4a3i

X-ray diffraction
3.8Å resolution

RNA Polymerase II binary complex with DNA

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:
ATP + D-ribose = ADP + D-ribose 5-phosphate
Chloride + O(2) = chlorite
(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
A pyrimidine 5'-nucleotide + H(2)O = D-ribose 5-phosphate + a pyrimidine base
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]
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
L-serine + L-homocysteine = L-cystathionine + H(2)O
L-alanine = D-alanine
L-glutamate = D-glutamate
CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein]
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH
NTP + H(2)O = NDP + phosphate
(1a) ATP + [RNA ligase]-L-lysine = [RNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
D-xylopyranose = D-xylulose
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
Methylamine + H(2)O + 2 oxidized [amicyanin] = formaldehyde + NH(3) + 2 reduced [amicyanin]
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).
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
ATP + AMP = 2 ADP
(+)-trans-carveol + NAD(+) = (+)-(S)-carvone + NADH
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
Orotidine 5'-phosphate = UMP + CO(2)
ATP + kanamycin = ADP + kanamycin 3'-phosphate
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate
RH + [reduced NADPH--hemoprotein reductase] + O(2) = ROH + [oxidized NADPH--hemoprotein reductase] + H(2)O
Carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate
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.
(1a) ATP + (R)-lipoate = lipoyl-AMP + diphosphate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
L-asparagine + H(2)O = L-aspartate + NH(3)
Urea + H(2)O = CO(2) + 2 NH(3)
ATP + [biotin carboxyl-carrier protein]-biotin-N(6)-L-lysine + hydrogencarbonate- = ADP + phosphate + [biotin carboxyl-carrier protein]-carboxybiotin-N(6)-L-lysine
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.
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]
Tetradecanoyl-CoA + an N-terminal-glycyl-[protein] = CoA + an N-terminal-N-tetradecanoylglycyl-[protein]
(R)-10-hydroxystearate = oleate + H(2)O
ATP + deamido-NAD(+) + NH(3) = AMP + diphosphate + NAD(+)
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
A chalcone = a flavanone
RX + glutathione = HX + R-S-glutathione
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
2 H(2)O(2) = O(2) + 2 H(2)O
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
Alpha-D-mannose 1-phosphate = D-mannose 6-phosphate
L-glutamate = 4-aminobutanoate + CO(2)
Beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA
Methyl-CoM + CoB = CoM-S-S-CoB + methane
Beta-D-ribopyranose = beta-D-ribofuranose
ATP + glycerol = ADP + sn-glycerol 3-phosphate
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
ATP + L-arginine = ADP + N(omega)-phospho-L-arginine
H(2)CO(3) = CO(2) + H(2)O
ATP + a protein = ADP + a phosphoprotein
ATP + L-methionine + H(2)O = phosphate + diphosphate + S-adenosyl-L-methionine
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Chorismate = prephenate
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
An acyl-[acyl-carrier protein] + NADP(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADPH
ADP + phosphate + acetyl-CoA + oxaloacetate = ATP + citrate + CoA
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
A beta-lactam + H(2)O = a substituted beta-amino acid
N-acetyl-D-glucosamine 6-phosphate + H(2)O = D-glucosamine 6-phosphate + acetate
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
D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Peptidylproline (omega=180) = peptidylproline (omega=0)
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
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
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Shikimate + NADP(+) = 3-dehydroshikimate + NADPH
Cytosine + H(2)O = uracil + NH(3)
ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys)
ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophyl-tRNA(Trp)
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA
1-(5-phospho-beta-D-ribosyl)-5-((5-phospho-beta-D-ribosylamino)methylideneamino)imidazole-4-carboxamide = 5-((5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino)-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide
Release of any N-terminal amino acid, including proline, that is linked to proline, even from a dipeptide or tripeptide.
Cleavage of peptide bonds with very broad specificity.
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
An aliphatic amide = a nitrile + H(2)O
Triacylglycerol + H(2)O = diacylglycerol + a carboxylate
A carboxylic ester + H(2)O = an alcohol + a carboxylate
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.
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
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
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.
ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO(2)
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).
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.
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'.
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.
Taurine + 2-oxoglutarate + O(2) = sulfite + aminoacetaldehyde + succinate + CO(2)
Choline = trimethylamine + acetaldehyde
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Anthranilate + N,N-dimethyl-1,4-phenylenediamine + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
Xylitol + NADP(+) = L-xylulose + NADPH
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
Hydrolysis of proteins in presence of ATP.
