3lnm

X-ray diffraction
2.9Å resolution

F233W mutant of the Kv2.1 paddle-Kv1.2 chimera channel

Released:
Source organism: Rattus norvegicus
Primary publication:
A gating charge transfer center in voltage sensors.
Science 328 67-73 (2010)
PMID: 20360102

Function and Biology Details

Reactions catalysed:
(2S)-2-amino-4-deoxychorismate + H(2)O = (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxylate + pyruvate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
ATP + a protein = ADP + a phosphoprotein
ATP-dependent breakage, passage and rejoining of double-stranded DNA
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.
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
O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
ATP-dependent cleavage of peptide bonds with broad specificity.
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
Diphosphate + H(2)O = 2 phosphate
L-aspartate = D-aspartate
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate
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
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
(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
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.
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.
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
Sucrose + ((1->6)-alpha-D-glucosyl)(n) = D-fructose + ((1->6)-alpha-D-glucosyl)(n+1)
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
Prephenate = phenylpyruvate + H(2)O + CO(2)
NTP + H(2)O = NDP + phosphate
Maltose = alpha,alpha-trehalose
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
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
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
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
ATP = 3',5'-cyclic AMP + diphosphate
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.
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'.
NAD(+) + glycine + sulfide = nicotinamide + ADP-5-ethyl-4-methylthiazole-2-carboxylate + 3 H(2)O
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 H(2)O
Peptidylproline (omega=180) = peptidylproline (omega=0)
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]
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
L-histidinol phosphate + H(2)O = L-histidinol + phosphate
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate
Succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + NAD(P)H
N(6)-(Delta(2)-isopentenyl)-adenosine 5'-phosphate + H(2)O = N(6)-(dimethylallyl)adenine + D-ribose 5'-phosphate
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
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
Geranylgeranyl diphosphate = (+)-copalyl diphosphate
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).
L-threonylcarbamoyladenylate + adenine(37) in tRNA = AMP + N(6)-L-threonylcarbamoyladenine(37) in tRNA
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and similar substrates, releasing cellobiose from the reducing ends of the chains.
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Adenosine + H(2)O = inosine + NH(3)
A (3R)-3-hydroxyacyl-[acyl-carrier-protein] + a UDP-3-O-((3R)-hydroxyacyl)-alpha-D-glucosamine = a UDP-2-N,3-O-bis((3R)-3-hydroxyacyl)-alpha-D-glucosamine + a holo-[acyl-carrier-protein]
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.
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
3-dehydroquinate = 3-dehydroshikimate + H(2)O
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
A primary alcohol + NAD(+) = an aldehyde + NADH
L-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)H
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu)
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
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
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
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
L-lysyl-tRNA(Lys) + phosphatidylglycerol = tRNA(Lys) + 3-O-L-lysyl-1-O-phosphatidylglycerol
Glutarate + 2-oxoglutarate + O(2) = (S)-2-hydroxyglutarate + succinate + CO(2)
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
A phosphate monoester + H(2)O = an alcohol + phosphate
2 ATP = 2 diphosphate + cyclic di-3',5'-adenylate
D-galactose + O(2) = D-galacto-hexodialdose + H(2)O(2)
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
Hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans
(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
Quercetin + O(2) = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H(+)
GTP + IMP + L-aspartate = GDP + phosphate + N(6)-(1,2-dicarboxyethyl)-AMP
RH + [reduced NADPH--hemoprotein reductase] + O(2) = ROH + [oxidized NADPH--hemoprotein reductase] + H(2)O
(1a) (2R,3S)-3-isopropylmalate = 2-isopropylmaleate + H(2)O
Carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
Chorismate = prephenate
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
4-phosphonooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + L-glutamate
ATP + [biotin carboxyl-carrier protein]-biotin-N(6)-L-lysine + hydrogencarbonate- = ADP + phosphate + [biotin carboxyl-carrier protein]-carboxybiotin-N(6)-L-lysine
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
2 glutathione + ROOH = glutathione disulfide + H(2)O + ROH
ATP + propanoyl-CoA + HCO(3)(-) = ADP + phosphate + (S)-methylmalonyl-CoA
ATP + RNA(n) = diphosphate + RNA(n+1)
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
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.
A 5'-phosphopolynucleotide + H(2)O = a polynucleotide + phosphate
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
Isocitrate = succinate + glyoxylate
2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
(1a) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-N(tau)-phospho-L-histidine + 2/3-phospho-D-glycerate
ATP + FMN = diphosphate + FAD
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.
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-.
A carboxylic ester + H(2)O = an alcohol + a carboxylate
Cutin + H(2)O = cutin monomers
Choline = trimethylamine + acetaldehyde
Acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an N-acetyldiamine
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine(34) in tRNA(Leu) = S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine(34) in tRNA(Leu)
D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
ADP-alpha-D-glucose + D-glucose 6-phosphate = ADP + alpha,alpha-trehalose 6-phosphate
Eliminative cleavage of alginate to give oligosaccharides with 4-deoxy-alpha-L-erythro-hex-4-enuronosyl groups at their non-reducing ends and beta-D-mannuronate at their reducing end.
ATP + thymidine = ADP + thymidine 5'-phosphate
ATP + riboflavin = ADP + FMN
Acetyl-CoA + glycine = CoA + 2-amino-3-oxobutanoate
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.
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Shikimate + NADP(+) = 3-dehydroshikimate + NADPH
Exolytic cleavage of the (1->4)-beta-glycosidic linkage between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues in peptidoglycan, from either the reducing or the non-reducing ends of the peptidoglycan chains, with concomitant formation of a 1,6-anhydrobond in the MurNAc residue.
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP + glycerol = ADP + sn-glycerol 3-phosphate
ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate = ADP + 1D-myo-inositol hexakisphosphate
O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
Random hydrolysis of (1->6)-alpha-D-mannosidic linkages in unbranched (1->6)-mannans
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
NH(3) + 2 H(2)O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H(+)
ADP-D-ribose 1''-phosphate + H(2)O = ADP-D-ribose + phosphate
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
Alpha-D-glucose = beta-D-glucose

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Voltage-gated potassium channel subunit beta-2 Chains: A, C
Molecule details ›
Chains: A, C
Length: 333 amino acids
Theoretical weight: 37.35 KDa
Source organism: Rattus norvegicus
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P62483 (Residues: 35-367; 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, D
Molecule details ›
Chains: B, D
Length: 514 amino acids
Theoretical weight: 58.86 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:

Ligands and Environments


Cofactor: Ligand NAP 2 x NAP
2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P4212
Unit cell:
a: 144.271Å b: 144.271Å c: 284.06Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.211 0.247
Expression system: Komagataella pastoris