yacF [2019-07-19 11:11:53]

putative tRNA-dihydrouridine synthase B

locus: BSU_00810

pI: 7.87

mw: 36.91 kDa

protein length: 333 aa

gene length: 1002 bp

function: tRNA maturation

product: putative tRNA-dihydrouridine synthase B

essential: no

synonyms: dusB,dus1

Genomic Context

categories

• [category|SW 3|Information processing] → [category|SW 3.3|Protein synthesis, modification and degradation] → [category|SW 3.3.1|Translation] → [category|SW 3.3.1.8|tRNA modification and maturation]

Gene

Coordinates: 87,634 → 88,635

The protein

Catalyzed reaction/ biological activity

• 5,6-dihydrouridine in tRNA + NAD⁺ --> uridine in tRNA + H⁺ + NADH (according to UniProt)
• 5,6-dihydrouridine in tRNA + NADP⁺ --> uridine in tRNA + H⁺ + NADPH

Protein family

• Dus family (with [protein|B1C2BD8CEEABF9BBAE2646E8E24457A485097CFC|YfjN], according to UniProt)

Paralogous protein(s)

• [protein|B1C2BD8CEEABF9BBAE2646E8E24457A485097CFC|YfjN]

[SW|Cofactors]

• FMN or FAD [Pubmed|21635694]

Structure

• [PDB|1VHN] (from ''Thermotoga maritima'', 35% identity, 54% similarity) [Pubmed|15103641]

Expression and Regulation

Operons

• genes: [gene|B189AD3E3D18876E1956763182D835A151727392|pabB]-[gene|956E33AAAADB302EB8663E4B75C917242D3AD2C0|pabA]-[gene|865678B10097C40337F5EEA77FF0F6E7BF5358DC|pabC]-[gene|FA9539CB701BC47FD4E849FBA6D7B201B27C6104|sul]-[gene|AAE44B4F73C7C02F7DB3574B6169E0DE46F4B787|folB]-[gene|D2B189C6292ACE1B25658B407C284E9A683EAE5B|folK]-[gene|F373EBC35805DC551E8AFF6FDC7E43D5587C4700|yazB]-[gene|CE45D56BC413555AF4E7914B5307AD967A358452|yacF]-[gene|24CC89DE55B3C19F80B11D106B9FD241174AE3E4|lysS]
  description: [Pubmed|9084182]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|9084182], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]

  regulation

  • translation repressed by tryptophan ([protein|E030E80134E9DED6ADBC73C7C7435024CDFD38B9|MtrB]) [Pubmed|9084182]

additional information

• the mRNA is very stable (> 15 min) [pubmed|12884008]

Biological materials

Mutant

• MGNA-B927 (yacF::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/1926 NBRP B. subtilis, Japan]
• BKE00810 (Δ[gene|CE45D56BC413555AF4E7914B5307AD967A358452|yacF]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE00810 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CAATTTTTCTCCTCCTTTCA, downstream forward: _UP4_TAATACTCACCTCTATTTGC
• BKK00810 (Δ[gene|CE45D56BC413555AF4E7914B5307AD967A358452|yacF]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK00810 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CAATTTTTCTCCTCCTTTCA, downstream forward: _UP4_TAATACTCACCTCTATTTGC

References

• 12884008,9084182,25902496