4a3e

X-ray diffraction
3.4Å resolution

RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid and soaked with AMPCPP

Released:
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis of initial RNA polymerase II transcription.
OpenAccess logo EMBO J. 30 4755-63 (2011)
PMID: 22056778

Function and Biology Details

Reactions catalysed:
Hydrolysis of proteins in presence of ATP.
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
Pimeloyl-[acyl-carrier protein] + L-alanine = 8-amino-7-oxononanoate + CO(2) + holo-[acyl-carrier protein]
A 4-O-methyl-D-glucopyranuronate ester + H(2)O = 4-O-methyl-D-glucuronic acid + an alcohol
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH
Sucrose + ((1->6)-alpha-D-glucosyl)(n) = D-fructose + ((1->6)-alpha-D-glucosyl)(n+1)
Succinate semialdehyde + NADP(+) + H(2)O = succinate + NADPH
D-glucose 6-phosphate = D-fructose 6-phosphate
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
D-glyceraldehyde 3-phosphate = glycerone phosphate
L-arabinose = L-ribulose
L-glutamate 5-semialdehyde + NAD(+) + H(2)O = L-glutamate + NADH
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
(1a) dTDP-beta-L-evernosamine + NADPH + O(2) = dTDP-N-hydroxy-beta-L-evernosamine + NADP(+) + H(2)O
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
S-formylglutathione + H(2)O = glutathione + formate
L-carnitine + NAD(P)H + O(2) = (3R)-3-hydroxy-4-oxobutanoate + trimethylamine + NAD(P)(+) + H(2)O
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
L-alanine + 3-oxopropanoate = pyruvate + beta-alanine
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
Betaine aldehyde + NAD(+) + H(2)O = betaine + NADH
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H(2)O
Tetradecanoyl-CoA + an N-terminal-glycyl-[protein] = CoA + an N-terminal-N-tetradecanoylglycyl-[protein]
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
(GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n)-diphosphoundecaprenol + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = (GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n+1)-diphosphoundecaprenol + undecaprenyl diphosphate
ATP + (L-Asp(4-L-Arg))(n) + L-Asp = ADP + phosphate + (L-Asp(4-L-Arg))(n)-L-Asp
(R)-lactate + N-acetyl-D-glucosamine 6-phosphate = N-acetylmuramate 6-phosphate + H(2)O
ATP + kanamycin = ADP + kanamycin 3'-phosphate
A beta-D-glucuronoside + H(2)O = D-glucuronate + an alcohol
Random hydrolysis of (1->4)-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate
Hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans
ATP-dependent breakage, passage and rejoining of double-stranded DNA
8 reduced ferredoxin + 8 H(+) + N(2) + 16 ATP + 16 H(2)O = 8 oxidized ferredoxin + H(2) + 2 NH(3) + 16 ADP + 16 phosphate
Carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Urea + H(2)O = CO(2) + 2 NH(3)
4-phosphonooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + L-glutamate
Prephenate = phenylpyruvate + H(2)O + CO(2)
NTP + H(2)O = NDP + phosphate
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
ATP + 5-formyltetrahydrofolate = ADP + phosphate + 5,10-methenyltetrahydrofolate
(1a) L-glutamine + H(2)O = L-glutamate + NH(4)(+)
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-alpha-D-glucose
RX + glutathione = HX + R-S-glutathione
2-phospho-D-glycerate = 3-phospho-D-glycerate
Random hydrolysis of (1->2)-glucosidic linkages in (1->2)-beta-D-glucans
Acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an N-acetyldiamine
ATP + H(2)O + H(+)(Side 1) + K(+)(Side 2) = ADP + phosphate + H(+)(Side 2) + K(+)(Side 1)
Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO(2)
(1a) acetyl-CoA + [acetyl-CoA C-acetyltransferase]-L-cysteine = [acetyl-CoA C-acetyltransferase]-S-acetyl-L-cysteine + CoA
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
Sucrose + (6)-beta-D-fructofuranosyl-(2->)(n) alpha-D-glucopyranoside = glucose + (6)-beta-D-fructofuranosyl-(2->)(n+1) alpha-D-glucopyranoside
UDP-glucose + D-fructose 6-phosphate = UDP + sucrose 6(F)-phosphate
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
L-aspartate = fumarate + NH(3)
An acyl-[acyl-carrier protein] + NADP(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADPH
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
2-iminobutanoate + H(2)O = 2-oxobutanoate + NH(3)
H(2)CO(3) = CO(2) + H(2)O
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
dUTP + H(2)O = dUMP + diphosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate 
ATP + a protein = ADP + a phosphoprotein
L-lysine = cadaverine + CO(2)
Formate + NAD(+) = CO(2) + NADH
(1a) S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
A beta-lactam + H(2)O = a substituted beta-amino acid
5,6-dihydrouracil + H(2)O = 3-ureidopropanoate
GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H(2)O
L-fuculose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
4-maleylacetoacetate = 4-fumarylacetoacetate
L-aspartate 4-semialdehyde + phosphate + NADP(+) = L-4-aspartyl phosphate + NADPH
L-proline + a quinone = (S)-1-pyrroline-5-carboxylate + a quinol
UDP-glucose + 2 NAD(+) + H(2)O = UDP-glucuronate + 2 NADH
Shikimate + NADP(+) = 3-dehydroshikimate + NADPH
5,10-methenyltetrahydrofolate + H(2)O = 10-formyltetrahydrofolate
ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro)
IMP + H(2)O = inosine + phosphate
A (3R)-3-hydroxyacyl-[acyl-carrier-protein] + UDP-N-acetyl-alpha-D-glucosamine = an [acyl-carrier-protein] + a UDP-3-O-(3-hydroxyacylyl)-N-acetyl-alpha-D-glucosamine
ATP + H(2)O + closed Cl(-) channel = ADP + phosphate + open Cl(-) channel
ATP + H(2)O = ADP + phosphate
L-proline + NAD(P)(+) = 1-pyrroline-5-carboxylate + NAD(P)H
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
5,10-methylenetetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH
Release of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro.
