Metabolism of RNA

Hocine S, Singer RH, Grunwald D. RNA Processing and Export. Cold Spring Harbor Perspectives in Biology. 2010 Oct 20;2(12):a000752. doi: 10.1101/cshperspect.a000752.

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

Magnesium cation

Formula: Mg (23.98505)

CAS ID: 22537-22-0

N7-Methylguanosine

Formula: C11H16N5O5 (298.1151386)

CAS ID: 20244-86-4

Oxygen

Formula: O2 (31.98983)

CAS ID: 7782-44-7

Zinc cation

Formula: Zn (63.929145)

CAS ID: 23713-49-7

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

ATP(4-)

Formula: C10H12N5O13P3 (502.9644492)

CAS ID:

GTP(4-)

Formula: C10H12N5O14P3 (518.9593642)

CAS ID: 86527-72-2

NAD(1-)

Formula: C21H26N7O14P2 (662.1012936000001)

CAS ID: 53-84-9

ADP(3-)

Formula: C10H12N5O10P2 (424.0059412)

CAS ID:



Enzyme

EC Number name full name note
2.1.1.-
1.1.1.159 7alpha-hydroxysteroid dehydrogenase 7alpha-hydroxysteroid:NAD+ 7-oxidoreductase
1.1.1.178 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (2S,3S)-3-hydroxy-2-methylbutanoyl-CoA:NAD+ oxidoreductase
1.1.1.239 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) 3alpha(or 17beta)-hydroxysteroid:NAD+ oxidoreductase
1.1.1.35 3-hydroxyacyl-CoA dehydrogenase (S)-3-hydroxyacyl-CoA:NAD+ oxidoreductase
1.1.1.53 3alpha(or 20beta)-hydroxysteroid dehydrogenase 3alpha(or 20beta)-hydroxysteroid:NAD+ oxidoreductase
1.1.1.62 17beta-estradiol 17-dehydrogenase 17beta-estradiol:NAD(P)+ 17-oxidoreductase
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
2.1.1.183 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase S-adenosyl-L-methionine:18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
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
2.1.1.218 tRNA (adenine9-N1)-methyltransferase S-adenosyl-L-methionine:tRNA (adenine9-N1)-methyltransferase
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
2.1.1.320 type II protein arginine methyltransferase S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-Nomega,Nomega'-dimethyl-L-arginine-forming)
2.1.1.33 tRNA (guanine46-N7)-methyltransferase S-adenosyl-L-methionine:tRNA (guanine-N7-)-methyltransferase
2.1.1.348 mRNA m6A methyltransferase S-adenosyl-L-methionine:adenine in mRNA methyltransferase
2.1.1.56 mRNA (guanine-N7)-methyltransferase S-adenosyl-L-methionine:mRNA (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
2.3.2.27 RING-type E3 ubiquitin transferase [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (isopeptide bond-forming; RING-type)
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
2.5.1.157 rRNA small subunit aminocarboxypropyltransferase S-adenosyl-L-methionine:rRNA N1-methylpseudouridine 3-[(3S)-3-amino-3-carboxypropyl]transferase
2.5.1.75 tRNA dimethylallyltransferase prenyl-diphosphate:adenine37 in tRNA prenyltransferase
2.7.1.78 polynucleotide 5'-hydroxyl-kinase ATP:5'-dephosphopolynucleotide 5'-phosphotransferase
2.7.10.2 non-specific protein-tyrosine kinase ATP:[protein]-L-tyrosine O-phosphotransferase (non-specific)
2.7.11.1 non-specific serine/threonine protein kinase ATP:protein phosphotransferase (non-specific)
2.7.11.13 protein kinase C ATP:protein phosphotransferase (diacylglycerol-dependent)
