thdF
168
GTP-binding protein, part of 5-carboxymethylaminomethyluridine-tRNA synthase complex (with [protein|7809B4F5B9172EBB6C91BDE7B673FB08E82763FF|gidA]), synthesis of mnm5s2U at the Wobble base position (U34) in tRNAs
locus
BSU_41020
Molecular weight
50.81 kDa
pI
4.64
function
tRNA modification
product
part of 5-carboxymethylaminomethyluridine-tRNA synthase complex (with [protein|7809B4F5B9172EBB6C91BDE7B673FB08E82763FF|gidA])
essential
no
synonyms
thdF, mnmE, trmE
Outlinks
Genomic Context
Categories containing this gene/protein
List of homologs in different organisms, belongs to COG0486 (Galperin et al., 2021)
This gene is a member of the following regulons
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]
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The protein
Catalyzed reaction/ biological activity
Binds and hydrolyzes GTP and readily exchanges GDP for GTP
(s2U34 in tRNA) + GTP + FAD + CH2-THF + NADH --> 5-carboxymethylaminomethyl-2- thiouridine [pubmed|36181794,38050996]
Protein family
[wiki|TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily] (according to UniProt)
[wiki|Domains]
TrmE-type G domain (aa 221-380) (according to UniProt)
Structure
[PDB|1XZP] (from ''Thermotoga maritima'', 44% identity) [Pubmed|15616586]
[AF|P25811]
Paralogous protein(s)
[protein|84E7D672DB40B114DC4D96A4D8834958B47401A7|obg], [protein|959C0ED7B9DA50F0EADCF1565405B878D36DA206|yqeH], [protein|9F6B78C1932FB56F7F71430DB16BC862A312407B|ynbA], [protein|B2270316642C66BC2DA86EBDCD1BF6A33CC6A1DC|engA], [protein|C0F5FAD6DF89DA9E0FFC8F888D7CED6AA42D9C73|yyaF], [protein|CB68B3393CA7862C45C624AF7B1ADD188243A01F|era], [protein|DF1A043F3D9817D9479B8C707F4ACEEF2BF2862C|ysxC], [protein|54CD247926F7FABE4ACE85EB7021B62500B47260|rbgA]
[wiki|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]
regulation
constitutively expressed [Pubmed|23701187]
regulatory mechanism
[protein|08CFA2C72931A75532D4289BC1D18A826DE9F9CA|comK]: activation, [Pubmed|11948146], in [regulon|protein:08CFA2C72931A75532D4289BC1D18A826DE9F9CA|comK regulon]
[protein|6740108089F13116F200C15F35C2E7561E990FEB|dnaA]: repression, [Pubmed|26020636], in [regulon|protein:6740108089F13116F200C15F35C2E7561E990FEB|dnaA regulon]
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 ([gene|66A6EC4F6CB91EE741BB9D7646913FF3EE602BD7|thdF]::erm trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKE41020 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATGTTGTTCACCTCTCTTT, downstream forward: _UP4_TAATTAAAGGAGGAACTAGA
BKK41020 ([gene|66A6EC4F6CB91EE741BB9D7646913FF3EE602BD7|thdF]::kan trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKK41020 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATGTTGTTCACCTCTCTTT, downstream forward: _UP4_TAATTAAAGGAGGAACTAGA
labs
[wiki|Naotake Ogasawara], Nara, Japan
References
Reviews
Original Publications
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Time of last update: 2024-04-19 18:42:42
Author of last update: Jstuelk