4jta

X-ray diffraction
2.5Å resolution

Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin

Released:

Function and Biology Details

Reactions catalysed:
(1a) an (RNA) containing cytidine = an (RNA)-3'-cytidine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-(RNA)
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 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
Cleavage of peptide bonds with very broad specificity.
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
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
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.
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).
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
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
(S)-dihydroorotate + fumarate = orotate + succinate
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
NTP + H(2)O = NDP + phosphate
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
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 + pyruvate = ADP + phosphoenolpyruvate
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
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 chalcone = a flavanone
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
D-ribose 5-phosphate = D-ribulose 5-phosphate
(R)-mandelonitrile = cyanide + benzaldehyde
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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'.
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
L-histidinol phosphate + H(2)O = L-histidinol + phosphate
Hydrolysis of terminal non-reducing alpha-L-rhamnose residues in alpha-L-rhamnosides
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
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
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.
Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose
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)
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
Beta-D-ribopyranose = beta-D-ribofuranose
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.
ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
Hydroxymethylbilane = uroporphyrinogen III + H(2)O
ATP + H(2)O = ADP + phosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
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
L-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)H
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
(R)-propane-1,2-diol + NAD(+) = (R)-lactaldehyde + NADH
Release of N-terminal proline from a peptide.
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.
Reduced riboflavin + NAD(P)(+) = riboflavin + NAD(P)H
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
ATP-dependent cleavage of peptide bonds with broad specificity.
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
L-asparagine + H(2)O = L-aspartate + NH(3)
A monocarboxylic acid amide + H(2)O = a monocarboxylate + NH(3)
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
A phenyl acetate + H(2)O = a phenol + acetate
Triacylglycerol + H(2)O = diacylglycerol + a carboxylate
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
(1a) NADP(+) = 2'-phospho-cyclic ADP-ribose + nicotinamide
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
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-|-
4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate
A beta-lactam + H(2)O = a substituted beta-amino acid
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
Myo-inositol phosphate + H(2)O = myo-inositol + phosphate
2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
ATP + L-phenylalanine + H(2)O = AMP + diphosphate + D-phenylalanine
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans
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-.
2 H(2)O(2) = O(2) + 2 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
ATP + H(2)O + H(+)(Side 1) + K(+)(Side 2) = ADP + phosphate + H(+)(Side 2) + K(+)(Side 1)
D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate
D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH
Succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + NAD(P)H
ATP + H(2)O + vitamin B12-[cobalamin-binding protein](Side 1) = ADP + phosphate + vitamin B12(Side 2) + [cobalamin-binding protein](Side 1)
GTP + IMP + L-aspartate = GDP + phosphate + N(6)-(1,2-dicarboxyethyl)-AMP
Quercetin + O(2) = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H(+)
S-adenosyl-L-homocysteine + H(2)O = L-homocysteine + adenosine
[Dinitrogen reductase]-N(omega)-alpha-(ADP-D-ribosyl)-L-arginine = ADP-D-ribose + [dinitrogen reductase]-L-arginine
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
ATP + AMP = 2 ADP
An alpha-L-fucoside + H(2)O = L-fucose + an alcohol
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
Protein L-glutamine + H(2)O = protein L-glutamate + NH(3)
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro)
ATP + glycerol = ADP + sn-glycerol 3-phosphate
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
H(2) + A = AH(2)
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
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
UDP-alpha-D-glucose = UDP-alpha-D-galactose
Palmitoyl-CoA + H(2)O = CoA + palmitate
(1a) NAD(+) = cyclic ADP-ribose + nicotinamide
A primary alcohol + NAD(+) = an aldehyde + NADH
AMP + H(2)O = D-ribose 5-phosphate + adenine
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 alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
1-haloalkane + H(2)O = a primary alcohol + halide
(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
2-iminobutanoate + H(2)O = 2-oxobutanoate + NH(3)
L-glutaminyl-peptide = 5-oxoprolyl-peptide + NH(3)
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H(2)O
ATP + D-ribose = ADP + D-ribose 5-phosphate
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
(1a) S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine
4-phosphonooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + L-glutamate
7,8-dihydroneopterin 3'-triphosphate + H(2)O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + triphosphate
NADH + ROOH + H(+) = NAD(+) + H(2)O + ROH
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
ATP = 3',5'-cyclic AMP + diphosphate
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.
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides
L-lysine = cadaverine + CO(2)
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
(S)-lactate + NAD(+) = pyruvate + NADH
Shikimate + NADP(+) = 3-dehydroshikimate + NADPH
L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH
ATP + thiamine = AMP + thiamine diphosphate
Adenosine + H(2)O = inosine + NH(3)
An aldehyde + NAD(+) + H(2)O = a carboxylate + NADH
Alpha-D-glucose = beta-D-glucose
ATP + a protein = ADP + a phosphoprotein

Structure analysis Details

Assemblies composition:
hetero octamer
hetero nonamer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Voltage-gated potassium channel subunit beta-2 Chains: A, P
Molecule details ›
Chains: A, P
Length: 333 amino acids
Theoretical weight: 37.35 KDa
Source organism: Rattus norvegicus
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P62483 (Residues: 36-367; Coverage: 91%)
Gene names: Ckbeta2, Kcnab2, Kcnb3
Sequence domains: Aldo/keto reductase family
Structure domains: NADP-dependent oxidoreductase domain
Potassium voltage-gated channel subfamily A member 2; Potassium voltage-gated channel subfamily B member 1 Chains: B, Q
Molecule details ›
Chains: B, Q
Length: 514 amino acids
Theoretical weight: 58.82 KDa
Source organism: Rattus norvegicus
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P15387 (Residues: 30-30, 274-307; Coverage: 4%)
  • Canonical: P63142 (Residues: 1-31, 33-266, 305-499; Coverage: 92%)
Gene names: Kcna2, Kcnb1
Sequence domains:
Structure domains:
Potassium channel toxin alpha-KTx 1.1 Chain: Y
Molecule details ›
Chain: Y
Length: 37 amino acids
Theoretical weight: 4.31 KDa
Source organism: Leiurus quinquestriatus hebraeus
Expression system: Escherichia coli
UniProt:
  • Canonical: P13487 (Residues: 23-59; Coverage: 100%)
Sequence domains: Scorpion short toxin, BmKK2

Ligands and Environments


Cofactor: Ligand NAP 2 x NAP
2 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P4212
Unit cell:
a: 144.4Å b: 144.4Å c: 284.103Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.21 0.236
Expression systems:
  • Komagataella pastoris
  • Escherichia coli