Oligoglycosylglucosyl-(1<->1)-ceramide + H(2)O = ceramide + oligoglycosylglucose
Release of N-terminal proline from a peptide.
Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low.
(S)-2-haloacid + H(2)O = (R)-2-hydroxyacid + halide
O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate
Cleavage of peptide bonds with very broad specificity.
Diphosphate + H(2)O = 2 phosphate
(1a) a nucleoside 5'-triphosphate + H(2)O = a nucleoside 5'-diphosphate + phosphate
Cinnamyl alcohol + NADP(+) = cinnamaldehyde + NADPH
An aliphatic amide = a nitrile + H(2)O
(R)-S-lactoylglutathione = glutathione + methylglyoxal
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
Thioredoxin + ROOH = thioredoxin disulfide + H(2)O + ROH
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
Maltose = alpha,alpha-trehalose
3-deoxy-D-manno-octulosonate 8-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate
2 reduced ferredoxin + NADP(+) + H(+) = 2 oxidized ferredoxin + NADPH
GTP = 3',5'-cyclic GMP + diphosphate
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
3-methyl-2-oxobutanoate + [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine = [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] S-(2-methylpropanoyl)dihydrolipoyllysine + CO(2)
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
(S)-malate = fumarate + H(2)O
S-adenosyl-L-methionine + cytidine(32) in tRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine(32) in tRNA
1D-chiro-inositol + NAD(+) = 2D-2,3,5/4,6-pentahydroxycyclohexanone + NADH
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
Cleaves proteins of the adenovirus and its host cell at two consensus sites: -Yaa-Xaa-Gly-Gly-|-Xaa- and -Yaa-Xaa-Gly-Xaa-|-Gly- (in which Yaa is Met, Ile or Leu, and Xaa is any amino acid).
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = 8 diphosphate + di-trans,octa-cis-undecaprenyl diphosphate
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O
ATP + (L-Asp(4-L-Arg))(n)-L-Asp + L-Arg = ADP + phosphate + (L-Asp(4-L-Arg))(n+1)
Myo-inositol + NAD(+) = 2,4,6/3,5-pentahydroxycyclohexanone + NADH
Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
An aromatic primary alcohol + O(2) = an aromatic aldehyde + H(2)O(2)
5-methyl-5,6,7,8-tetrahydromethanopterin + coenzyme M + 2 Na(+)(In) = 5,6,7,8-tetrahydromethanopterin + 2-(methylsulfanyl)ethane-1-sulfonate + 2 Na(+)(Out)
(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
L-arginine + H(2)O = L-ornithine + urea
S-(hydroxymethyl)glutathione + NAD(P)(+) = S-formylglutathione + NAD(P)H
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
A C(21)-steroid + [reduced NADPH--hemoprotein reductase] + O(2) = a 17-alpha-hydroxy-C(21)-steroid + [oxidized NADPH--hemoprotein reductase] + H(2)O
UDP-alpha-D-glucose = UDP-alpha-D-galactose
L-asparagine + H(2)O = L-aspartate + NH(3)
(1a) (2R,3S)-3-isopropylmalate + NAD(+) = (2S)-2-isopropyl-3-oxosuccinate + NADH
(Ribonucleotide)(n)-2',3'-cyclic phosphate + H(2)O = (ribonucleotide)(n)-2'-phosphate
ATP + biotin + [biotin carboxyl-carrier protein]-L-lysine = AMP + diphosphate + [biotin carboxyl-carrier protein]-N(6)-biotinyl-L-lysine
Similar to that of papain.
Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans
2 H(2)O(2) = O(2) + 2 H(2)O
(R)-mevalonate + CoA + 2 NADP(+) = (S)-3-hydroxy-3-methylglutaryl-CoA + 2 NADPH
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends
UDP-N-acetyl-alpha-D-mannosamine + N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = UDP + N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
(1a) N(6)-(3-methylbut-2-en-1-yl)-adenine(37) in tRNA + sulfur-(sulfur carrier) + S-adenosyl-L-methionine + reduced electron acceptor = N(6)-(3-methylbut-2-en-1-yl)-2-thioadenine(37) in tRNA + (sulfur carrier) + L-methionine + 5'-deoxyadenosine + electron acceptor
Methyl-CoM + CoB = CoM-S-S-CoB + methane
Alpha-D-glucosamine 6-phosphate + H(2)O = D-fructose 6-phosphate + NH(3)
ATP + glycerol = ADP + sn-glycerol 3-phosphate
A pyrimidine nucleoside + H(2)O = D-ribose + a pyrimidine base
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
A 3-beta-hydroxy-Delta(5)-steroid + NAD(+) = a 3-oxo-Delta(5)-steroid + NADH
UDP-N-acetyl-alpha-D-glucosamine = UDP-2-acetamido-2,6-dideoxy-alpha-D-xylo-hex-4-ulose + H(2)O
H(2) + 5,10-methenyltetrahydromethanopterin = H(+) + 5,10-methylenetetrahydromethanopterin
4-coumarate = 4-vinylphenol + CO(2)
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains
17-alpha-hydroxypregnenolone + [reduced NADPH--hemoprotein reductase] + O(2) = 3-beta-hydroxyandrost-5-en-17-one + acetate + [oxidized NADPH--hemoprotein reductase] + H(2)O
Oxalyl-CoA = formyl-CoA + CO(2)
Aceneneuramate = N-acetyl-D-mannosamine + pyruvate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Peptidylproline (omega=180) = peptidylproline (omega=0)
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
N,N-dimethylformamide + H(2)O = dimethylamine + formate
D-glucosyl-N-acylsphingosine + H(2)O = D-glucose + N-acylsphingosine
Formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin
(S)-3-hydroxybutanoyl-CoA + NADP(+) = 3-acetoacetyl-CoA + NADPH
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
D-gluconate + NAD(P)(+) = 5-dehydro-D-gluconate + NAD(P)H
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
2 glutathione + ROOH = glutathione disulfide + H(2)O + ROH
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
Taurine + 2-oxoglutarate + O(2) = sulfite + aminoacetaldehyde + succinate + CO(2)
[Dinitrogen reductase]-N(omega)-alpha-(ADP-D-ribosyl)-L-arginine = ADP-D-ribose + [dinitrogen reductase]-L-arginine
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate
Hg + NADP(+) + H(+) = Hg(2+) + NADPH
ATP + L-asparagine + tRNA(Asn) = AMP + diphosphate + L-asparaginyl-tRNA(Asn)
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Acts on substrates that are at least partially unfolded. The cleavage site P1 residue is normally between a pair of hydrophobic residues, such as Val-|-Val
Endonucleolytic cleavage to 5'-phosphomonoester.
Chloride + O(2) = chlorite
Hydrolysis of Xaa-|-Pro dipeptides. Also acts on aminoacyl-hydroxyproline analogs. No action on Pro-|-Pro.
L-serine + L-homocysteine = L-cystathionine + H(2)O
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
Trypanothione + NADP(+) = trypanothione disulfide + NADPH
CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein]
ATP + UMP = ADP + UDP
5,10-methylenetetrahydrofolate + dUMP + NADPH = dTMP + tetrahydrofolate + NADP(+)
(1a) S-adenosyl-L-methionine + L-histidine = S-adenosyl-L-homocysteine + N(alpha)-methyl-L-histidine
D-ribose 5-phosphate = D-ribulose 5-phosphate
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
A (3R)-3-hydroxyacyl-[acyl-carrier-protein] + a UDP-3-O-((3R)-hydroxyacyl)-alpha-D-glucosamine = a UDP-2-N,3-O-bis((3R)-3-hydroxyacyl)-alpha-D-glucosamine + a holo-[acyl-carrier-protein]
4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate
(+)-trans-carveol + NAD(+) = (+)-(S)-carvone + NADH
O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate
2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O
Orotidine 5'-phosphate = UMP + CO(2)
sn-glycerol 3-phosphate + NAD(P)(+) = glycerone phosphate + NAD(P)H
A monocarboxylic acid amide + H(2)O = a monocarboxylate + NH(3)
(1a) S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N(omega)-methyl-L-arginine
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
L-methionine + thioredoxin disulfide + H(2)O = L-methionine (S)-S-oxide + thioredoxin
A chalcone = a flavanone
(1a) L-methionine = methanethiol + 2-aminobut-2-enoate
ATP + thiamine phosphate = ADP + thiamine diphosphate
A primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L) + 2 H(+)
A primary alcohol + 2 cytochrome c = an aldehyde + 2 reduced cytochrome c + 2 H(+)
D-fructose 6-phosphate + phosphate = acetyl phosphate + D-erythrose 4-phosphate + H(2)O
Alpha-D-glucose = beta-D-glucose
Acetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacetyl-[acyl-carrier-protein] + CoA + CO(2) 
L-ornithine = L-proline + NH(3)
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
(9Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate = (15Z)-12-oxophyto-10,15-dienoate
ATP + D-fructose = ADP + D-fructose 6-phosphate
Chorismate = prephenate
5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2)
Hydrolysis of proteins and small molecule substrates at -Asn-|-Xaa- bonds.
