3lut

X-ray diffraction
2.9Å resolution

A Structural Model for the Full-length Shaker Potassium Channel Kv1.2

Released:
Source organism: Rattus norvegicus
Primary publication:
Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement.
Proc. Natl. Acad. Sci. U.S.A. 107 11352-7 (2010)
PMID: 20534430

Function and Biology Details

Reactions catalysed:
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
(1a) S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N(omega)-methyl-L-arginine
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
ATP = 3',5'-cyclic AMP + diphosphate
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
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 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).
A glutathione-S-conjugate + H(2)O = an (L-cysteinylglycine)-S-conjugate + L-glutamate
Hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and similar substrates, releasing cellobiose from the reducing ends of the chains.
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
Alpha-D-glucosamine 6-phosphate + H(2)O = D-fructose 6-phosphate + NH(3)
NH(3) + 2 H(2)O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H(+)
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
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.
ATP + thymidine = ADP + thymidine 5'-phosphate
Pectin + n H(2)O = n methanol + pectate
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.
Peptidylproline (omega=180) = peptidylproline (omega=0)
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
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.
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]
4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate
NTP + H(2)O = NDP + phosphate
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA 
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
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).
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
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
(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
L-asparagine + H(2)O = L-aspartate + NH(3)
A (5-L-glutamyl)-peptide + an amino acid = a peptide + a 5-L-glutamyl amino acid
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
RX + glutathione = HX + R-S-glutathione
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
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.
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
(2R)-2,3-dihydroxy-3-methylbutanoate + NADP(+) = (2S)-2-hydroxy-2-methyl-3-oxobutanoate + NADPH
Catechol + O(2) = cis,cis-muconate
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
5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H(2)O
5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
2 nitric oxide + 2 O(2) + NAD(P)H = 2 nitrate + NAD(P)(+) + H(+)
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-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)H
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
(S)-dihydroorotate + fumarate = orotate + succinate
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'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
1-haloalkane + H(2)O = a primary alcohol + halide
Succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + NAD(P)H
H(2)CO(3) = CO(2) + H(2)O
dUTP + H(2)O = dUMP + diphosphate
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
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
A beta-lactam + H(2)O = a substituted beta-amino acid
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
L-lysyl-tRNA(Lys) + phosphatidylglycerol = tRNA(Lys) + 3-O-L-lysyl-1-O-phosphatidylglycerol
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Voltage-gated potassium channel subunit beta-2 Chain: A
Molecule details ›
Chain: A
Length: 367 amino acids
Theoretical weight: 41.07 KDa
Source organism: Rattus norvegicus
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P62483 (Residues: 1-367; Coverage: 100%)
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 Chain: B
Molecule details ›
Chain: B
Length: 499 amino acids
Theoretical weight: 56.76 KDa
Source organism: Rattus norvegicus
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P63142 (Residues: 1-499; Coverage: 100%)
Gene name: Kcna2
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAP 1 x NAP
1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: I4
Unit cell:
a: 113.605Å b: 113.605Å c: 260.473Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.211 0.221
Expression system: Komagataella pastoris