RNA Polymerase II Transcription

Bernecky C, Herzog F, Baumeister W, Plitzko JM, Cramer P. Structure of transcribing mammalian RNA polymerase II. Nature. 2016 Jan 28;529(7587):551–4. doi: 10.1038/nature16482. PMID: 26789250.; Cramer P. Structure and function of RNA polymerase II. Adv Protein Chem. 2004;67():1–42. doi: 10.1016/s0065-3233(04)67001-x. PMID: 14969722.

Metabolites

CO

Formula: CO (27.994915)

CAS ID: 630-08-0

H+

Formula: H (1.0078246)

CAS ID: 12408-02-5

H2O

Formula: H2O (18.0105642)

CAS ID: 7732-18-5

Hydrogen peroxide

Formula: H2O2 (34.0054792)

CAS ID: 7722-84-1

Nicotinamide

Formula: C6H6N2O (122.0480106)

CAS ID: 98-92-0

Oxygen

Formula: O2 (31.98983)

CAS ID: 7782-44-7

Retinoate

Formula: C20H28O2 (300.2089188)

CAS ID: 302-79-4

Zinc cation

Formula: Zn (63.929145)

CAS ID: 23713-49-7

acetate

Formula: C2H3O2 (59.0133038)

CAS ID: 71-50-1

NADPH(4-)

Formula: C21H26N7O17P3 (741.0598016)

CAS ID: 53-57-6

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:

NADP(3-)

Formula: C21H25N7O17P3 (740.051977)

CAS ID: 53-59-8



Enzyme

EC Number name full name note
1.-.-.-
1.1.1.49 glucose-6-phosphate dehydrogenase (NADP+) D-glucose-6-phosphate:NADP+ 1-oxidoreductase
1.11.1.12 phospholipid-hydroperoxide glutathione peroxidase glutathione:lipid-hydroperoxide oxidoreductase
1.11.1.2 NADPH peroxidase NADPH:hydrogen-peroxide oxidoreductase
1.11.1.24 thioredoxin-dependent peroxiredoxin thioredoxin:hydroperoxide oxidoreductase
1.11.1.9 glutathione peroxidase glutathione:hydrogen-peroxide oxidoreductase
1.14.11.67 [histone H3]-trimethyl-L-lysine4 demethylase [histone H3]-N6,N6,N6-trimethyl-L-lysine4,2-oxoglutarate:oxygen oxidoreductase
1.3.1.70 DELTA14-sterol reductase 4,4-dimethyl-5alpha-cholesta-8,24-dien-3beta-ol:NADP+ DELTA14-oxidoreductase
1.8.1.7 glutathione-disulfide reductase glutathione:NADP+ oxidoreductase
1.8.1.9 thioredoxin-disulfide reductase thioredoxin:NADP+ oxidoreductase
2.1.1.319 type I protein arginine methyltransferase S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-Nomega,Nomega-dimethyl-L-arginine-forming)
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)
2.1.1.354 [histone H3]-lysine4 N-trimethyltransferase S-adenosyl-L-methionine:[histone H3]-L-lysine4 N6-methyltransferase
2.1.1.356 [histone H3]-lysine27 N-trimethyltransferase S-adenosyl-L-methionine:[histone H3]-L-lysine27 N6-methyltransferase
2.1.1.361 [histone H4]-lysine20 N-methyltransferase S-adenosyl-L-methionine:[histone H4]-L-lysine20 N6-methyltransferase
2.1.1.364 [histone H3]-lysine4 N-methyltransferase S-adenosyl-L-methionine:[histone H3]-L-lysine4 N6-methyltransferase
2.1.1.367 [histone H3]-lysine9 N-methyltransferase S-adenosyl-L-methionine:[histone H3]-L-lysine9 N6-methyltransferase
2.1.1.56 mRNA (guanine-N7)-methyltransferase S-adenosyl-L-methionine:mRNA (guanine-N7)-methyltransferase
2.3.1.48 histone acetyltransferase acetyl-CoA:[protein]-L-lysine acetyltransferase
2.3.1.57 diamine N-acetyltransferase acetyl-CoA:alkane-alpha,omega-diamine N-acetyltransferase
2.3.2.26 HECT-type E3 ubiquitin transferase [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (isopeptide bond-forming)
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)
2.3.2.32 cullin-RING-type E3 NEDD8 transferase [E2 NEDD8-conjugating enzyme]-S-[NEDD8-protein]-yl-L-cysteine:[cullin] [NEDD8-protein] transferase (isopeptide bond-forming; RING-type)
2.3.2.36 RING-type E3 ubiquitin transferase (cysteine targeting) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (thioester bond-froming; RING-type)
2.4.2.30 NAD+ ADP-ribosyltransferase NAD+:poly(ADP-D-ribosyl)-acceptor ADP-D-ribosyl-transferase
2.5.1.60 protein geranylgeranyltransferase type II geranylgeranyl-diphosphate:protein-cysteine geranyltransferase
2.7.1.149 1-phosphatidylinositol-5-phosphate 4-kinase ATP:1-phosphatidyl-1D-myo-inositol-5-phosphate 4-phosphotransferase
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)
2.7.11.21 polo kinase ATP:protein phosphotransferase (spindle-pole-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
2.7.11.24 mitogen-activated protein kinase ATP:protein phosphotransferase (MAPKK-activated)
2.7.12.1 dual-specificity kinase ATP:protein phosphotransferase (Ser/Thr- and Tyr-phosphorylating)
2.7.12.2 mitogen-activated protein kinase kinase ATP:protein phosphotransferase (MAPKKK-activated)
2.7.7.19 polynucleotide adenylyltransferase ATP:polynucleotide adenylyltransferase
2.7.7.48 RNA-directed RNA polymerase nucleoside-triphosphate:RNA nucleotidyltransferase (RNA-directed)
2.7.7.50 mRNA guanylyltransferase GTP:mRNA guanylyltransferase
2.7.7.6 DNA-directed RNA polymerase nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed)
3.1.3.16 protein-serine/threonine phosphatase protein-serine/threonine-phosphate phosphohydrolase
3.1.3.46 fructose-2,6-bisphosphate 2-phosphatase beta-D-fructose-2,6-bisphosphate 2-phosphohydrolase
3.1.3.48 protein-tyrosine-phosphatase protein-tyrosine-phosphate phosphohydrolase
3.1.3.78 phosphatidylinositol-4,5-bisphosphate 4-phosphatase 1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate 4-phosphohydrolase
3.4.19.12 ubiquitinyl hydrolase 1
3.4.21.75 Furin
3.4.22.15 cathepsin L
3.4.22.38 cathepsin K
3.4.22.55 caspase-2
3.5.1.2 glutaminase L-glutamine amidohydrolase
3.5.1.98 histone deacetylase histone amidohydrolase
3.6.1.74 mRNA 5'-phosphatase 5'-triphospho-mRNA 5'-phosphohydrolase
5.2.1.8 peptidylprolyl isomerase Peptidylproline cis-trans-isomerase
5.3.1.9 glucose-6-phosphate isomerase alpha-D-glucose-6-phosphate aldose-ketose-isomerase (configuration-inverting)
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)


Proteins

Protein ID name full name