yfkN

168

cell wall-anchored 3'5' cyclic dinucleotide 3' phosphodiesterase, degrades c-di-AMP

Locus: BSU_07840

Molecular weight: 159.47 kDa

Isoelectric point: 5.02

Protein length: 1462 aa

Gene length: 4389 bp

Function: degradation of c-di-AMP

Product: cell wall-anchored 3'5' cyclic dinucleotide 3′ phosphodiesterase, degrades c-di-AMP

Essential: no

E.C.: 3.1.4.16

Synonyms: yfkN

Genomic Context

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List of homologs in different organisms, belongs to COG0737 (Galperin et al., 2021)

Gene

Coordinates: 855,114 → 859,502

Phenotypes of a mutant

• essential according to Kobayshi et al. PubMed, but a deletion mutant could be constructed PubMed

The protein

Catalyzed reaction/ biological activity

• degrades c-di-AMP two 5′ AMP molecules PubMed
• nucleoside 2',3'-cyclic phosphate + H₂O --> nucleoside 3'-phosphate + H⁺ (according to UniProt)
• ribonucleoside 3'-phosphate + H₂O --> ribonucleoside + phosphate (according to UniProt)
• ribonucleoside 5'-phosphate + H₂O --> ribonucleoside + phosphate (according to UniProt)

Protein family

• 5'-nucleotidase family (with YhcR, according to UniProt)

Cofactors

• Mn2+ PubMed

Structure

• 3GVE (PDB) (fragment, aa 37 - 374)
• 2Z1A (PDB) (aa 665 ... 1184, from Thermus thermophilus, 40% identity)
• O34313 (AlphaFold)

Paralogous protein(s)

• YhcR

Localization

• extracellular (signal peptide) PubMed, the transmembrane domain serves as retention signal, attached to the cell wall PubMed

Expression and Regulation

Operons

• Genes: yfkN

  Description: PubMed

  Regulation

  • expressed under conditions of phosphate limitation (PhoP) PubMed

  Regulatory mechanism

  • CcpA: repression, PubMed, in ccpA regulon
  • PhoP: activation, PubMed, in phoP regulon

Biological materials

Mutant

• GP2026 (ΔyfkN::aphA3), available in Jörg Stülke's lab PubMed
• MGNA-C263 (yfkN::erm), available at the NBRP B. subtilis, Japan
• BKE07840 (ΔyfkN::erm  trpC2) available at BGSC,  PubMed, upstream reverse: _UP1_CACCAGTTCTCCACCTTTCA,  downstream forward: _UP4_TAAAAAAGAGCTGCTCGCTA
• BKK07840 (ΔyfkN::kan  trpC2) available at BGSC,  PubMed, upstream reverse: _UP1_CACCAGTTCTCCACCTTTCA,  downstream forward: _UP4_TAAAAAAGAGCTGCTCGCTA

References

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