6uvq

X-ray diffraction
1.84Å resolution

Crystal structure of Apo AtmM

Released:
Source organism: Actinomadura melliaura
Entry authors: Alvarado SK, Wang Z, Miller MD, Thorson JS, Phillips Jr GN

Function and Biology Details

Reactions catalysed:
3 ATP = pppA2'p5'A2'p5'A + 2 diphosphate
Hydrolysis of proteins in presence of ATP.
dUTP + H(2)O = dUMP + diphosphate
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
ATP + deamido-NAD(+) + L-glutamine + H(2)O = AMP + diphosphate + NAD(+) + L-glutamate
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + a protein = ADP + a phosphoprotein
1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate = 1-C-(3-indolyl)-glycerol 3-phosphate + CO(2) + H(2)O
S-adenosyl-L-methionine + phospholipid olefinic fatty acid = S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid
(1a) [acetyl-CoA C-acyltransferase]-S-acyl-L-cyteine + acetyl-CoA = 3-oxoacyl-CoA + [acetyl-CoA C-acyltransferase]-L-cyteine
4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + H(2)O = 4-O-(beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose
tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate
(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
Acyl-CoA + H(2)O = CoA + a carboxylate
L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
1-haloalkane + H(2)O = a primary alcohol + halide
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
Diphosphate + H(2)O = 2 phosphate
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
S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
Chorismate = prephenate
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
A phenyl acetate + H(2)O = a phenol + acetate
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
4-phosphonooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + L-glutamate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
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
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(+)
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.
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
Reduced riboflavin + NAD(P)(+) = riboflavin + NAD(P)H
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
Isochorismate = salicylate + pyruvate
NTP + H(2)O = NDP + phosphate
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-.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
ATP + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine = ADP + phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole
[Biotin carboxyl-carrier protein]-N(6)-carboxybiotinyl-L-lysine + acetyl-CoA = [biotin carboxyl-carrier protein]-N(6)-biotinyl-L-lysine + malonyl-CoA
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
A chalcone = a flavanone
A beta-lactam + H(2)O = a substituted beta-amino acid
RX + glutathione = HX + R-S-glutathione
(1a) cholest-4-en-3-one + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H(+) + O(2) = (25S)-26-hydroxycholest-4-en-3-one + 2 oxidized ferredoxin [iron-sulfur] cluster + H(2)O
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
ATP = 3',5'-cyclic AMP + diphosphate
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
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.
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'.
ATP + sulfate = diphosphate + adenylyl sulfate
NAD(+) + glycine + sulfide = nicotinamide + ADP-5-ethyl-4-methylthiazole-2-carboxylate + 3 H(2)O
Trans,octacis-decaprenylphospho-beta-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose + FADH(2)
All bonds known to be hydrolyzed by this endopeptidase have arginine in P1 and an acidic residue in P4. P6 is often occupied by an acidic residue or by a hydroxy-amino-acid residue, the phosphorylation of which enhances cleavage.
(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate
(2E,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + ditrans,polycis-polyprenyl diphosphate (n = 10-55)
Peptidylproline (omega=180) = peptidylproline (omega=0)
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO(2)
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
(S)-malate = fumarate + H(2)O
Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
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
Geranylgeranyl diphosphate = (+)-copalyl diphosphate
ATP + adenylyl sulfate = ADP + 3'-phosphoadenylyl sulfate
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).
Acetyl-CoA + H(2)O + glyoxylate = (S)-malate + CoA
Chorismate = isochorismate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
DNA (containing 4-O-methylthymine) + protein L-cysteine = DNA (without 4-O-methylthymine) + protein S-methyl-L-cysteine
Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H(2)O = CoA + N-succinyl-L-2-amino-6-oxoheptanedioate
L-alanine + H(2)O + NAD(+) = pyruvate + NH(3) + NADH
An alpha-L-fucoside + H(2)O = L-fucose + an alcohol
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
NAD(P)H + a quinone = NAD(P)(+) + a hydroquinone
ATP + protoporphyrin IX + Mg(2+) + H(2)O = ADP + phosphate + Mg-protoporphyrin IX + 2 H(+)
ATP + (R)-pantothenate = ADP + (R)-4'-phosphopantothenate
H(2) + A = AH(2)
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.
An aldehyde + NAD(+) + H(2)O = a carboxylate + NADH
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O
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
Palmitoyl-CoA + H(2)O = CoA + palmitate
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
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
O-phospho-L-homoserine + H(2)O = L-threonine + phosphate
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 superoxide + 2 H(+) = O(2) + H(2)O(2)
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
N(1)-methylguanine(37) in tRNA(Phe) + pyruvate + S-adenosyl-L-methionine = 4-demethylwyosine(37) in tRNA(Phe) + L-methionine + 5'-deoxyadenosine + CO(2) + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo tetramer
homo dimer
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
PKS_MT domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 268 amino acids
Theoretical weight: 28.67 KDa
Source organism: Actinomadura melliaura
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q0H2W9 (Residues: 1-268; Coverage: 100%)
Gene name: atM
Sequence domains: Methyltransferase domain

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P2
Unit cell:
a: 69.463Å b: 52.997Å c: 70.842Å
α: 90° β: 93.34° γ: 90°
R-values:
R R work R free
0.183 0.181 0.224
Expression system: Escherichia coli BL21(DE3)