7asa

Electron Microscopy
3.5Å resolution

Bacillus subtilis ribosome-associated quality control complex state B, multibody refinement focussed on RqcH. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabO

Released:

Function and Biology Details

Reactions catalysed:
ATP + a protein = ADP + a phosphoprotein
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
Diphosphate + H(2)O = 2 phosphate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
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.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
NTP + H(2)O = NDP + phosphate
A beta-lactam + H(2)O = a substituted beta-amino acid
RX + glutathione = HX + R-S-glutathione
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'.
2 H(2)O(2) = O(2) + 2 H(2)O
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 H(2)O
L-histidinol phosphate + H(2)O = L-histidinol + 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).
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
(S)-lactate + NAD(+) = pyruvate + NADH
ATP + AMP = 2 ADP
An alpha-L-fucoside + H(2)O = L-fucose + an alcohol
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
Succinate + a quinone = fumarate + a quinol
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.
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
ATP + H(2)O = ADP + 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
L-lysyl-tRNA(Lys) + phosphatidylglycerol = tRNA(Lys) + 3-O-L-lysyl-1-O-phosphatidylglycerol
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate 
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
A phosphate monoester + H(2)O = an alcohol + phosphate
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
A monocarboxylic acid amide + H(2)O = a monocarboxylate + NH(3)
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
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 + [biotin carboxyl-carrier protein]-biotin-N(6)-L-lysine + hydrogencarbonate- = ADP + phosphate + [biotin carboxyl-carrier protein]-carboxybiotin-N(6)-L-lysine
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
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate
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.
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
L-arginine + H(2)O = L-ornithine + urea
ATP = 3',5'-cyclic AMP + diphosphate
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).
ATP + acetate + CoA = ADP + phosphate + acetyl-CoA
Maleate = fumarate
Peptidylproline (omega=180) = peptidylproline (omega=0)
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]
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
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.
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
ATP + thymidine = ADP + thymidine 5'-phosphate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
Beta-D-ribopyranose = beta-D-ribofuranose
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
1-haloalkane + H(2)O = a primary alcohol + halide
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
2-iminobutanoate + H(2)O = 2-oxobutanoate + NH(3)
3 ATP = pppA2'p5'A2'p5'A + 2 diphosphate
(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH
Beta-nicotinate D-ribonucleotide + diphosphate + CO(2) = pyridine-2,3-dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
(S)-2-hydroxy acid + O(2) = 2-oxo acid + H(2)O(2)
D-glyceraldehyde 3-phosphate = glycerone phosphate
2 alpha,alpha'-trehalose 6-mycolate = alpha,alpha'-trehalose + alpha,alpha'-trehalose 6,6'-bismycolate
7,8-dihydroneopterin = 7,8-dihydromonapterin
Cleavage of peptide bonds with very broad specificity.
S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate
Chorismate = prephenate
(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]
Cyclo(L-tyrosyl-L-tyrosyl) + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H(+) + O(2) = mycocyclosin + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H(2)O
ATP + shikimate = ADP + shikimate 3-phosphate
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
Isochorismate = salicylate + pyruvate
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
L-fuculose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
ATP + dTMP = ADP + dTDP
(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate
5,10-methylenetetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
Hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose
ATP + NAD(+) = ADP + NADP(+)
(R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH
Chorismate = isochorismate
Acyl-CoA + 1,2-diacylglycerol = CoA + triacylglycerol
DNA (containing 4-O-methylthymine) + protein L-cysteine = DNA (without 4-O-methylthymine) + protein S-methyl-L-cysteine
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
An ultra-long-chain mono-unsaturated acyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = an ultra-long-chain mono-unsaturated 3-oxo-fatty acyl-[acyl-carrier protein] + CO(2) + a holo-[acyl-carrier protein]
(2E,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + ditrans,polycis-polyprenyl diphosphate (n = 10-55)
5,10-methenyltetrahydrofolate + H(2)O = 10-formyltetrahydrofolate
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(27) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(27)
NAD(P)H + a quinone = NAD(P)(+) + a hydroquinone
Nucleoside 3',5'-cyclic phosphate + H(2)O = nucleoside 5'-phosphate
Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 3'-phosphate
7,8-dihydroneopterin + O(2) = 7,8-dihydroxanthopterin + formate + glycolaldehyde
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
Hydrolysis of --Pro-|- and to a lesser extent --Ala-|- in oligopeptides.
7,8-dihydroneopterin = 6-hydroxymethyl-7,8-dihydropterin + glycolaldehyde
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (5 distinct):
Rqc2 homolog RqcH Chain: 0
Molecule details ›
Chain: 0
Length: 597 amino acids
Theoretical weight: 68.34 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: O34693 (Residues: 1-570; Coverage: 100%)
Gene names: BSU15640, rqcH, yloA
Sequence domains:
Uncharacterized protein YabO Chain: 1
Molecule details ›
Chain: 1
Length: 86 amino acids
Theoretical weight: 9.74 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P37557 (Residues: 1-86; Coverage: 100%)
Gene names: BSU00590, yabO
Sequence domains: S4 domain
50S ribosomal protein L11 Chain: K
Molecule details ›
Chain: K
Length: 141 amino acids
Theoretical weight: 14.95 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: Q06796 (Residues: 1-141; Coverage: 100%)
Gene names: BSU01020, relC, rplK, tsp6
Sequence domains:
tRNA-Ala-1-1 Chain: 2
Molecule details ›
Chain: 2
Length: 76 nucleotides
Theoretical weight: 24.49 KDa
Sequence domains: tRNA
23S ribosomal RNA Chain: A

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-11891
Expression system: Bacillus subtilis subsp. subtilis str. 168