tRNA modification in the nucleus and cytosol

Hou YM, Gamper H, Yang W. Post-transcriptional modifications to tRNA--a response to the genetic code degeneracy. RNA. 2015 Apr;21(4):642–4. PMID: 25780173; PMCID: PMC4371315.; Sarin LP, Leidel SA. Modify or die? - RNA modification defects in metazoans. RNA Biology. 2014 Dec 02;11(12):1555–67. doi: 10.4161/15476286.2014.992279.; Gu C, Begley TJ, Dedon PC. tRNA modifications regulate translation during cellular stress. FEBS Letters. 2014 Oct 07;588(23):4287–96. doi: 10.1016/j.febslet.2014.09.038.; Li S, Mason CE. The pivotal regulatory landscape of RNA modifications. Annu Rev Genomics Hum Genet. 2014;15():127–50. doi: 10.1146/annurev-genom-090413-025405. PMID: 24898039.; Torres AG, Batlle E, Ribas de Pouplana L. Role of tRNA modifications in human diseases. Trends Mol Med. 2014 Jun;20(6):306–14. doi: 10.1016/j.molmed.2014.01.008. PMID: 24581449.; Helm M, Alfonzo J. Posttranscriptional RNA Modifications: Playing Metabolic Games in a Cell’s Chemical Legoland. Chemistry & Biology. 2014 Feb;21(2):174–85. doi: 10.1016/j.chembiol.2013.10.015.; Boschi-Muller S, Motorin Y. Chemistry enters nucleic acids biology: enzymatic mechanisms of RNA modification. Biochemistry (Mosc). 2013 Dec;78(13):1392–404. doi: 10.1134/s0006297913130026. PMID: 24490730.; Jackman JE, Alfonzo JD. Transfer RNA modifications: nature's combinatorial chemistry playground. Wiley Interdiscip Rev RNA. 2013 Jan;4(1):35–48. PMID: 23139145; PMCID: PMC3680101.

Metabolites

5'-Deoxyadenosine

Formula: C10H13N5O3 (251.10183480000003)

CAS ID: 4754-39-6

5'-Methylthioadenosine

Formula: C11H15N5O3S (297.089556)

CAS ID: 2457-80-9

Ammonia

Formula: NH3 (17.0265478)

CAS ID: 7664-41-7

CO2

Formula: CO2 (43.98983)

CAS ID: 124-38-9

Fe2+

Formula: Fe (55.934939)

CAS ID: 15438-31-0

H2O

Formula: H2O (18.0105642)

CAS ID: 7732-18-5

L-Threonylcarbamoyladenylate

Formula: C15H21N6O11P (492.1005886)

CAS ID:

Oxygen

Formula: O2 (31.98983)

CAS ID: 7782-44-7

2-oxoglutarate(2-)

Formula: C5H4O5 (144.00587339999998)

CAS ID: 64-15-3

succinate(2-)

Formula: C4H4O4 (116.01095839999999)

CAS ID: 56-14-4

pyruvate

Formula: C3H3O3 (87.00821880000001)

CAS ID: 57-60-3

adenosine 5'-monophosphate(2-)

Formula: C10H12N5O7P (345.0474332)

CAS ID:

ATP(4-)

Formula: C10H12N5O13P3 (502.9644492)

CAS ID:

GTP(4-)

Formula: C10H12N5O14P3 (518.9593642)

CAS ID: 86527-72-2



Enzyme

EC Number name full name note
2.1.1.-
1.14.11.42 tRNAPhe (7-(3-amino-3-carboxypropyl)wyosine37-C2)-hydroxylase tRNAPhe 7-(3-amino-3-carboxypropyl)wyosine37,2-oxoglutarate:oxygen oxidoreductase (2-hydroxylating)
1.3.1.91 tRNA-dihydrouridine20 synthase [NAD(P)+] tRNA-5,6-dihydrouracil20:NAD(P)+ oxidoreductase
2.1.1.203 tRNA (cytosine34-C5)-methyltransferase S-adenosyl-L-methionine:tRNA (cytosine34-C5)-methyltransferase
2.1.1.204 tRNA (cytosine38-C5)-methyltransferase S-adenosyl-L-methionine:tRNA (cytosine38-C5)-methyltransferase
2.1.1.205 tRNA (cytidine32/guanosine34-2'-O)-methyltransferase S-adenosyl-L-methionine:tRNA (cytidine32/guanosine34-2'-O)-methyltransferase
2.1.1.211 tRNASer (uridine44-2'-O)-methyltransferase S-adenosyl-L-methionine:tRNASer (uridine44-2'-O)-methyltransferase
2.1.1.214 tRNA (guanine10-N2)-methyltransferase S-adenosyl-L-methionine:tRNA (guanine10-N2)-methyltransferase
2.1.1.216 tRNA (guanine26-N2)-dimethyltransferase S-adenosyl-L-methionine:tRNA (guanine26-N2)-dimethyltransferase
2.1.1.220 tRNA (adenine58-N1)-methyltransferase S-adenosyl-L-methionine:tRNA (adenine58-N1)-methyltransferase
2.1.1.221 tRNA (guanine9-N1)-methyltransferase S-adenosyl-L-methionine:tRNA (guanine9-N1)-methyltransferase
2.1.1.225 tRNA:m4X modification enzyme S-adenosyl-L-methionine:tRNAPro/His/Gly(GCC) (cytidine/adenosine4-2'-O)-methyltransferase
2.1.1.228 tRNA (guanine37-N1)-methyltransferase S-adenosyl-L-methionine:tRNA (guanine37-N1)-methyltransferase
2.1.1.229 tRNA (carboxymethyluridine34-5-O)-methyltransferase S-adenosyl-L-methionine:tRNA (carboxymethyluridine34-5-O)-methyltransferase
2.1.1.282 tRNAPhe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase S-adenosyl-L-methionine:tRNAPhe 7-[(3S)-(3-amino-3-carboxypropyl)-4-demethylwyosine-N4]-methyltransferase
2.1.1.290 tRNAPhe [7-(3-amino-3-carboxypropyl)wyosine37-O]-methyltransferase S-adenosyl-L-methionine:tRNAPhe {7-[(3S)-3-amino-3-carboxypropyl]wyosine37-O}-methyltransferase
2.1.1.33 tRNA (guanine46-N7)-methyltransferase S-adenosyl-L-methionine:tRNA (guanine-N7-)-methyltransferase
2.3.1.231 tRNAPhe {7-[3-amino-3-(methoxycarbonyl)propyl]wyosine37-N}-methoxycarbonyltransferase S-adenosyl-L-methionine:tRNAPhe {7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine37-N}-methyltransferase (carbon dioxide-adding)
2.3.1.234 N6-L-threonylcarbamoyladenine synthase L-threonylcarbamoyladenylate:adenine37 in tRNA N6-L-threonylcarbamoyltransferase
2.4.2.64 tRNA-guanosine34 queuine transglycosylase tRNA-guanosine34:queuine tRNA-D-ribosyltransferase
2.5.1.114 tRNAPhe (4-demethylwyosine37-C7) aminocarboxypropyltransferase S-adenosyl-L-methionine:tRNAPhe (4-demethylwyosine37-C7) [(3S)-3-amino-3-carboxypropyl]transferase
2.5.1.75 tRNA dimethylallyltransferase prenyl-diphosphate:adenine37 in tRNA prenyltransferase
2.7.11.1 non-specific serine/threonine protein kinase ATP:protein phosphotransferase (non-specific)
2.7.7.79 tRNAHis guanylyltransferase p-tRNAHis:GTP guanylyltransferase (ATP-hydrolysing)
2.8.4.5 tRNA (N6-L-threonylcarbamoyladenosine37-C2)-methylthiotransferase tRNA (N6-L-threonylcarbamoyladenosine37):sulfur-(sulfur carrier),S-adenosyl-L-methionine C2-methylthiotransferase
3.5.4.33 tRNA(adenine34) deaminase tRNA(adenine34) aminohydrolase
3.5.4.34 tRNAAla(adenine37) deaminase tRNAAla(adenine37) aminohydrolase
4.1.3.44 tRNA 4-demethylwyosine synthase (AdoMet-dependent) tRNAPhe N1-methylguanine,pyruvate acetaldehyde-lyase (tRNAPhe 4-demethylwyosine-forming, decarboxylating, dehydrating)
5.4.99.45 tRNA pseudouridine38/39 synthase tRNA-uridine38/39 uracil mutase
6.1.1.15 proline-tRNA ligase L-proline:tRNAPro ligase (AMP-forming)
6.1.1.17 glutamate-tRNA ligase L-glutamate:tRNAGlu ligase (AMP-forming)


Proteins

Protein ID name full name