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
(2S)-2-hydroxy-2-methyl-3-oxobutanoate = (3R)-3-hydroxybutan-2-one + CO(2)
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholan-24-oylglycine + H(2)O = 3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholanate + glycine
Maleate = fumarate
7-alpha,12-alpha-dihydroxy-3-oxochol-4-en-24-oyl-CoA = 12-alpha-hydroxy-3-oxochola-4,6-dien-24-oyl-CoA + H(2)O
Cytosine + H(2)O = uracil + NH(3)
Adenosine + H(2)O = inosine + NH(3)
ATP + L-glutamine + tRNA(Gln) = AMP + diphosphate + L-glutaminyl-tRNA(Gln)
NAD(+) + protein-L-arginine = nicotinamide + N(omega)-(ADP-D-ribosyl)-protein-L-arginine
Succinate + a quinone = fumarate + a quinol
ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys)
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Catechol + O(2) = 2-hydroxymuconate-6-semialdehyde
(1a) (2R,3S)-3-isopropylmalate = 2-isopropylmaleate + H(2)O
A phosphate monoester + H(2)O = an alcohol + phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
Triacylglycerol + H(2)O = diacylglycerol + a carboxylate
(2E,6E)-farnesyl diphosphate + H(2)O = (2E,6E)-farnesol + diphosphate
(S)-dihydroorotate + fumarate = orotate + succinate
ATP = 3',5'-cyclic AMP + diphosphate
Cleaves -Ala-|-Ser- and -Ala-|-Ala- bonds in the scaffold protein.
Autocatalytically cleaves itself from the polyprotein of the foot-and-mouth disease virus by hydrolysis of a Lys-|-Gly bond, but then cleaves host cell initiation factor eIF-4G at bonds -Gly-|-Arg- and -Lys-|-Arg-.
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine(34) in tRNA(Leu) = S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine(34) in tRNA(Leu)
Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
CoB + CoM + methanophenazine = CoM-S-S-CoB + dihydromethanophenazine
ATP + H(2)O + K(+)(Side 1) = ADP + phosphate + K(+)(Side 2)
A (Z)-hexadec-9-enoyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = a (Z)-3-oxooctadec-11-enoyl-[acyl-carrier protein] + CO(2) + an [acyl-carrier protein]
A primary alcohol + NAD(+) = an aldehyde + NADH
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
[Molybdopterin-synthase sulfur-carrier protein]-Gly-Gly-AMP + [cysteine desulfurase]-S-sulfanyl-L-cysteine + reduced acceptor = AMP + [molybdopterin-synthase sulfur-carrier protein]-Gly-NH-CH(2)-C(O)SH + [cysteine desulfurase] + oxidized acceptor
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
Protein dithiol + NAD(P)(+) = protein disulfide + NAD(P)H
CO + H(2)O + 2 oxidized ferredoxin = CO(2) + 2 reduced ferredoxin + 2 H(+)
Methylamine + H(2)O + 2 oxidized [amicyanin] = formaldehyde + NH(3) + 2 reduced [amicyanin]
Geranylgeranyl diphosphate = (+)-copalyl diphosphate
A glutathione-S-conjugate + H(2)O = an (L-cysteinylglycine)-S-conjugate + L-glutamate
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
S-methyl-5'-thioadenosine + H(2)O = 5-(methylsulfanyl)-D-ribose + adenine
ATP + AMP = 2 ADP
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(36) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(36)
3-dehydroquinate = 3-dehydroshikimate + H(2)O
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
Produces alpha-D-fructofuranose beta-D-fructofuranose 1,2':2,1'-dianhydride (DFA I) by successively eliminating the diminishing (2->1)-beta-D-fructan (inulin) chain from the terminal D-fructosyl-D-fructosyl disaccharide.
