Bacimethrin
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| Category | Antibiotics |
| Catalog number | BBF-00249 |
| CAS | 3690-12-8 |
| Molecular Weight | 155.15 |
| Molecular Formula | C6H9N3O2 |
| Purity | ≥98% |
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Description
Bacimethrin is produced by the strain of Bacillus megatheriumy and Streptomyces albus. It has anti-fungal and gram-positive bacteria, negative bacteria activity, and vitamin B1 and B6 can reduce its activity.
Specification
| Synonyms | 4-amino-2-methoxy-5-pyrimidinemethanol; 5-pyrimidinemethanol, 4-amino-2-methoxy- |
| IUPAC Name | (4-amino-2-methoxypyrimidin-5-yl)methanol |
| Canonical SMILES | COC1=NC=C(C(=N1)N)CO |
| InChI | InChI=1S/C6H9N3O2/c1-11-6-8-2-4(3-10)5(7)9-6/h2,10H,3H2,1H3,(H2,7,8,9) |
| InChI Key | ZPNHGSNYBLXGOL-UHFFFAOYSA-N |
Properties
| Appearance | White Acicular Crystalline |
| Antibiotic Activity Spectrum | gram-positive bacterial; gram-negative bacteria; fungi |
| Melting Point | 174 °C |
| Density | 1.337 g/cm3 |
| Solubility | Soluble in water, methanol, glacial acetic acid. |
Reference Reading
1. Competence of Thiamin Diphosphate-Dependent Enzymes with 2'-Methoxythiamin Diphosphate Derived from Bacimethrin, a Naturally Occurring Thiamin Anti-vitamin
Natalia S Nemeria, Brateen Shome, Alicia A DeColli, Kathryn Heflin, Tadhg P Begley, Caren Freel Meyers, Frank Jordan Biochemistry. 2016 Feb 23;55(7):1135-48. doi: 10.1021/acs.biochem.5b01300. Epub 2016 Feb 8.
Bacimethrin (4-amino-5-hydroxymethyl-2-methoxypyrimidine), a natural product isolated from some bacteria, has been implicated as an inhibitor of bacterial and yeast growth, as well as in inhibition of thiamin biosynthesis. Given that thiamin biosynthetic enzymes could convert bacimethrin to 2'-methoxythiamin diphosphate (MeOThDP), it is important to evaluate the effect of this coenzyme analogue on thiamin diphosphate (ThDP)-dependent enzymes. The potential functions of MeOThDP were explored on five ThDP-dependent enzymes: the human and Escherichia coli pyruvate dehydrogenase complexes (PDHc-h and PDHc-ec, respectively), the E. coli 1-deoxy-D-xylulose 5-phosphate synthase (DXPS), and the human and E. coli 2-oxoglutarate dehydrogenase complexes (OGDHc-h and OGDHc-ec, respectively). Using several mechanistic tools (fluorescence, circular dichroism, kinetics, and mass spectrometry), it was demonstrated that MeOThDP binds in the active centers of ThDP-dependent enzymes, however, with a binding mode different from that of ThDP. While modest activities resulted from addition of MeOThDP to E. coli PDHc (6-11%) and DXPS (9-14%), suggesting that MeOThDP-derived covalent intermediates are converted to the corresponding products (albeit with rates slower than that with ThDP), remarkably strong activity (up to 75%) resulted upon addition of the coenzyme analogue to PDHc-h. With PDHc-ec and PDHc-h, the coenzyme analogue could support all reactions, including communication between components in the complex. No functional substitution of MeOThDP for ThDP was in evidence with either OGDH-h or OGDH-ec, shown to be due to tight binding of ThDP.
2. A strictly monofunctional bacterial hydroxymethylpyrimidine phosphate kinase precludes damaging errors in thiamin biosynthesis
Antje M Thamm, Gengnan Li, Marlene Taja-Moreno, Svetlana Y Gerdes, Valérie de Crécy-Lagard, Steven D Bruner, Andrew D Hanson Biochem J. 2017;474(16):2887-2895. doi: 10.1042/BCJ20170437. Epub 2017 Jul 20.
The canonical kinase (ThiD) that converts the thiamin biosynthesis intermediate hydroxymethylpyrimidine (HMP) monophosphate to the diphosphate can also very efficiently convert free HMP to the monophosphate in prokaryotes, plants, and fungi. This HMP kinase activity enables salvage of HMP, but it is not substrate-specific and so allows toxic HMP analogs and damage products to infiltrate the thiamin biosynthesis pathway. Comparative analysis of bacterial genomes uncovered a gene, thiD2 , that is often fused to the thiamin synthesis gene thiE and could potentially encode a replacement for ThiD. Standalone ThiD2 proteins and ThiD2 fusion domains are small (~130-residues) and do not belong to any previously known protein family. Genetic and biochemical analyses showed that representative standalone and fused ThiD2 proteins catalyze phosphorylation of HMP monophosphate, but not of HMP or its toxic analogs and damage products such as bacimethrin and 5-(hydroxymethyl)-2-methylpyrimidin-4-ol. As strictly monofunctional HMP monophosphate kinases, ThiD2 proteins eliminate a potentially fatal vulnerability of canonical ThiD, at the cost of the ability to reclaim HMP formed by thiamin turnover.
3. Structure of the N-glycosidase MilB in complex with hydroxymethyl CMP reveals its Arg23 specifically recognizes the substrate and controls its entry
Gong Zhao, Geng Wu, Yan Zhang, Guang Liu, Tiesheng Han, Zixin Deng, Xinyi He Nucleic Acids Res. 2014 Jul;42(12):8115-24. doi: 10.1093/nar/gku486. Epub 2014 Jun 11.
5-Hydroxymethylcytosine (5hmC) is present in T-even phage and mammalian DNA as well as some nucleoside antibiotics, including mildiomycin and bacimethrin, during whose synthesis 5hmC is produced by the hydrolysis of 5-hydroxymethyl cytidine 5'-monophosphate (hmCMP) by an N-glycosidase MilB. Recently, the MilB-CMP complex structure revealed its substrate specificity for CMP over dCMP. However, hmCMP instead of CMP is the preferred substrate for MilB as supported by that its KM for CMP is ~27-fold higher than that for hmCMP. Here, we determined the crystal structures of MilB and its catalytically inactive E103A mutant in complex with hmCMP. In the structure of the complex, Phe22 and Arg23 are positioned in a cage-like active site resembling the binding pocket for the flipped 5-methylcytosine (5mC) in eukaryotic 5mC-binding proteins. Van der Waals interaction between the benzene ring of Phe22 and the pyrimidine ring of hmCMP stabilizes its binding. Remarkably, upon hmCMP binding, the guanidinium group of Arg23 was bent ~65° toward hmCMP to recognize its 5-hydroxymethyl group, inducing semi-closure of the cage-like pocket. Mutagenesis studies of Arg23 and bioinformatics analysis demonstrate that the positively charged Arg/Lys at this site is critical for the specific recognition of the 5-hydroxymethyl group of hmCMP.
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Bio Calculators
* Our calculator is based on the following equation:
Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C1V1 = C2V2
* Total Molecular Weight:
g/mol
Tip: Chemical formula is case sensitive. C22H30N4O √ c22h30n40 ╳
