4jtd

X-ray diffraction
2.54Å resolution

Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Lys27Met mutant of Charybdotoxin

Released:

Function and Biology Details

Reactions catalysed:
Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction)
A phosphate monoester + H(2)O = an alcohol + phosphate
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
dUTP + H(2)O = dUMP + diphosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate 
ATP + molybdopterin = diphosphate + adenylyl-molybdopterin
UDP-N-acetyl-alpha-D-glucosamine = UDP-2-acetamido-2,6-dideoxy-alpha-D-xylo-hex-4-ulose + H(2)O
3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholanate + NAD(+) = 3-alpha,12-alpha-dihydroxy-7-oxo-5-beta-cholanate + NADH
(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
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
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
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
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
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).
L-asparagine + H(2)O = L-aspartate + NH(3)
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
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.
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(+)
Pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2)
ATP + RNA(n) = diphosphate + RNA(n+1)
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
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
(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
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
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.
A beta-lactam + H(2)O = a substituted beta-amino acid
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
Angiotensin II + H(2)O = angiotensin-(1-7) + L-phenylalanine
ATP = 3',5'-cyclic AMP + diphosphate
(R)-mandelonitrile = cyanide + benzaldehyde
(1a) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-N(tau)-phospho-L-histidine + 2/3-phospho-D-glycerate
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.
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'.
L-glutamate 5-semialdehyde + NAD(+) + H(2)O = L-glutamate + NADH
Peptidylproline (omega=180) = peptidylproline (omega=0)
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
Hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose
Hydrolysis of terminal non-reducing alpha-L-rhamnose residues in alpha-L-rhamnosides
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
RH + Cl(-) + H(2)O(2) = RCl + 2 H(2)O
L-lysine = cadaverine + CO(2)
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
ATP + thymidine = ADP + thymidine 5'-phosphate
L-proline + a quinone = (S)-1-pyrroline-5-carboxylate + a quinol
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)
S-formylglutathione + H(2)O = glutathione + formate
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
ATP + AMP = 2 ADP
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro)
NAD(+) + protein-L-arginine = nicotinamide + N(omega)-(ADP-D-ribosyl)-protein-L-arginine
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.
((1->2)-beta-D-glucosyl)(n) + H(2)O = sophorose + ((1->2)-beta-D-glucosyl)(n-2)
2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
A phosphatidylcholine + H(2)O = 1,2-diacyl-sn-glycerol + phosphocholine
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
1-haloalkane + H(2)O = a primary alcohol + halide
ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamate 5-phosphate
2-iminobutanoate + H(2)O = 2-oxobutanoate + NH(3)
L-lysyl-tRNA(Lys) + phosphatidylglycerol = tRNA(Lys) + 3-O-L-lysyl-1-O-phosphatidylglycerol
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
Phosphoenolpyruvate + D-erythrose 4-phosphate + H(2)O = 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate + phosphate
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + D-xylulose = ADP + D-xylulose 5-phosphate
S-adenosyl-L-methionine + pseudouridine(1915) in 23S rRNA = S-adenosyl-L-homocysteine + N(3)-methylpseudouridine(1915) in 23S rRNA
L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H(2)O
(2S)-2-hydroxy-3,4-dioxopentyl phosphate = 3-hydroxy-2,4-dioxopentyl phosphate
6-phospho-D-glucono-1,5-lactone + H(2)O = 6-phospho-D-gluconate
(S)-ureidoglycolate = glyoxylate + urea
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
GTP + H(2)O = GDP + phosphate
O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate
(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
ATP-dependent cleavage of peptide bonds with broad specificity.
Blasticidin S + H(2)O = deaminohydroxyblasticidin S + NH(3)
S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol
Chorismate = prephenate
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
Triacylglycerol + H(2)O = diacylglycerol + a carboxylate
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein]
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
NADH + ROOH + H(+) = NAD(+) + H(2)O + ROH
GTP + alpha-D-mannose 1-phosphate = diphosphate + GDP-mannose
Hydrolyzes poly(ADP-D-ribose) at glycosidic (1''-2') linkage of ribose-ribose bond to produce free ADP-D-ribose
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
Isocitrate = succinate + glyoxylate
N-acetyl-D-glucosamine 6-phosphate + H(2)O = D-glucosamine 6-phosphate + acetate
GTP = 3',5'-cyclic GMP + diphosphate
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
D-xylopyranose = D-xylulose
Cleaves -Ala-|-Ser- and -Ala-|-Ala- bonds in the scaffold protein.
Maltose = alpha,alpha-trehalose
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
An aldehyde + H(2)O + 2 oxidized ferredoxin = a carboxylate + 2 H(+) + 2 reduced ferredoxin
5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
Preferential cleavage: Glu-|-, Asp-|-.
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
ATP-dependent breakage, passage and rejoining of double-stranded DNA
An alpha-L-fucoside + H(2)O = L-fucose + an alcohol
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
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]
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
NAD(P)H + a quinone = NAD(P)(+) + a hydroquinone
ATP + glycerol = ADP + sn-glycerol 3-phosphate
2 nitric oxide + 2 O(2) + NAD(P)H = 2 nitrate + NAD(P)(+) + H(+)
An aldehyde + NAD(+) + H(2)O = a carboxylate + NADH
3-dehydroquinate = 3-dehydroshikimate + 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.
A primary alcohol + NAD(+) = an aldehyde + NADH
AMP + H(2)O = D-ribose 5-phosphate + adenine
L-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)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.
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
(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
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
4-fumarylacetoacetate + H(2)O = acetoacetate + fumarate
NADPH + NAD(+) + H(+)(Side 1) = NADP(+) + H(+)(Side 2) + NADH
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + a protein = ADP + a phosphoprotein
A C(21)-steroid + [reduced NADPH--hemoprotein reductase] + O(2) = a 17-alpha-hydroxy-C(21)-steroid + [oxidized NADPH--hemoprotein reductase] + H(2)O
Cleavage of peptide bonds with very broad specificity.
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
A phenyl acetate + H(2)O = a phenol + acetate
17-alpha-hydroxypregnenolone + [reduced NADPH--hemoprotein reductase] + O(2) = 3-beta-hydroxyandrost-5-en-17-one + acetate + [oxidized NADPH--hemoprotein reductase] + H(2)O
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = (S)-allantoin + CO(2)
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
ATP + thiamine = AMP + thiamine diphosphate
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
H(2) + A = AH(2)
ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
Palmitoyl-CoA + H(2)O = CoA + palmitate
An N-acyl-L-homoserine lactone + H(2)O = an N-acyl-L-homoserine

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, G
Molecule details ›
Chains: A, G
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, H
Molecule details ›
Chains: B, H
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: 144.867Å b: 144.867Å c: 284.292Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.21 0.235
Expression systems:
  • Komagataella pastoris
  • Escherichia coli