A (3R)-3-hydroxyacyl-[acyl-carrier protein] = a trans-2-enoyl-[acyl-carrier protein] + H(2)O
Eliminative cleavage of alginate to give oligosaccharides with 4-deoxy-alpha-L-erythro-hex-4-enuronosyl groups at their non-reducing ends and beta-D-mannuronate at their reducing end.
Beta-D-ribopyranose = beta-D-ribofuranose
ATP + [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly = diphosphate + [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly-AMP
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
ATP + D-glucose = ADP + D-glucose 6-phosphate
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
(1a) cyanate + HCO(3)(-) + H(+) = carbamate + CO(2)
Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates
Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
ATP + pyruvate = ADP + phosphoenolpyruvate
Hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose
Acetyl-CoA + n malonyl-CoA + 2n NADPH = a long-chain fatty acid + (n+1) CoA + n CO(2) + 2n NADP(+)
Malonyl-CoA + an [acyl-carrier-protein] = CoA + a malonyl-[acyl-carrier-protein]
Acetyl-CoA + [acyl-carrier-protein] = CoA + acetyl-[acyl-carrier-protein]
Glycerone phosphate = methylglyoxal + phosphate
A (5-L-glutamyl)-peptide + an amino acid = a peptide + a 5-L-glutamyl amino acid
2 5-aminolevulinate = porphobilinogen + 2 H(2)O
L-glutamate = D-glutamate
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
ATP + RNA(n) = diphosphate + RNA(n+1)
((1->4)-alpha-D-glucosyl)(n) + phosphate = ((1->4)-alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate
L-aspartate = D-aspartate
An L-amino acid = a D-amino acid
(2E,6E)-farnesyl diphosphate = amorpha-4,11-diene + diphosphate
N(6)-prenyladenine + acceptor + H(2)O = adenine + 3-methylbut-2-enal + reduced acceptor
(1a) L-tyrosine + 1/2 O(2) = L-dopa
dTDP-beta-L-rhamnose + NADP(+) = dTDP-4-dehydro-beta-L-rhamnose + NADPH
ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
(R)-3-hydroxyacyl-CoA + NADP(+) = 3-oxoacyl-CoA + NADPH
S-adenosyl-L-homocysteine + H(2)O = L-homocysteine + adenosine
S-adenosyl-L-methionine + 3-((1-carboxyvinyl)oxy)benzoate + H(2)O = 6-amino-6-deoxyfutalosine + L-methionine + HCO(3)(-)
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
NH(3) + 2 H(2)O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H(+)
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
L-fucopyranose = L-fuculose
Benzoylformate = benzaldehyde + CO(2)
D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
(S)-lactate + NAD(+) = pyruvate + NADH
ATP + L-pyrrolysine + tRNA(Pyl) = AMP + diphosphate + L-pyrrolysyl-tRNA(Pyl)
ATP + propanoyl-CoA + HCO(3)(-) = ADP + phosphate + (S)-methylmalonyl-CoA
NAD(+) + glycine + sulfide = nicotinamide + ADP-5-ethyl-4-methylthiazole-2-carboxylate + 3 H(2)O
ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
H(2) + NAD(+) = H(+) + NADH
H(2) + A = AH(2)
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
ATP + D-ribulose 5-phosphate = ADP + D-ribulose 1,5-bisphosphate
Propane-1,2-diol = propanal + H(2)O
2 glutathione + NADP(+) = glutathione disulfide + NADPH
Urate + O(2) + H(2)O = 5-hydroxyisourate + H(2)O(2)
CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
(R)-10-hydroxystearate = oleate + H(2)O
L-alanine = D-alanine
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 H(2)O
Alpha-maltose 1-phosphate + ((1->4)-alpha-D-glucosyl)(n) = phosphate + ((1->4)-alpha-D-glucosyl)(n+2)
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
NADH + ubiquinone + n Na(+)(Side 1) = NAD(+) + ubiquinol + n Na(+)(Side 2)
D-ribulose 5-phosphate = D-xylulose 5-phosphate
Endohydrolysis of beta-(1->4)-linkages between D-glucosamine residues in a partly acetylated chitosan
AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate
The peptide bond hydrolyzed can be designated -C-|-A-A-X in which C is an S-isoprenylated cysteine residue, A is usually aliphatic and X is the C-terminal residue of the substrate protein, and may be any of several amino acids.