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
6-phospho-D-glucono-1,5-lactone + H(2)O = 6-phospho-D-gluconate
7,8-dihydroneopterin 3'-triphosphate = 6-pyruvoyl-5,6,7,8-tetrahydropterin + triphosphate
((1->4)-alpha-D-glucosyl)(n) + phosphate = ((1->4)-alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate
ATP + 3-methylbut-3-en-1-yl phosphate = ADP + 3-methylbut-3-en-1-yl diphosphate
5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH
Sucrose = 6-O-alpha-D-glucopyranosyl-D-fructofuranose
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H(2)O
O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
(S)-4-hydroxy-2-oxohexanoate = propanal + pyruvate
Diphosphate + D-fructose 6-phosphate = phosphate + D-fructose 1,6-bisphosphate
Carbamoyl phosphate + N(2)-acetyl-L-ornithine = phosphate + N-acetyl-L-citrulline
(Ribonucleotide)(n)-2',3'-cyclic phosphate + H(2)O = (ribonucleotide)(n)-2'-phosphate
Acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an N-acetyldiamine
(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
6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
UDP-alpha-D-glucose + D-glucose 6-phosphate = UDP + alpha,alpha-trehalose 6-phosphate
A purine nucleoside + H(2)O = D-ribose + a purine base
D-ribulose 5-phosphate = D-xylulose 5-phosphate
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
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
(1a) [acetyl-CoA C-acyltransferase]-S-acyl-L-cyteine + acetyl-CoA = 3-oxoacyl-CoA + [acetyl-CoA C-acyltransferase]-L-cyteine
Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H(2)O = 5-amino-6-(5-phosphoribosylamino)uracil + NH(3)
(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
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
Cellobiose = 4-O-beta-D-glucopyranosyl-D-mannose
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
S-adenosyl-L-methionine + 3-((1-carboxyvinyl)oxy)benzoate + H(2)O = 6-amino-6-deoxyfutalosine + L-methionine + HCO(3)(-)
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
Hydrolysis of terminal non-reducing alpha-L-rhamnose residues in alpha-L-rhamnosides
N,N-dimethylformamide + H(2)O = dimethylamine + formate
L-histidinol + H(2)O + 2 NAD(+) = L-histidine + 2 NADH
Isocitrate = succinate + glyoxylate
IMP + H(2)O = inosine + phosphate
L-proline + NAD(P)(+) = 1-pyrroline-5-carboxylate + NAD(P)H
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.
Diphosphate + H(2)O = 2 phosphate
An acylphosphate + H(2)O = a carboxylate + phosphate
A long-chain aldehyde + O(2) + 2 NADPH = an alkane + formate + H(2)O + 2 NADP(+)
(1,4-alpha-D-galacturonosyl)(n+m) + H(2)O = (1,4-alpha-D-galacturonosyl)(n) + (1,4-alpha-D-galacturonosyl)(m)
Hydrolysis of Xaa-|-Pro dipeptides. Also acts on aminoacyl-hydroxyproline analogs. No action on Pro-|-Pro.
N-isopropylammelide + H(2)O = cyanuric acid + isopropylamine
3-deoxy-D-manno-octulosonate 8-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
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-.
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
Hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose
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.
(S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate
Glycerol + NAD(+) = glycerone + NADH
L-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)H
Hg + NADP(+) + H(+) = Hg(2+) + NADPH
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
(S)-ureidoglycolate = glyoxylate + urea
Linoleate + O(2) = (9Z,12Z)-(11S)-11-hydroperoxyoctadeca-9,12-dienoate
L-threonylcarbamoyladenylate + adenine(37) in tRNA = AMP + N(6)-L-threonylcarbamoyladenine(37) in tRNA
L-arginine + H(2)O = L-ornithine + urea
Angiotensin II + H(2)O = angiotensin-(1-7) + L-phenylalanine
D-glyceraldehyde 3-phosphate = glycerone phosphate
4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate
2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O
(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
A beta-D-glucuronoside + H(2)O = D-glucuronate + an alcohol
Hydrolysis of (1->4)-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini
L-erythrulose 1-phosphate = D-erythrulose 4-phosphate
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
3'-phosphoadenylyl sulfate + a phenol = adenosine 3',5'-bisphosphate + an aryl sulfate
Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans
Propane-1,2-diol = propanal + H(2)O
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 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.
