7b0p

X-ray diffraction
1.94Å resolution

In meso structure of the membrane integral lipoprotein intramolecular transacylase Lit from Bacillus cereus in space group P21212

Released:

Function and Biology Details

Reactions catalysed:
dUTP + H(2)O = dUMP + diphosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
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
(8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate
Galactarate = (2R,3S)-2,3-dihydroxy-5-oxohexanedioate + H(2)O
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
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
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
D-glyceraldehyde 3-phosphate = glycerone phosphate
GTP + H(2)O = GDP + phosphate
D-mannose = D-fructose
(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
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
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
Cleaves -Ala-|-Ser- and -Ala-|-Ala- bonds in the scaffold protein.
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
(1a) (2R,3S)-3-isopropylmalate + NAD(+) = (2S)-2-isopropyl-3-oxosuccinate + NADH
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
L-asparagine + H(2)O = L-aspartate + NH(3)
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
(1a) S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N(omega)-methyl-L-arginine
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
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 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.
CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[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
2 H(2)O(2) = O(2) + 2 H(2)O
ATP + shikimate = ADP + shikimate 3-phosphate
NH(3) + 2 H(2)O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H(+)
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
ATP + acetate + CoA = ADP + phosphate + acetyl-CoA
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
NTP + H(2)O = NDP + phosphate
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
ATP + pyruvate = ADP + phosphoenolpyruvate
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
[Biotin carboxyl-carrier protein]-N(6)-carboxybiotinyl-L-lysine + acetyl-CoA = [biotin carboxyl-carrier protein]-N(6)-biotinyl-L-lysine + malonyl-CoA
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
5,10-methylenetetrahydrofolate + dUMP + NADPH = dTMP + tetrahydrofolate + NADP(+)
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.
Endonucleolytic cleavage to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end-products
A beta-lactam + H(2)O = a substituted beta-amino acid
3'-phosphoadenylyl sulfate + a phenol = adenosine 3',5'-bisphosphate + an aryl sulfate
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
ATP = 3',5'-cyclic AMP + diphosphate
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
6-hydroxymethyl-7,8-dihydropterin diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate
2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
The primary cleavage site is at 67-His-|-Lys-68 in human C5a with a minor secondary cleavage site at 58-Ala-|-Ser-59
L-fuculose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
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
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
ATP + pantetheine 4'-phosphate = diphosphate + 3'-dephospho-CoA
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
S-adenosyl-L-methionine + phospholipid olefinic fatty acid = S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid
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-.
D-glucose 6-phosphate + oxidized coenzyme F420 = D-glucono-1,5-lactone 6-phosphate + reduced coenzyme F420
Peptidylproline (omega=180) = peptidylproline (omega=0)
Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose
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]
(1E,2Z)-3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta-1(10),2-dien-4-oate + H(2)O = 3-((3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl)propanoate + (2Z,4Z)-2-hydroxyhexa-2,4-dienoate
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
H(2)CO(3) = CO(2) + H(2)O
S-adenosyl-L-homocysteine + H(2)O = L-homocysteine + adenosine
ATP + thymidine = ADP + thymidine 5'-phosphate
ATP + NAD(+) = ADP + NADP(+)
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 glutathione-S-conjugate + H(2)O = an (L-cysteinylglycine)-S-conjugate + L-glutamate
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).
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and similar substrates, releasing cellobiose from the reducing ends of the chains.
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
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
Acetyl-CoA + 3-methyl-2-oxobutanoate + H(2)O = (2S)-2-isopropylmalate + CoA
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).
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
S-adenosyl-L-methionine + DNA cytosine = S-adenosyl-L-homocysteine + DNA N(4)-methylcytosine
ATP + 6-hydroxymethyl-7,8-dihydropterin = AMP + 6-hydroxymethyl-7,8-dihydropterin diphosphate
Alpha-D-glucosamine 6-phosphate + H(2)O = D-fructose 6-phosphate + NH(3)
Beta-D-ribopyranose = beta-D-ribofuranose
ATP + glycerol = ADP + sn-glycerol 3-phosphate
2 nitric oxide + 2 O(2) + NAD(P)H = 2 nitrate + NAD(P)(+) + H(+)
tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate
Succinate + a quinone = fumarate + a quinol
Pectin + n H(2)O = n methanol + pectate
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.
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O
3-dehydroquinate = 3-dehydroshikimate + H(2)O
ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys)
A phosphatidylcholine + H(2)O = 1,2-diacyl-sn-glycerol + phosphocholine
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
Acetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacetyl-[acyl-carrier-protein] + CoA + CO(2) 
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
(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
2,6-dioxo-6-phenylhexa-3-enoate + H(2)O = benzoate + 2-oxopent-4-enoate
Tuberculosinyl diphosphate + adenosine = 1-tuberculosinyladenosine + diphosphate
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
NADPH + NAD(+) + H(+)(Side 1) = NADP(+) + H(+)(Side 2) + NADH
A (5-L-glutamyl)-peptide + an amino acid = a peptide + a 5-L-glutamyl amino acid
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Hypothetical Membrane Spanning Protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 237 amino acids
Theoretical weight: 27.64 KDa
Source organism: Bacillus cereus ATCC 14579
Expression system: Escherichia coli
UniProt:
  • Canonical: Q813T3 (Residues: 1-218; Coverage: 100%)
Gene name: BC_1526
Sequence domains: Protein of unknown function (DUF1461)

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P21212
Unit cell:
a: 51.166Å b: 192.235Å c: 76.801Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.232 0.246
Expression system: Escherichia coli