD]': the mRNA is substantially stabilized upon depletion of [gene|872CCB5A49C9000BD95E4B0472556D5F60F7D7A4|RNase Y] (the half-life of the monocistronic 'speD' mRNA increases from 1.4 to 36 min) [PubMed|21815947]

• genes: [gene|CDD5C7B1CE58352D29BB86BCC2C3685D1D8898ED|speD]
  description: [Pubmed|10844697]

  regulation

  • ''[protein|search|gapB]'': repressed in the presence of glucose ([protein|search|CcpN]) [Pubmed|15720552]

  additional information

  • '[protein|search|speD]': the mRNA is substantially stabilized upon depletion of [gene|872CCB5A49C9000BD95E4B0472556D5F60F7D7A4|RNase Y] (the half-life of the monocistronic 'speD' mRNA increases from 1.4 to 36 min) [PubMed|21815947]

Biological materials

Mutant

• MGNA-A122 (ytcF::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/122 NBRP B. subtilis, Japan]
• BKE29010 (Δ[gene|CDD5C7B1CE58352D29BB86BCC2C3685D1D8898ED|speD]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE29010 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATAGTCATGGACCCCCCTT, downstream forward: _UP4_TAAAGTAAATTGCGAACACA
• BKK29010 (Δ[gene|CDD5C7B1CE58352D29BB86BCC2C3685D1D8898ED|speD]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK29010 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATAGTCATGGACCCCCCTT, downstream forward: _UP4_TAAAGTAAATTGCGAACACA
• GP2599 (Δ[gene|CDD5C7B1CE58352D29BB86BCC2C3685D1D8898ED|speD]::tet comIQ12L) (in DK1042), available in[SW|Jörg Stülke]'s lab

Expression vector

• pGP2324: for expression in B. subtilis, in [SW|pBQ200],available in[SW|Jörg Stülke]'s lab

References

• 10844697,15720552,9723923,21815947,24529384,28546427