A 2-oxo acid = an aldehyde + CO(2)
ATP + pantetheine 4'-phosphate = diphosphate + 3'-dephospho-CoA
2 pyruvate = 2-acetolactate + CO(2)
N(4)-acetyl-L-2,4-diaminobutanoate = L-ectoine + H(2)O
2'-deoxycytidine + H(2)O = 2'-deoxyuridine + NH(3)
4 sulfur + 4 H(2)O + O(2) = 2 H(2)S + 2 HSO(3)(-) + 2 H(+)
Glycerol = 3-hydroxypropanal + H(2)O
NADH + ROOH + H(+) = NAD(+) + H(2)O + ROH
N-acyl-D-glutamate + H(2)O = a carboxylate + D-glutamate
Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. Alpha-Casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec; and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs).
Acetyl-CoA + L-2,4-diaminobutanoate = CoA + N(4)-acetyl-L-2,4-diaminobutanoate
Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved.
Hydrolyzes a Gly-|-Gly bond at its own C-terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the processing of the potyviral polyprotein.
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
(1a) Man(9)GlcNAc(2)-[protein] + H(2)O = Man(8)GlcNAc(2)-[protein] (isomer 8A(1,2,3)B(1,2)) + beta-D-mannopyranose
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
(S)-lactaldehyde + NAD(+) + H(2)O = (S)-lactate + NADH
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
O-phospho-L-homoserine + H(2)O = L-threonine + phosphate
ATP + D-ribose = ADP + D-ribose 5-phosphate
Hydrolyzes poly(ADP-D-ribose) at glycosidic (1''-2') linkage of ribose-ribose bond to produce free ADP-D-ribose
L-erythro-3,5-diaminohexanoate + H(2)O + NAD(+) = (S)-5-amino-3-oxohexanoate + NH(3) + NADH
A nitroalkane + H(2)O + O(2) = an aldehyde or ketone + nitrite + H(2)O(2)
Random hydrolysis of (1->6)-alpha-D-mannosidic linkages in unbranched (1->6)-mannans
S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical
Hydrolysis of terminal, non-reducing branched (1->3)-alpha-D-galactosidic residues, producing free D-galactose
Triphosphate + [microsomal-membrane protein] = diphosphate + [microsomal-membrane protein] phosphate
Hydrolysis of (1->4)-beta-D-glucosidic linkages in beta-D-glucans containing (1->3)- and (1->4)-bonds
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA
A purine nucleoside + H(2)O = D-ribose + a purine base
ATP + (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = ADP + phosphate + NADH
L-histidinol + H(2)O + 2 NAD(+) = L-histidine + 2 NADH
S-adenosyl-L-methionine + a 5-hydroxyfurocoumarin = S-adenosyl-L-homocysteine + a 5-methoxyfurocoumarin
ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys)
Hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains
Hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides
Exolytic cleavage of the (1->4)-beta-glycosidic linkage between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues in peptidoglycan, from either the reducing or the non-reducing ends of the peptidoglycan chains, with concomitant formation of a 1,6-anhydrobond in the MurNAc residue.
Hydrolysis of (1->6)-alpha-D-glucosidic linkages in pullulan, amylopectin and glycogen, and in the alpha- and beta-limit dextrins of amylopectin and glycogen.
Linoleate + O(2) = (9Z,12Z)-(11S)-11-hydroperoxyoctadeca-9,12-dienoate
Xyloglucan + H(2)O = xyloglucan oligosaccharides
Feruloyl-polysaccharide + H(2)O = ferulate + polysaccharide
S-adenosyl-L-methionine + 3,4-dihydroxy-trans-cinnamate = S-adenosyl-L-homocysteine + 3-methoxy-4-hydroxy-trans-cinnamate
ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate
Release of an N-terminal dipeptide from a peptide comprising four or more residues, with broad specificity. Also acts on dipeptidyl 2-naphthylamides.
Acetyl-CoA + H(2)O + acetoacetyl-CoA = (S)-3-hydroxy-3-methylglutaryl-CoA + CoA
ATP + L-methionine + H(2)O = phosphate + diphosphate + S-adenosyl-L-methionine
ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec)
ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met)
UDP-N,N'-diacetylbacillosamine + tritrans,heptacis-undecaprenyl phosphate = UMP + N,N'-diacetyl-alpha-D-bacillosaminyl-diphospho-tritrans,heptacis-undecaprenol
A carboxylic ester + H(2)O = an alcohol + a carboxylate
D-mannitol + NAD(+) = D-fructose + NADH
(R)-2-haloacid + H(2)O = (S)-2-hydroxyacid + halide
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
Anthranilate + N,N-dimethyl-1,4-phenylenediamine + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH
Acetyl-CoA + n malonyl-CoA + 2n NADPH = long-chain-acyl-CoA + n CoA + n CO(2) + 2n NADP(+)
(S)-2-hydroxy acid + O(2) = 2-oxo acid + H(2)O(2)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(27) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(27)
sn-glycerol 3-phosphate + O(2) = glycerone phosphate + H(2)O(2)
Isovaleryl-CoA + electron-transfer flavoprotein = 3-methylcrotonyl-CoA + reduced electron-transfer flavoprotein
(+)-muconolactone = cis,cis-muconate
6-hydroxymethyl-7,8-dihydropterin diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate
(S)-malate + NAD(+) = oxaloacetate + NADH
N-acetyl-alpha-D-glucosamine 1-phosphate = N-acetyl-D-glucosamine 6-phosphate
Beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate
Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain
(S)-mandelate = (R)-mandelate
H(2) + oxidized coenzyme F420 = reduced coenzyme F420
Coproporphyrinogen III + 3 O(2) = coproporphyrin III + 3 H(2)O(2)
Cellobiose = 4-O-beta-D-glucopyranosyl-D-mannose
Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides
UTP + alpha-D-glucose 1-phosphate = diphosphate + UDP-glucose
n UDP-alpha-D-glucose + 4-O-(poly((2R)-glycerophospho)-(2R)-glycerophospho)-N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = n UDP + 4-O-(poly((2R)-2-alpha-D-glucosyl-1-glycerophospho)-(2R)-glycerophospho)-N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
(S)-3-hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate
(S)(+)-allantoin = (R)(-)-allantoin
1-haloalkane + H(2)O = a primary alcohol + halide
ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe)
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA 
Cyclic pyranopterin phosphate + 2 [molybdopterin-synthase sulfur-carrier protein]-Gly-NH-CH(2)-C(O)SH + H(2)O = molybdopterin + 2 [molybdopterin-synthase sulfur-carrier protein]
(1a) 2 Fe(2+) + O(2) + 4 H(2)O = 2 (FeO(OH)) + 4 H(+) + H(2)O(2)
Putrescine + O(2) + H(2)O = 4-aminobutanal + NH(3) + H(2)O(2)
(1a) ATP + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-N(epsilon)-phosphono-L-lysine + diphosphate
Cutin + H(2)O = cutin monomers
(2S,3S)-3-hydroxy-2-methylbutanoyl-CoA + NAD(+) = 2-methylacetoacetyl-CoA + NADH
An aldehyde + NAD(+) + H(2)O = a carboxylate + NADH
ATP + acetate = ADP + acetyl phosphate
NADPH + n oxidized hemoprotein = NADP(+) + n reduced hemoprotein
Hydrolysis of (1->4)-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini
RH + [reduced NADPH--hemoprotein reductase] + O(2) = ROH + [oxidized NADPH--hemoprotein reductase] + H(2)O
FAD + [protein]-L-threonine = [protein]-FMN-L-threonine + AMP
[Amino group carrier protein]-C-terminal-gamma-(L-lysyl)-L-glutamate + H(2)O = [amino group carrier protein]-C-terminal-L-glutamate + L-lysine
H(2) + 2 ferricytochrome c3 = 2 H(+) + 2 ferrocytochrome c3
Transfers a segment of a (1->4)-alpha-D-glucan to a new position in an acceptor, which may be glucose or a (1->4)-alpha-D-glucan
ADP + phosphate + acetyl-CoA + oxaloacetate = ATP + citrate + CoA
ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate = ADP + 1D-myo-inositol hexakisphosphate
2 ATP = 2 diphosphate + cyclic di-3',5'-adenylate
Phosphoenolpyruvate + D-erythrose 4-phosphate + H(2)O = 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate + phosphate
Prenyl phosphate + FMNH(2) = prenylated FMNH(2) + phosphate
NAD(P)H + O(2) = NAD(P)(+) + H(2)O(2)
dTDP-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H(2)O
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate
1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + thiocarboxy-[sulfur-carrier protein ThiS] = 2-((2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + [sulfur-carrier protein ThiS] + 2 H(2)O
A long-chain aldehyde + O(2) + 2 NADPH = an alkane + formate + H(2)O + 2 NADP(+)
R-CHOH-R' + NADP(+) = R-CO-R' + NADPH
Endohydrolysis of (1->3)- or (1->4)-linkages in beta-D-glucans when the glucose residue whose reducing group is involved in the linkage to be hydrolyzed is itself substituted at C-3.
