3tt9

X-ray diffraction
1.55Å resolution

Crystal structure of the stable degradation fragment of human plakophilin 2 isoform a (PKP2a) C752R variant

Released:

Function and Biology Details

Reactions catalysed:
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
D-galactose + O(2) = D-galacto-hexodialdose + H(2)O(2)
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
ATP + a protein = ADP + a phosphoprotein
N-(5-phospho-D-ribosyl)-anthranilate + diphosphate = anthranilate + 5-phospho-alpha-D-ribose 1-diphosphate
L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H(2)O
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Naphthalene + NADH + O(2) = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD(+)
2 alpha,alpha'-trehalose 6-mycolate = alpha,alpha'-trehalose + alpha,alpha'-trehalose 6,6'-bismycolate
Release of N-terminal proline from a peptide.
D-ribose 5-phosphate = D-ribulose 5-phosphate
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.
(1a) (2R,3S)-3-isopropylmalate = 2-isopropylmaleate + H(2)O
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
A phosphate monoester + H(2)O = an alcohol + phosphate
O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate
Cleavage of peptide bonds with very broad specificity.
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
Diphosphate + H(2)O = 2 phosphate
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
Triacylglycerol + H(2)O = diacylglycerol + a carboxylate
A carboxylic ester + H(2)O = an alcohol + a carboxylate
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.
Preferential cleavage: hydrophobic, preferably aromatic, residues in P1 and P1' positions. Cleaves 1-Phe-|-Val-2, 4-Gln-|-His-5, 13-Glu-|-Ala-14, 14-Ala-|-Leu-15, 15-Leu-|-Tyr-16, 16-Tyr-|-Leu-17, 23-Gly-|-Phe-24, 24-Phe-|-Phe-25 and 25-Phe-|-Tyr-26 bonds in the B chain of insulin.
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
2 glutathione + ROOH = glutathione disulfide + H(2)O + ROH
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
ATP + shikimate = ADP + shikimate 3-phosphate
Tuberculosinyl diphosphate + adenosine = 1-tuberculosinyladenosine + diphosphate
(R)-10-hydroxystearate = oleate + H(2)O
(S)-dihydroorotate + fumarate = orotate + succinate
5-methyltetrahydrofolate + L-homocysteine = tetrahydrofolate + L-methionine
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
Prephenate = phenylpyruvate + H(2)O + CO(2)
Hydrolysis of (1->4)-alpha-D-glucosidic linkage in 4-alpha-D-((1->4)-alpha-D-glucanosyl)(n) trehalose to yield trehalose and (1->4)-alpha-D-glucan
NTP + H(2)O = NDP + phosphate
Succinate semialdehyde + NADP(+) + H(2)O = succinate + NADPH
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
ATP + UMP = ADP + UDP
S-adenosyl-L-methionine + phospholipid olefinic fatty acid = S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid
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.
A beta-lactam + H(2)O = a substituted beta-amino acid
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
(1a) 2 cob(II)alamin + 2 [corrinoid adenosyltransferase] = 2 [corrinoid adenosyltransferase]-cob(II)alamin
6-hydroxymethyl-7,8-dihydropterin diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate
D-xylopyranose = D-xylulose
Cleaves -Ala-|-Ser- and -Ala-|-Ala- bonds in the scaffold protein.
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'.
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.
Trans,octacis-decaprenylphospho-beta-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose + FADH(2)
L-lysine + 2-oxoglutarate = (S)-2-amino-6-oxohexanoate + L-glutamate
Cutin + H(2)O = cutin monomers
Choline = trimethylamine + acetaldehyde
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
(S)-malate = fumarate + H(2)O
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
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
ATP + adenosine = ADP + AMP
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
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Acyl-CoA + 1,2-diacylglycerol = CoA + triacylglycerol
ATP + H(2)O + H(+)(Side 1) + K(+)(Side 2) = ADP + phosphate + H(+)(Side 2) + K(+)(Side 1)
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
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 + (R)-5-phosphomevalonate = ADP + (R)-5-diphosphomevalonate
ATP + AMP = 2 ADP
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
ATP + 6-hydroxymethyl-7,8-dihydropterin = AMP + 6-hydroxymethyl-7,8-dihydropterin diphosphate
2'-deoxycytidine + H(2)O = 2'-deoxyuridine + NH(3)
Adenosine + H(2)O = inosine + NH(3)
2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH
Beta-D-ribopyranose = beta-D-ribofuranose
Succinate + a quinone = fumarate + a quinol
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
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
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
S-adenosyl-L-methionine + adenine(2030) in 23S rRNA = S-adenosyl-L-homocysteine + N(6)-methyladenine(2030) in 23S rRNA
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
Limited hydrolysis of proteins of the neuroexocytosis apparatus, synaptobrevin (also known as neuronal vesicle-associated membrane protein, VAMP), synaptosome-associated protein of 25 kDa (SNAP25) or syntaxin. No detected action on small molecule substrates.
L-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)H
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
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
L-fuconate = 2-dehydro-3-deoxy-L-fuconate + H(2)O
CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
L-histidine-[translation elongation factor 2] + S-adenosyl-L-methionine = 2-((3S)-3-amino-3-carboxypropyl)-L-histidine-[translation elongation factor 2] + S-methyl-5'-thioadenosine
Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Plakophilin-2 Chain: A
Molecule details ›
Chain: A
Length: 233 amino acids
Theoretical weight: 26.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99959 (Residues: 346-620; Coverage: 26%)
  • Best match: Q99959-2 (Residues: 346-576)
Gene name: PKP2
Sequence domains: Armadillo/beta-catenin-like repeat
Structure domains: Leucine-rich Repeat Variant

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P212121
Unit cell:
a: 46.35Å b: 63.038Å c: 74.953Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.158 0.192
Expression system: Escherichia coli