D-glucose + NAD(P)(+) = D-glucono-1,5-lactone + NAD(P)H
Sucrose + (6)-beta-D-fructofuranosyl-(2->)(n) alpha-D-glucopyranoside = glucose + (6)-beta-D-fructofuranosyl-(2->)(n+1) alpha-D-glucopyranoside
L-ornithine = L-proline + NH(3)
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate 
2-deoxy-D-ribosyl-base(1) + base(2) = 2-deoxy-D-ribosyl-base(2) + base(1) 
L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H(2)O
Meso-2,6-diaminoheptanedioate = L-lysine + CO(2)
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
Benzoylformate = benzaldehyde + CO(2)
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
Succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + NAD(P)H
2 pyruvate = 2-acetolactate + CO(2)
5,10-methenyltetrahydrofolate + H(2)O = 10-formyltetrahydrofolate
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
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.
(S)-3-hydroxybutanoyl-CoA + NADP(+) = 3-acetoacetyl-CoA + NADPH
Glycerol = 3-hydroxypropanal + H(2)O
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
Endohydrolysis of (1->6)-alpha-D-glucosidic linkages in dextran
Maltose = alpha,alpha-trehalose
ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA
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
(S)-malate = fumarate + H(2)O
Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine
Chitin + H(2)O = chitosan + acetate
An alpha-L-fucoside + H(2)O = L-fucose + an alcohol
CoB + CoM + methanophenazine = CoM-S-S-CoB + dihydromethanophenazine
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)
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
3-beta-D-glucosyl-D-glucose + phosphate = D-glucose + alpha-D-glucose 1-phosphate
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
L-glutamate 5-semialdehyde + NAD(+) + H(2)O = L-glutamate + NADH
ATP + adenylyl sulfate = ADP + 3'-phosphoadenylyl sulfate
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH
Oxalate + O(2) + 2 H(+) = 2 CO(2) + H(2)O(2)
Betaine aldehyde + NAD(+) + H(2)O = betaine + NADH
Hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans
(1a) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [RBR-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [RBR-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine
S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol
(1a) S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N(omega)-methyl-L-arginine
ATP + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-alanyl-D-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine
A (3R)-3-hydroxyacyl-[acyl-carrier protein] = a trans-2-enoyl-[acyl-carrier protein] + H(2)O
4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O
(1a) L-methionine = methanethiol + 2-aminobut-2-enoate
Hydrolysis of (1->4)-beta-D-glucosidic linkages in beta-D-glucans containing (1->3)- and (1->4)-bonds
Random hydrolysis of (1->2)-glucosidic linkages in (1->2)-beta-D-glucans
(1a) S-adenosyl-L-methionine + precorrin-6B = S-adenosyl-L-homocysteine + precorrin-7 + CO(2)
7,8-dihydroneopterin = 6-hydroxymethyl-7,8-dihydropterin + glycolaldehyde
D-fructose 6-phosphate + phosphate = acetyl phosphate + D-erythrose 4-phosphate + H(2)O
Alpha-D-glucose = beta-D-glucose
(S)-malate + NAD(+) = oxaloacetate + NADH
Hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains
H(2) + oxidized coenzyme F420 = reduced coenzyme F420
(R)-mevalonate + CoA + 2 NAD(+) = 3-hydroxy-3-methylglutaryl-CoA + 2 NADH
ATP + D-glucose = ADP + D-glucose 6-phosphate
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
ATP + pantetheine 4'-phosphate = diphosphate + 3'-dephospho-CoA
D-glucosyl-N-acylsphingosine + H(2)O = D-glucose + N-acylsphingosine
L-proline + a quinone = (S)-1-pyrroline-5-carboxylate + a quinol
(1a) cyanate + HCO(3)(-) + H(+) = carbamate + CO(2)
UDP-glucose + 2 NAD(+) + H(2)O = UDP-glucuronate + 2 NADH
NAD(P)H + a quinone = NAD(P)(+) + a hydroquinone
Succinate + a quinone = fumarate + a quinol