ADP-alpha-D-glucose + D-glucose 6-phosphate = ADP + alpha,alpha-trehalose 6-phosphate
(R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH
RH + H(2)O(2) = ROH + H(2)O
Prephenate + NADP(+) = 4-hydroxyphenylpyruvate + CO(2) + NADPH
2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH
(2S)-flavan-4-ol + NADP(+) = (2S)-flavanone + NADPH
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
D-xylopyranose = D-xylulose
ATP + adenylyl sulfate = ADP + 3'-phosphoadenylyl sulfate
ATP + 6-hydroxymethyl-7,8-dihydropterin = AMP + 6-hydroxymethyl-7,8-dihydropterin diphosphate
Phenylacetaldehyde + NAD(+) + H(2)O = phenylacetate + NADH
Eliminative cleavage of the terminal beta-D-mannosyl-(1->4)-beta-D-glucuronosyl linkage of the side-chain of the polysaccharide xanthan, leaving a 4-deoxy-alpha-L-threo-hex-4-enuronosyl group at the terminus of the side-chain
A 3-oxosteroid + acceptor = a 3-oxo-Delta(1)-steroid + reduced acceptor
(1a) 1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate
Chorismate = isochorismate
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate
Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products
(R)-mevalonate + CoA + 2 NAD(+) = 3-hydroxy-3-methylglutaryl-CoA + 2 NADH
ATP + 3-methylbut-3-en-1-yl phosphate = ADP + 3-methylbut-3-en-1-yl diphosphate
L-allo-threonine = glycine + acetaldehyde
S-adenosyl-L-methionine + precorrin-5 + H(2)O = S-adenosyl-L-homocysteine + precorrin-6A + acetate
ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO(2)
ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
S-adenosyl-L-methionine + [peptide chain release factor 1 or 2]-L-glutamine = S-adenosyl-L-homocysteine + [peptide chain release factor 1 or 2]-N(5)-methyl-L-glutamine

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
Entry contents:
12 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (15 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
DNA-directed RNA polymerase II subunit RPB3 Chain: C
Molecule details ›
Chain: C
Length: 318 amino acids
Theoretical weight: 35.33 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P16370 (Residues: 1-318; Coverage: 100%)
Gene names: RPB3, YIL021W
Sequence domains:
Structure domains:
DNA-directed RNA polymerase II subunit RPB4 Chain: D
Molecule details ›
Chain: D
Length: 221 amino acids
Theoretical weight: 25.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20433 (Residues: 1-221; Coverage: 100%)
Gene names: J0654, RPB4, YJL140W
Sequence domains: RNA polymerase Rpb4
Structure domains: Growth Hormone; Chain: A;
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
Molecule details ›
Chain: E
Length: 215 amino acids
Theoretical weight: 25.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20434 (Residues: 1-215; Coverage: 100%)
Gene names: RPA7, RPB5, RPC9, YBR1204, YBR154C
Sequence domains:
Structure domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 155 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20435 (Residues: 1-155; Coverage: 100%)
Gene names: P9677.8, RPB6, RPO26, YPR187W
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
DNA-directed RNA polymerase II subunit RPB7 Chain: G
Molecule details ›
Chain: G
Length: 171 amino acids
Theoretical weight: 19.08 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P34087 (Residues: 1-171; Coverage: 100%)
Gene names: D9509.22, RPB7, YDR404C
Sequence domains:
Structure domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20436 (Residues: 1-146; Coverage: 100%)
Gene names: RPB8, YOR224C, YOR50-14
Sequence domains: RNA polymerase Rpb8
Structure domains: Nucleic acid-binding proteins
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 122 amino acids
Theoretical weight: 14.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P27999 (Residues: 1-122; Coverage: 100%)
Gene names: RPB9, YGL070C
Sequence domains:
Structure domains: N-terminal domain of TfIIb
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 70 amino acids
Theoretical weight: 8.29 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22139 (Residues: 1-70; Coverage: 100%)
Gene names: RPB10, YOR210W
Sequence domains: RNA polymerases N / 8 kDa subunit
Structure domains: Homeodomain-like
DNA-directed RNA polymerase II subunit RPB11 Chain: K
Molecule details ›
Chain: K
Length: 120 amino acids
Theoretical weight: 13.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38902 (Residues: 1-120; Coverage: 100%)
Gene names: RPB11, YOL005C
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
Structure domains: RNA polymerase, RBP11-like subunit
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
Molecule details ›
Chain: L
Length: 70 amino acids
Theoretical weight: 7.73 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40422 (Residues: 1-70; Coverage: 100%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Structure domains: RNA polymerase ii, chain L
NON TEMPLATE DNA 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP *GP*CP*TP)-3' Chain: N
Molecule details ›
Chain: N
Length: 14 nucleotides
Theoretical weight: 4.29 KDa
TEMPLATE DNA 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP *TP*TP*TP*CP*CP*BRU*GP*GP*TP*CP*AP*TP*TP)-3' Chain: T
Molecule details ›
Chain: T
Length: 26 nucleotides
Theoretical weight: 7.98 KDa
TRANSCRIPT RNA 5'-R(*CP*AP*GP*GP*AP)-3' Chain: P
Molecule details ›
Chain: P
Length: 5 nucleotides
Theoretical weight: 1.61 KDa

Ligands and Environments

3 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2221
Unit cell:
a: 223.68Å b: 394.17Å c: 283.29Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.16 0.188