Cloned (Comment) | Organism |
---|---|
gene trm5a, recombinant expression of wild-type and mutant enzymes | Pyrococcus abyssi |
Crystallization (Comment) | Organism |
---|---|
purified recombinant apo-PaTrm5a and PaTrm5a in complex with tRNAPhe, and PaTrm5a-tRNAPhe (imG-14)-SAH ternary complex, X-ray diffraction structure determination and analysis | Pyrococcus abyssi |
Protein Variants | Comment | Organism |
---|---|---|
D243A | site-directed mutagenesis, substrate binding compared to wild-type enzyme | Pyrococcus abyssi |
E213A | site-directed mutagenesis, substrate binding compared to wild-type enzyme | Pyrococcus abyssi |
H128A | site-directed mutagenesis, substrate binding compared to wild-type enzyme | Pyrococcus abyssi |
R133A | site-directed mutagenesis, substrate binding compared to wild-type enzyme | Pyrococcus abyssi |
R135A | site-directed mutagenesis, substrate binding compared to wild-type enzyme | Pyrococcus abyssi |
R174A | site-directed mutagenesis, substrate binding compared to wild-type enzyme | Pyrococcus abyssi |
Y318A | site-directed mutagenesis, substrate binding compared to wild-type enzyme | Pyrococcus abyssi |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Mg2+ | required | Pyrococcus abyssi |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
additional information | Pyrococcus abyssi | bifunctional Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4 demethylwyosine at position 37 to produce isowyosine (EC 2.1.1.228 and EC 2.1.1.282, respectively) | ? | - |
- |
|
S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe | Pyrococcus abyssi | - |
S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Pyrococcus abyssi | Q9V2G1 | - |
- |
Purification (Comment) | Organism |
---|---|
recombinant wild-type and mutant enzymes | Pyrococcus abyssi |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
additional information | bifunctional Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4 demethylwyosine at position 37 to produce isowyosine (EC 2.1.1.228 and EC 2.1.1.282, respectively) | Pyrococcus abyssi | ? | - |
- |
|
additional information | structural basis for substrate recognition, the D1 domain of the enzyme undergoes large conformational changes upon the binding of tRNA., the enzyme recognizes the overall shape of tRNA. PaTrm5a adopts distinct open conformations before and after the binding of tRNA. Enzyme-substrate interactions in the catalytic domain. The anticodon interactions mostly concentrate on the A36-G37-A38 triplet. Proposed reaction mechanism of Trm5a with modified yeast tRNAPhe, overview | Pyrococcus abyssi | ? | - |
- |
|
S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe | - |
Pyrococcus abyssi | S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe | - |
? | |
S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe | imG-14 | Pyrococcus abyssi | S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe | - |
? |
Subunits | Comment | Organism |
---|---|---|
More | substrate interactions with the catalytic region in the PaTrm5a-tRNAPhe-(imG-14)-SAH ternary complex, overview. In the model, imG-14 is flipped into a hydrophobic pocket formed by Phe165, Phe284, Tyr318, Met170, Tyr197, and the 260PTPK263 fragment | Pyrococcus abyssi |
Synonyms | Comment | Organism |
---|---|---|
More | see also EC 2.1.1.228 | Pyrococcus abyssi |
PaTrm5a | - |
Pyrococcus abyssi |
TAW22 | - |
Pyrococcus abyssi |
Trm5a | - |
Pyrococcus abyssi |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
37 | - |
assay at | Pyrococcus abyssi |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
8 | - |
assay at | Pyrococcus abyssi |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
S-adenosyl-L-methionine | - |
Pyrococcus abyssi |
General Information | Comment | Organism |
---|---|---|
malfunction | deletion of the D1 domain greatly reduces the affinity and activity of PaTrm5a toward its RNA substrate | Pyrococcus abyssi |
additional information | structure comparison of the Pyrococcus abyssii Trm5a enzyme structure (PDB ID 5WT1) with the structure of its orthologue Trm5b (MjTrm5b, PDB IDs 2YX1 and 3AY0) from Methanococcus jannaschii, overview | Pyrococcus abyssi |
physiological function | the methyltransferase Trm5a from Pyrococcus abyssi (PaTrm5a) plays a key role in this hypermodification process in generating m1G37 (EC 2.1.1.228) and imG2 (EC 2.1.1.282), two products of the wyosine biosynthetic pathway, through two methyl transfers to distinct substrates | Pyrococcus abyssi |