5xou

X-ray diffraction
2.63Å resolution

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 7T8 on the guide strand

Released:

Function and Biology Details

Reactions catalysed:
Glutarate + 2-oxoglutarate + O(2) = (S)-2-hydroxyglutarate + succinate + CO(2)
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
dUTP + H(2)O = dUMP + diphosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
(8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + a protein = ADP + a phosphoprotein
Beta-nicotinate D-ribonucleotide + diphosphate + CO(2) = pyridine-2,3-dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate
GTP + IMP + L-aspartate = GDP + phosphate + N(6)-(1,2-dicarboxyethyl)-AMP
Acyl-CoA + H(2)O = CoA + a carboxylate
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.
GTP + H(2)O = GDP + phosphate
Cleavage of peptide bonds with very broad specificity.
Carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate
S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate
Diphosphate + H(2)O = 2 phosphate
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Chorismate = prephenate
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
L-alanine = D-alanine
Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
(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
4-phosphonooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + L-glutamate
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
CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein]
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
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
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH
2 glutathione + ROOH = glutathione disulfide + H(2)O + ROH
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
ATP + shikimate = ADP + shikimate 3-phosphate
NH(3) + 2 H(2)O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H(+)
A [lipoyl-carrier protein]-N(6)-((R)-dihydrolipoyl)-L-lysine + ROOH = a [lipoyl-carrier protein]-N(6)-((R)-lipoyl)-L-lysine + H(2)O + ROH
5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2)
Geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2Z,6E)-farnesyl diphosphate
Vanillyl alcohol + O(2) = vanillin + H(2)O(2)
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
(S)-dihydroorotate + fumarate = orotate + succinate
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
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.
A 5'-phosphopolynucleotide + H(2)O = a polynucleotide + phosphate
Isochorismate = salicylate + pyruvate
Prephenate = phenylpyruvate + H(2)O + CO(2)
NTP + H(2)O = NDP + phosphate
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
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.
Isocitrate = succinate + glyoxylate
1-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H(2)O = 1-alkyl-sn-glycero-3-phosphocholine + acetate
Endonucleolytic cleavage to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end-products
A beta-lactam + H(2)O = a substituted beta-amino acid
2-carboxy-2,5-dihydro-5-oxofuran-2-acetate = cis,cis-butadiene-1,2,4-tricarboxylate
3-deoxy-D-manno-octulosonate 8-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
L-arginine + H(2)O = L-ornithine + urea
ATP = 3',5'-cyclic AMP + diphosphate
Myo-inositol phosphate + H(2)O = myo-inositol + phosphate
D-xylopyranose = D-xylulose
2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
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).
(1a) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-N(tau)-phospho-L-histidine + 2/3-phospho-D-glycerate
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.
ATP + pantetheine 4'-phosphate = diphosphate + 3'-dephospho-CoA
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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'.
NAD(+) + glycine + sulfide = nicotinamide + ADP-5-ethyl-4-methylthiazole-2-carboxylate + 3 H(2)O
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.
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-.
A carboxylic ester + H(2)O = an alcohol + a carboxylate
Cutin + H(2)O = cutin monomers
Acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an N-acetyldiamine
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
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]
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
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
2 a mycocerosyl-[mycocerosic acid synthase] + a phenolphthiocerol = a dimycocerosyl phenolphthiocerol + 2 holo-[mycocerosic acid synthase]
D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH
L-aspartate 4-semialdehyde + phosphate + NADP(+) = L-4-aspartyl phosphate + NADPH
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate = ADP + phosphate + (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate
H(2)CO(3) = CO(2) + H(2)O
ADP-alpha-D-glucose + D-glucose 6-phosphate = ADP + alpha,alpha-trehalose 6-phosphate
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.
ATP + thymidine = ADP + thymidine 5'-phosphate
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).
N(6)-prenyladenine + acceptor + H(2)O = adenine + 3-methylbut-2-enal + reduced acceptor
Chorismate = isochorismate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
ATP + dTMP = ADP + dTDP
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
Shikimate + NADP(+) = 3-dehydroshikimate + NADPH
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP + glycerol = ADP + sn-glycerol 3-phosphate
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
Naphthalene + NADH + O(2) = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD(+)
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.
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
AMP + H(2)O = D-ribose 5-phosphate + adenine
NAD(+) + H(2)O = ADP-D-ribose + nicotinamide
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
ATP + RNA(n) = diphosphate + RNA(n+1)
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
ADP-D-ribose 1''-phosphate + H(2)O = ADP-D-ribose + phosphate
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
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
Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids.
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA
ATP + propanoyl-CoA + HCO(3)(-) = ADP + phosphate + (S)-methylmalonyl-CoA
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Piwi domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 685 amino acids
Theoretical weight: 76.73 KDa
Source organism: Thermus thermophilus HB27
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q746M7 (Residues: 1-685; Coverage: 100%)
Gene name: TT_P0026
Sequence domains:
DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*TP*GP*GP*TP*TP*GP*T)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 22 nucleotides
Theoretical weight: 6.89 KDa
Source organism: Thermus thermophilus
Expression system: Not provided
DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 19 nucleotides
Theoretical weight: 5.71 KDa
Source organism: Thermus thermophilus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 112.747Å b: 114.982Å c: 160.441Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.235 0.276
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided