1o4u

X-ray diffraction
2.5Å resolution

Function and Biology Details

Reactions catalysed:
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
Hydrolysis of proteins in presence of ATP.
dUTP + H(2)O = dUMP + diphosphate
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate 
(8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate
Catechol + O(2) = cis,cis-muconate
D-arabinose 5-phosphate = D-ribulose 5-phosphate
ATP + a protein = ADP + a phosphoprotein
Beta-nicotinate D-ribonucleotide + diphosphate + CO(2) = pyridine-2,3-dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate
N-(5-phospho-D-ribosyl)-anthranilate + diphosphate = anthranilate + 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
Protein L-glutamine + H(2)O = protein L-glutamate + NH(3)
Quercetin + O(2) = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H(+)
(2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (3E)-2-oxohex-3-enedioate
Release of N-terminal proline from a peptide.
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
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.
Release of an N-terminal amino acid, Xaa-|-Yaa- from a peptide, amide or arylamide. Xaa is preferably Ala, but may be most amino acids including Pro (slow action). When a terminal hydrophobic residue is followed by a prolyl residue, the two may be released as an intact Xaa-Pro dipeptide.
ATP + L-methionine + H(2)O = phosphate + diphosphate + S-adenosyl-L-methionine
1-haloalkane + H(2)O = a primary alcohol + halide
Cleavage of peptide bonds with very broad specificity.
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
(1a) 2 Fe(2+) + O(2) + 4 H(2)O = 2 (FeO(OH)) + 4 H(+) + H(2)O(2)
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD(+) = 2-oxoadipate + CO(2) + NADH
The enzyme specifically hydrolyzes (1->4)-beta-D-galactosidic linkages in type I arabinogalactans.
(R)-mandelonitrile = cyanide + benzaldehyde
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
A phenyl acetate + H(2)O = a phenol + acetate
Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans
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
Beta-D-ribopyranose = beta-D-ribofuranose
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.
Cyclic di-3',5'-guanylate + H(2)O = 5'-phosphoguanylyl(3'->5')guanosine
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
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
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
dCTP + 2 H(2)O = dUMP + diphosphate + NH(3)
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.
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
Protein dithiol + NAD(P)(+) = protein disulfide + NAD(P)H
Chorismate = 3-((1-carboxyvinyl)oxy)benzoate + H(2)O
(S)-dihydroorotate + fumarate = orotate + succinate
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
(3R)-3-hydroxybutanoyl-CoA = crotonoyl-CoA + H(2)O
4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate
(R)-10-hydroxystearate = oleate + H(2)O
NTP + H(2)O = NDP + phosphate
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
(+)-muconolactone = 5-oxo-4,5-dihydrofuran-2-acetate
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
ATP + deamido-NAD(+) + L-glutamine + H(2)O = AMP + diphosphate + NAD(+) + L-glutamate
5,10-methylenetetrahydrofolate + dUMP + NADPH = dTMP + tetrahydrofolate + NADP(+)
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
Isocitrate = succinate + glyoxylate
A chalcone = a flavanone
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
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
(1a) 2 cob(II)alamin + 2 [corrinoid adenosyltransferase] = 2 [corrinoid adenosyltransferase]-cob(II)alamin
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).
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.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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.
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-.
Protoheme + 3 reduced acceptor + 3 O(2) = mycobilin a + Fe(2+) + 3 acceptor + 3 H(2)O
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 H(2)O
Peptidylproline (omega=180) = peptidylproline (omega=0)
Choline = trimethylamine + acetaldehyde
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
ATP + H(2)O + H(+)(Side 1) + K(+)(Side 2) = ADP + phosphate + H(+)(Side 2) + K(+)(Side 1)
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate
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.
Hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose
D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
(S)-malate = fumarate + H(2)O
H(2)CO(3) = CO(2) + H(2)O
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).
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H(2)O = CoA + N-succinyl-L-2-amino-6-oxoheptanedioate
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
ATP + (R)-pantothenate = ADP + (R)-4'-phosphopantothenate
ATP + choline = ADP + phosphocholine
NAD(+) + protein-L-arginine = nicotinamide + N(omega)-(ADP-D-ribosyl)-protein-L-arginine
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate = ADP + 1D-myo-inositol hexakisphosphate
Succinate + a quinone = fumarate + a quinol
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H(2)O
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
NADPH + acceptor = NADP(+) + reduced acceptor
Random hydrolysis of (1->6)-alpha-D-mannosidic linkages in unbranched (1->6)-mannans
A phosphatidylcholine + H(2)O = 1,2-diacyl-sn-glycerol + phosphocholine
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
Palmitoyl-CoA + H(2)O = CoA + palmitate
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione + FMNH(2) + O(2) = 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione + FMN + H(2)O
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
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)
NADPH + NAD(+) + H(+)(Side 1) = NADP(+) + H(+)(Side 2) + NADH
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Quinolinate phosphoribosyltransferase [decarboxylating] Chains: A, B
Molecule details ›
Chains: A, B
Length: 285 amino acids
Theoretical weight: 31.68 KDa
Source organism: Thermotoga maritima
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9X1X8 (Residues: 1-273; Coverage: 100%)
Gene name: TM_1645
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: I222
Unit cell:
a: 96.371Å b: 126.125Å c: 138.372Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.213 0.272
Expression system: Escherichia coli