yfkN
168
cell wall-anchored 3'5' cyclic dinucleotide 3' phosphodiesterase, degrades c-di-AMP
locus
BSU_07840
Molecular weight
159.47 kDa
pI
5.02
function
degradation of c-di-AMP
product
cell wall-anchored 3'5' cyclic dinucleotide 3′ phosphodiesterase, degrades c-di-AMP
essential
no
ec
3.1.4.16
synonyms
yfkN
Outlinks
Genomic Context
Categories containing this gene/protein
List of homologs in different organisms, belongs to COG0737 (Galperin et al., 2021)
This gene is a member of the following regulons
Gene
Coordinates
855,114 → 859,502
Phenotypes of a mutant
essential according to Kobayshi ''et al.'' [Pubmed|17114254], but a deletion mutant could be constructed [Pubmed|27681641]
The protein
Catalyzed reaction/ biological activity
degrades c-di-AMP two 5′ AMP molecules [Pubmed|27414497]
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 [protein|DAFBC470DA0FA437B117716DE899A8D3EC454672|yhcR], according to UniProt)
[wiki|Cofactors]
Mn2+ [Pubmed|27414497]
Structure
[PDB|3GVE] (fragment, aa 37 - 374)
[PDB|2Z1A] (aa 665 ... 1184, from Thermus thermophilus, 40% identity)
[AF|O34313]
Paralogous protein(s)
[protein|DAFBC470DA0FA437B117716DE899A8D3EC454672|yhcR]
[wiki|Localization]
extracellular (signal peptide) [Pubmed|18957862], the transmembrane domain serves as retention signal, attached to the cell wall [Pubmed|21800427,22767609]
Expression and Regulation
Operons
genes
[gene|B791B0603042603CB5B5E03CA129B20D02BC02BC|yfkN]
description
[Pubmed|16291680]
regulation
expressed under conditions of phosphate limitation ([protein|search|PhoP]) [Pubmed|16291680]
regulatory mechanism
[protein|E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|ccpA]: repression, [Pubmed|12850135], in [regulon|protein:E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|ccpA regulon]
[protein|638D6D2FCCA2A167EFED05CB4E60C2D78D5319AE|phoP]: activation, [Pubmed|16291680], in [regulon|protein:638D6D2FCCA2A167EFED05CB4E60C2D78D5319AE|phoP regulon]
Biological materials
Mutant
GP2026 (Δ''yfkN::aphA3''), available in [wiki|Jörg Stülke]'s lab [Pubmed|27681641]
MGNA-C263 (yfkN::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/2261 NBRP B. subtilis, Japan]
BKE07840 (Δ[gene|B791B0603042603CB5B5E03CA129B20D02BC02BC|yfkN]::erm trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKE07840 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CACCAGTTCTCCACCTTTCA, downstream forward: _UP4_TAAAAAAGAGCTGCTCGCTA
BKK07840 (Δ[gene|B791B0603042603CB5B5E03CA129B20D02BC02BC|yfkN]::kan trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKK07840 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CACCAGTTCTCCACCTTTCA, downstream forward: _UP4_TAAAAAAGAGCTGCTCGCTA
References
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Time of last update: 2024-12-21 05:12:05
Author of last update: Jstuelk