n ATP + n H(2)O + a microtubule = n ADP + n phosphate + (n+1) alpha/beta tubulin heterodimers
4-trimethylammoniobutanoate + 2-oxoglutarate + O(2) = 3-hydroxy-4-trimethylammoniobutanoate + succinate + CO(2) 
A phosphate monoester + H(2)O = an alcohol + phosphate
Myo-inositol hexakisphosphate + H(2)O = 1D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate
N-carbamoyl-L-2-amino acid (a 2-ureido carboxylate) + H(2)O = L-2-amino acid + NH(3) + CO(2)
NAD(+) + glycine + sulfide = nicotinamide + ADP-5-ethyl-4-methylthiazole-2-carboxylate + 3 H(2)O
1D-chiro-inositol + NAD(+) = 2D-2,3,5/4,6-pentahydroxycyclohexanone + NADH
Acetyl-CoA + n malonyl-CoA + 2n NADPH = a long-chain fatty acid + (n+1) CoA + n CO(2) + 2n NADP(+)
H(2) + A = AH(2)
Malonyl-CoA + an [acyl-carrier-protein] = CoA + a malonyl-[acyl-carrier-protein]
Acetyl-CoA + [acyl-carrier-protein] = CoA + acetyl-[acyl-carrier-protein]
Myo-inositol + NAD(+) = 2,4,6/3,5-pentahydroxycyclohexanone + NADH
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
L-aspartate 4-semialdehyde + phosphate + NADP(+) = L-4-aspartyl phosphate + NADPH
[Protein]-N(pi)-phospho-L-histidine + D-mannose(Side 1) = [protein]-L-histidine + D-mannose 6-phosphate(Side 2)
(1a) 1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate
Xyloglucan + H(2)O = xyloglucan oligosaccharides
D-ribose 5-phosphate = D-ribulose 5-phosphate
Cutin + H(2)O = cutin monomers
S-adenosyl-L-methionine + 3,4-dihydroxy-trans-cinnamate = S-adenosyl-L-homocysteine + 3-methoxy-4-hydroxy-trans-cinnamate
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
A glutathione-S-conjugate + H(2)O = an (L-cysteinylglycine)-S-conjugate + L-glutamate
ATP + 6-hydroxymethyl-7,8-dihydropterin = AMP + 6-hydroxymethyl-7,8-dihydropterin diphosphate
An aryl sulfate + H(2)O = a phenol + sulfate
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
Hydrolyzes poly(ADP-D-ribose) at glycosidic (1''-2') linkage of ribose-ribose bond to produce free ADP-D-ribose
Succinate semialdehyde + NADP(+) + H(2)O = succinate + NADPH
(1a) L-glutamine + H(2)O = L-glutamate + NH(4)(+)
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
(R)-mevalonate + CoA + 2 NADP(+) = (S)-3-hydroxy-3-methylglutaryl-CoA + 2 NADPH
D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate
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
Prenyl phosphate + FMNH(2) = prenylated FMNH(2) + phosphate
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
Hydrolysis of --Pro-|- and to a lesser extent --Ala-|- in oligopeptides.
((1->2)-beta-D-glucosyl)(n) + H(2)O = sophorose + ((1->2)-beta-D-glucosyl)(n-2)
D-sorbitol 6-phosphate + NAD(+) = D-fructose 6-phosphate + NADH
dUTP + H(2)O = dUMP + diphosphate
UDP-alpha-D-galactopyranose = UDP-alpha-D-galactofuranose
An archaeal dolichyl phosphooligosaccharide + [protein]-L-asparagine = an archaeal dolichyl phosphate + a glycoprotein with the oligosaccharide chain attached by N-beta-D-glycosyl linkage to a protein L-asparagine
5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2)
L-fucopyranose = L-fuculose
An aryl sulfate + a phenol = a phenol + an aryl sulfate
N(4)-acetyl-L-2,4-diaminobutanoate = L-ectoine + H(2)O
2'-deoxycytidine + H(2)O = 2'-deoxyuridine + NH(3)
ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
N(6)-(L-1,3-dicarboxypropyl)-L-lysine + NAD(+) + H(2)O = L-lysine + 2-oxoglutarate + NADH
ATP + propanoyl-CoA + HCO(3)(-) = ADP + phosphate + (S)-methylmalonyl-CoA
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
H(2) + NAD(+) = H(+) + NADH
FAD + [protein]-L-threonine = [protein]-FMN-L-threonine + AMP
GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
O-phospho-L-homoserine + H(2)O = L-threonine + phosphate
A (5-L-glutamyl)-peptide + an amino acid = a peptide + a 5-L-glutamyl amino acid
4-coumaroyl-CoA + shikimate = CoA + 4-coumaroylshikimate
Endonucleolytic cleavage of RNA, removing 21 and 42 nucleotides, respectively, from the 5'- and 3'-termini of a 5S-rRNA precursor.
