thdF [2018-02-11T23:32:32.000Z]

GTP-binding protein, putative tRNA modification GTPase

locus: BSU41020

pI: 4.64

mw: 50.81 kDa

protein length: 459 aa

gene length: 1377 bp

function: tRNA modification

product: putative tRNA modification GTPase

essential: no

synonyms: mnmE,trmE

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]
• [category|SW 6|Groups of genes] → [category|SW 6.3|GTP-binding proteins]

Gene

Coordinates: 4,211,510 → 4,212,889

Phenotypes of a mutant

• inactivation of ''[gene|66A6EC4F6CB91EE741BB9D7646913FF3EE602BD7|thdF]'' reduces sporulation efficiency to 21.9% that of wild type cells; longer mother cells, some with aberrant septa and forespores [Pubmed|26735940]

The protein

Catalyzed reaction/ biological activity

• Binds and hydrolyzes GTP and readily exchanges GDP for GTP

Protein family

• MnmE subfamily (according to Swiss-Prot) Era/Obg family

Paralogous protein(s)

• [protein|CB68B3393CA7862C45C624AF7B1ADD188243A01F|Era], [protein|84E7D672DB40B114DC4D96A4D8834958B47401A7|Obg], [protein|B2270316642C66BC2DA86EBDCD1BF6A33CC6A1DC|YphC], [protein|DF1A043F3D9817D9479B8C707F4ACEEF2BF2862C|YsxC], [protein|54CD247926F7FABE4ACE85EB7021B62500B47260|RbgA], [protein|959C0ED7B9DA50F0EADCF1565405B878D36DA206|YqeH], [protein|C0F5FAD6DF89DA9E0FFC8F888D7CED6AA42D9C73|YyaF], [protein|9F6B78C1932FB56F7F71430DB16BC862A312407B|YnbA]

Structure

• [PDB|1XZP] (from ''Thermotoga maritima'', 44% identity) [Pubmed|15616586]

[SW|Localization]

• cytoplasm (according to Swiss-Prot)

Additional information

• Information on the corresponding protein from ''E. coli'': [http://BioCyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=EG10997-MONOMER EcoCyc]
• MnmE required for wild-type 5-methylaminomethyl-2-thiouridine modification of tRNA, interacts with [protein|7809B4F5B9172EBB6C91BDE7B673FB08E82763FF|GidA]. MnmE also appears to play a role in oxidation of thiophene and furan compounds and regulates glutamate-dependent acid resistance.

Expression and Regulation

Operons

• genes: [gene|66A6EC4F6CB91EE741BB9D7646913FF3EE602BD7|thdF]-[gene|7809B4F5B9172EBB6C91BDE7B673FB08E82763FF|gidA]-[gene|CCB7EE1D049585979303148FBDE0D42549E648DE|gidB]-[gene|559DEDC9887B811EF80994526256ADC48BA51CE3|noc]
  description: [Pubmed|11807071]

  regulatory mechanism

  • [protein|08CFA2C72931A75532D4289BC1D18A826DE9F9CA|ComK]: activation, [Pubmed|11948146], in [regulon|08CFA2C72931A75532D4289BC1D18A826DE9F9CA|ComK regulon]
  • [protein|6740108089F13116F200C15F35C2E7561E990FEB|DnaA]: repression, [Pubmed|26020636], in [regulon|6740108089F13116F200C15F35C2E7561E990FEB|DnaA regulon]

  regulation

  • constitutively expressed [Pubmed|23701187]

Biological materials

Mutant

• MGNA-B877 (thdF::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/1876 NBRP B. subtilis, Japan]
• BKE41020 (Δ[gene|66A6EC4F6CB91EE741BB9D7646913FF3EE602BD7|thdF]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE41020 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATGTTGTTCACCTCTCTTT, downstream forward: _UP4_TAATTAAAGGAGGAACTAGA
• BKK41020 (Δ[gene|66A6EC4F6CB91EE741BB9D7646913FF3EE602BD7|thdF]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK41020 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATGTTGTTCACCTCTCTTT, downstream forward: _UP4_TAATTAAAGGAGGAACTAGA

Labs working on this gene/protein

• [SW|Naotake Ogasawara], Nara, Japan

References

Reviews

• 21885683

Original publications

• 12427945,11807071,11948146,23630314,26020636,15616586,26735940