2.7.11.22 cyclin-dependent kinase ATP:cyclin phosphotransferase
2.7.11.23 [RNA-polymerase]-subunit kinase ATP:[DNA-directed RNA polymerase] phosphotransferase
2.7.11.26 tau-protein kinase ATP:[tau-protein] O-phosphotransferase
2.7.7.19 polynucleotide adenylyltransferase ATP:polynucleotide adenylyltransferase
2.7.7.50 mRNA guanylyltransferase GTP:mRNA guanylyltransferase
2.7.7.72 CCA tRNA nucleotidyltransferase CTP,CTP,ATP:tRNA cytidylyl,cytidylyl,adenylyltransferase
2.7.7.79 tRNAHis guanylyltransferase p-tRNAHis:GTP guanylyltransferase (ATP-hydrolysing)
2.7.7.8 polyribonucleotide nucleotidyltransferase polyribonucleotide:phosphate nucleotidyltransferase
2.7.7.87 L-threonylcarbamoyladenylate synthase ATP:L-threonyl,bicarbonate adenylyltransferase
2.8.1.14 tRNA-5-taurinomethyluridine 2-sulfurtransferase [protein]-S-sulfanyl-L-cysteine:tRNA (5-taurinomethyluridine34 2-O)-sulfurtransferase
2.8.4.5 tRNA (N6-L-threonylcarbamoyladenosine37-C2)-methylthiotransferase tRNA (N6-L-threonylcarbamoyladenosine37):sulfur-(sulfur carrier),S-adenosyl-L-methionine C2-methylthiotransferase
3.1.13.1 exoribonuclease II
3.1.13.4 poly(A)-specific ribonuclease
3.1.26.11 tRNase Z
3.1.26.5 ribonuclease P
3.1.3.16 protein-serine/threonine phosphatase protein-serine/threonine-phosphate phosphohydrolase
3.1.3.5 5'-nucleotidase 5'-ribonucleotide phosphohydrolase
3.1.3.91 7-methylguanosine nucleotidase N7-methyl-GMP phosphohydrolase
3.4.19.12 ubiquitinyl hydrolase 1
3.5.4.33 tRNA(adenine34) deaminase tRNA(adenine34) aminohydrolase
3.5.4.34 tRNAAla(adenine37) deaminase tRNAAla(adenine37) aminohydrolase
3.5.4.37 double-stranded RNA adenine deaminase double-stranded RNA(adenine) aminohydrolase
3.6.1.15 nucleoside-triphosphate phosphatase unspecific diphosphate phosphohydrolase
3.6.1.59 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] N7-methylguanosine 5'-phosphate phosphohydrolase
3.6.1.62 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] N7-methylguanosine-5'-diphosphate phosphohydrolase
3.6.1.74 mRNA 5'-phosphatase 5'-triphospho-mRNA 5'-phosphohydrolase
3.6.4.10 non-chaperonin molecular chaperone ATPase ATP phosphohydrolase (polypeptide-polymerizing)
3.6.4.12 DNA helicase
3.6.4.13 RNA helicase
4.1.3.44 tRNA 4-demethylwyosine synthase (AdoMet-dependent) tRNAPhe N1-methylguanine,pyruvate acetaldehyde-lyase (tRNAPhe 4-demethylwyosine-forming, decarboxylating, dehydrating)
4.2.99.18 DNA-(apurinic or apyrimidinic site) lyase DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase
4.6.1.16 tRNA-intron lyase pretRNA lyase (intron-removing; cyclic-2',3'-phosphate-forming)
5.2.1.8 peptidylprolyl isomerase Peptidylproline cis-trans-isomerase
5.4.99.25 tRNA pseudouridine55 synthase tRNA-uridine55 uracil mutase
5.4.99.45 tRNA pseudouridine38/39 synthase tRNA-uridine38/39 uracil mutase
5.6.2.3 DNA 5'-3' helicase DNA 5'-3' helicase (ATP-hydrolysing)
5.6.2.4 DNA 3'-5' helicase DNA 3'-5' helicase (ATP-hydrolysing)
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)
6.5.1.8 3'-phosphate/5'-hydroxy nucleic acid ligase poly(ribonucleotide)-3'-phosphate:5'-hydroxy-poly(ribonucleotide) ligase (GMP-forming)


Proteins

Protein ID name full name