Thiosulfate + cyanide = sulfite + thiocyanate
Prephenate = phenylpyruvate + H(2)O + CO(2)
ATP + 7,8-dihydropteroate + L-glutamate = ADP + phosphate + 7,8-dihydropteroylglutamate
Cyclohexanone + NADPH + O(2) = hexano-6-lactone + NADP(+) + H(2)O
Myo-inositol phosphate + H(2)O = myo-inositol + phosphate
A nitroalkane + H(2)O + O(2) = an aldehyde or ketone + nitrite + H(2)O(2)
S-(hydroxymethyl)glutathione + NAD(P)(+) = S-formylglutathione + NAD(P)H
Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 3'-phosphate
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
3-dehydroquinate = 3-dehydroshikimate + H(2)O
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
[Amino group carrier protein]-C-terminal-gamma-(L-lysyl)-L-glutamate + H(2)O = [amino group carrier protein]-C-terminal-L-glutamate + L-lysine
ATP + tetrahydropteroyl-(gamma-Glu)(n) + L-glutamate = ADP + phosphate + tetrahydropteroyl-(gamma-Glu)(n+1)
6-hydroxymethyl-7,8-dihydropterin diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate
NAD(H) + H(2)O = AMP + NMN(H)
Formate + NAD(+) = CO(2) + NADH
(2S)-2-hydroxy-2-methyl-3-oxobutanoate = (3R)-3-hydroxybutan-2-one + CO(2)
A short-chain acyl-CoA + electron-transfer flavoprotein = a short-chain trans-2,3-dehydroacyl-CoA + reduced electron-transfer flavoprotein
(S)-lactate + NAD(+) = pyruvate + NADH
4 sulfur + 4 H(2)O + O(2) = 2 H(2)S + 2 HSO(3)(-) + 2 H(+)
Penicillin + H(2)O = a carboxylate + 6-aminopenicillanate
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate
Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain
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
ATP + pyruvate = ADP + phosphoenolpyruvate
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
Cleaves -Ala-|-Ser- and -Ala-|-Ala- bonds in the scaffold protein.
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO(2)
(R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH
Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose
Glycerone phosphate = methylglyoxal + phosphate
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA 
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
S-formylglutathione + H(2)O = glutathione + formate
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
Pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2)
Limited hydrolysis of proteins of the neuroexocytosis apparatus, synaptobrevin (also known as neuronal vesicle-associated membrane protein, VAMP), synaptosome-associated protein of 25 kDa (SNAP25) or syntaxin. No detected action on small molecule substrates.
A C(21)-steroid + [reduced NADPH--hemoprotein reductase] + O(2) = a 17-alpha-hydroxy-C(21)-steroid + [oxidized NADPH--hemoprotein reductase] + H(2)O
Phosphatidylinositol 3,4,5-trisphosphate + H(2)O = phosphatidylinositol 4,5-bisphosphate + phosphate
NADPH + n oxidized hemoprotein = NADP(+) + n reduced hemoprotein
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO(3)(-) = ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-alpha-D-glucose
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate
17-alpha-hydroxypregnenolone + [reduced NADPH--hemoprotein reductase] + O(2) = 3-beta-hydroxyandrost-5-en-17-one + acetate + [oxidized NADPH--hemoprotein reductase] + H(2)O
ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp)
Quercetin + O(2) = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H(+)
ATP + D-ribulose 5-phosphate = ADP + D-ribulose 1,5-bisphosphate
2 glutathione + NADP(+) = glutathione disulfide + NADPH
Urate + O(2) + H(2)O = 5-hydroxyisourate + H(2)O(2)
N(6)-prenyladenine + acceptor + H(2)O = adenine + 3-methylbut-2-enal + reduced acceptor
CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
Alpha-maltose 1-phosphate + ((1->4)-alpha-D-glucosyl)(n) = phosphate + ((1->4)-alpha-D-glucosyl)(n+2)
NADH + ubiquinone + n Na(+)(Side 1) = NAD(+) + ubiquinol + n Na(+)(Side 2)
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
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
UDP-N-acetyl-alpha-D-glucosamine = UDP-2-acetamido-2,6-dideoxy-alpha-D-xylo-hex-4-ulose + H(2)O
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.
