2hkn

X-ray diffraction
1.87Å resolution

Crystal structure of the CAP-Gly domain of human Dynactin-1 (p150-Glued)

Released:
Source organism: Homo sapiens

Function and Biology Details

Reactions catalysed:
Hydrolysis of terminal, non-reducing branched (1->3)-alpha-D-galactosidic residues, producing free D-galactose
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
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
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
ATP + deamido-NAD(+) + L-glutamine + H(2)O = AMP + diphosphate + NAD(+) + L-glutamate
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH
N-(5-phospho-D-ribosyl)-anthranilate + diphosphate = anthranilate + 5-phospho-alpha-D-ribose 1-diphosphate
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
6-phospho-D-glucono-1,5-lactone + H(2)O = 6-phospho-D-gluconate
ATP-dependent breakage, passage and rejoining of double-stranded DNA
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
1-haloalkane + H(2)O = a primary alcohol + halide
(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.
D-tagatose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
Diphosphate + H(2)O = 2 phosphate
Blasticidin S + H(2)O = deaminohydroxyblasticidin S + NH(3)
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
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
Chorismate = prephenate
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
A phenyl acetate + H(2)O = a phenol + acetate
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
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 + RNA(n) = diphosphate + RNA(n+1)
NH(3) + 2 H(2)O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H(+)
Thioredoxin + NADP(+) = thioredoxin disulfide + NADPH
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
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Isochorismate = salicylate + pyruvate
Hydrolyzes poly(ADP-D-ribose) at glycosidic (1''-2') linkage of ribose-ribose bond to produce free ADP-D-ribose
NTP + H(2)O = NDP + phosphate
A 5'-phosphopolynucleotide + H(2)O = a polynucleotide + phosphate
N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate
L-methionine + thioredoxin disulfide + H(2)O = L-methionine (S)-S-oxide + thioredoxin
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin
Maltose = alpha,alpha-trehalose
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
[Biotin carboxyl-carrier protein]-N(6)-carboxybiotinyl-L-lysine + acetyl-CoA = [biotin carboxyl-carrier protein]-N(6)-biotinyl-L-lysine + malonyl-CoA
ATP + succinate + CoA = ADP + phosphate + succinyl-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.
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
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).
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'.
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
L-lysine + 2-oxoglutarate = (S)-2-amino-6-oxohexanoate + L-glutamate
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinose
(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate
L-alanine = D-alanine
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
Peptidylproline (omega=180) = peptidylproline (omega=0)
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
5,10-methylenetetrahydrofolate + 3-methyl-2-oxobutanoate + H(2)O = tetrahydrofolate + 2-dehydropantoate
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
ATP + H(2)O + vitamin B12-[cobalamin-binding protein](Side 1) = ADP + phosphate + vitamin B12(Side 2) + [cobalamin-binding protein](Side 1)
Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
ATP + thymidine = ADP + thymidine 5'-phosphate
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.
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).
Chorismate = isochorismate
Preferential cleavage at the carboxyl of hydrophobic amino acids, but fails to cleave 15-Leu-|-Tyr-16, 16-Tyr-|-Leu-17 and 24-Phe-|-Phe-25 of insulin B chain. Activates trypsinogen, and degrades keratin.
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).
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
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)
DNA (containing 4-O-methylthymine) + protein L-cysteine = DNA (without 4-O-methylthymine) + protein S-methyl-L-cysteine
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]
ATP + AMP = 2 ADP
L-alanine + H(2)O + NAD(+) = pyruvate + NH(3) + NADH
(2E,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + ditrans,polycis-polyprenyl diphosphate (n = 10-55)
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu)
Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 3'-phosphate
ATP + (R)-pantothenate = ADP + (R)-4'-phosphopantothenate
(S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate
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.
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O
N-acetyl-L-glutamate 5-semialdehyde + NADP(+) + phosphate = N-acetyl-L-glutamyl 5-phosphate + NADPH
Pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2)
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
AMP + H(2)O = D-ribose 5-phosphate + adenine
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Nucleoside 3',5'-cyclic phosphate + H(2)O = nucleoside 5'-phosphate
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
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
ADP-D-ribose 1''-phosphate + H(2)O = ADP-D-ribose + phosphate
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
1-O-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-1D-myo-inositol + H(2)O = 1-O-(2-amino-2-deoxy-alpha-D-glucopyranosyl)-1D-myo-inositol + acetate
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA
ATP + propanoyl-CoA + HCO(3)(-) = ADP + phosphate + (S)-methylmalonyl-CoA
UDP-alpha-D-glucuronate + NAD(+) = UDP-beta-L-threo-pentapyranos-4-ulose + CO(2) + NADH
(S)-4-hydroxy-2-oxohexanoate = propanal + pyruvate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dynactin subunit 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 97 amino acids
Theoretical weight: 10.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q14203 (Residues: 18-111; Coverage: 7%)
Gene name: DCTN1
Sequence domains: CAP-Gly domain
Structure domains: CAP Gly-rich-like domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ENRAF-NONIUS FR591
Spacegroup: P212121
Unit cell:
a: 43.3Å b: 55.2Å c: 66.6Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.199 0.251
Expression system: Escherichia coli