Oxalyl-CoA = formyl-CoA + CO(2)
A 2-oxo acid = an aldehyde + CO(2)
Aceneneuramate = N-acetyl-D-mannosamine + pyruvate
Thioredoxin + ROOH = thioredoxin disulfide + H(2)O + ROH
NADH + ROOH + H(+) = NAD(+) + H(2)O + ROH
N-acyl-D-glutamate + H(2)O = a carboxylate + D-glutamate
ATP = 3',5'-cyclic AMP + diphosphate
(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
(S)-lactaldehyde + NAD(+) + H(2)O = (S)-lactate + NADH
ATP + D-xylulose = ADP + D-xylulose 5-phosphate
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
Sucrose + ((1->6)-alpha-D-glucosyl)(n) = D-fructose + ((1->6)-alpha-D-glucosyl)(n+1)
A 3-oxo-Delta(5)-steroid = a 3-oxo-Delta(4)-steroid
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.
UDP-alpha-D-glucose = UDP-alpha-D-galactose
ATP + 3-phospho-D-glycerate = ADP + 3-phospho-D-glyceroyl phosphate
Xylitol + NAD(P)(+) = D-xylose + NAD(P)H
Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline
Endohydrolysis of (1->4)-beta-D-linkages between D-galactose 4-sulfate and 3,6-anhydro-D-galactose in kappa-carrageenans.
A monocarboxylic acid amide + H(2)O = a monocarboxylate + NH(3)
ATP + thiamine phosphate = ADP + thiamine diphosphate
L-histidinol phosphate + H(2)O = L-histidinol + phosphate
N(6)-(Delta(2)-isopentenyl)-adenosine 5'-phosphate + H(2)O = N(6)-(dimethylallyl)adenine + D-ribose 5'-phosphate
Acetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacetyl-[acyl-carrier-protein] + CoA + CO(2) 
ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate
UDP-N-acetyl-alpha-D-glucosamine + H(2)O = N-acetyl-D-mannosamine + UDP
Nitrous oxide + 2 ferricytochrome c + H(2)O = 2 nitric oxide + 2 ferrocytochrome c + 2 H(+)
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
GDP-mannose + 3-phospho-D-glycerate = GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
5,6-dihydrouracil + H(2)O = 3-ureidopropanoate
L-fuculose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
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
N-((R)-4'-phosphopantothenoyl)-L-cysteine = pantotheine 4'-phosphate + CO(2)
2 reduced ferredoxin + NADP(+) + H(+) = 2 oxidized ferredoxin + NADPH
3 malonyl-CoA + benzoyl-CoA = 4 CoA + 3,5-dihydroxybiphenyl + 4 CO(2)
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine(34) in tRNA(Leu) = S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine(34) in tRNA(Leu)
CTP + (R)-4'-phosphopantothenate + L-cysteine = CMP + diphosphate + N-((R)-4'-phosphopantothenoyl)-L-cysteine
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).
Endonucleolytic cleavage to 5'-phosphomonoester.
Phosphoenolpyruvate + D-arabinose 5-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
Thioredoxin + NADP(+) = thioredoxin disulfide + NADPH
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(79) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(79)
ATP + acetate = ADP + acetyl phosphate
4-phosphonooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + L-glutamate
1-haloalkane + H(2)O = a primary alcohol + halide
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)(+) + H(2)O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H
(R)-mandelonitrile = cyanide + benzaldehyde
Formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin
Hydrolysis of proteins and small molecule substrates at -Asn-|-Xaa- bonds.
A primary alcohol + NAD(+) = an aldehyde + NADH
Hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides
L-glutaminyl-peptide = 5-oxoprolyl-peptide + NH(3)

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
Entry contents:
12 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (14 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
5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*GP*CP*T)-3' Chain: N
Molecule details ›
Chain: N
Length: 15 nucleotides
Theoretical weight: 4.59 KDa
TEMPLATE DNA 27-MER Chain: T
Molecule details ›
Chain: T
Length: 27 nucleotides
Theoretical weight: 8.39 KDa

Ligands and Environments

2 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2221
Unit cell:
a: 221.14Å b: 393.18Å c: 282.48Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.159 0.159 0.191