5ke9

X-ray diffraction
2.34Å resolution

mouse Klf4 E446P ZnF1-3 and TpG/CpA sequence DNA complex structure

Released:

Function and Biology Details

Reactions catalysed:
Phosphoenolpyruvate + D-arabinose 5-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
4 sulfur + 4 H(2)O + O(2) = 2 H(2)S + 2 HSO(3)(-) + 2 H(+)
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
dUTP + H(2)O = dUMP + diphosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
ATP + D-ribose = ADP + D-ribose 5-phosphate
ATP + a protein = ADP + a phosphoprotein
GTP + H(2)O = formate + 2-amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)-dihydropteridine triphosphate
Hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans
(1a) [acetyl-CoA C-acyltransferase]-S-acyl-L-cyteine + acetyl-CoA = 3-oxoacyl-CoA + [acetyl-CoA C-acyltransferase]-L-cyteine
An aryl sulfate + H(2)O = a phenol + sulfate
Chloride + O(2) = chlorite
Oligoglycosylglucosyl-(1<->1)-ceramide + H(2)O = ceramide + oligoglycosylglucose
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
Glycolate + NADP(+) = glyoxylate + NADPH
(2R,3S)-catechin + NADP(+) + H(2)O = 2,3-trans-3,4-cis-leucocyanidin + NADPH
IMP + H(2)O = inosine + phosphate
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Diphosphate + H(2)O = 2 phosphate
S-adenosyl-L-methionine = S-adenosyl 3-(methylthio)propylamine + CO(2)
D-glycerate + NAD(P)(+) = hydroxypyruvate + NAD(P)H
(1a) 2 Fe(2+) + O(2) + 4 H(2)O = 2 (FeO(OH)) + 4 H(+) + H(2)O(2)
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
UDP-alpha-D-galactopyranose = UDP-alpha-D-galactofuranose
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
L-glutamine + H(2)O = L-glutamate + NH(3)
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O
Urea + H(2)O = CO(2) + 2 NH(3)
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
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 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.
Trypanothione + NADP(+) = trypanothione disulfide + NADPH
Triphosphate + [microsomal-membrane protein] = diphosphate + [microsomal-membrane protein] phosphate
(Ribonucleotide)(n)-2',3'-cyclic phosphate + H(2)O = (ribonucleotide)(n)-2'-phosphate
ATP + phenylacetate + CoA = AMP + diphosphate + phenylacetyl-CoA
FAD + [protein]-L-threonine = [protein]-FMN-L-threonine + AMP
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
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
Hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains
Hydrolysis of Xaa-|-Pro dipeptides. Also acts on aminoacyl-hydroxyproline analogs. No action on Pro-|-Pro.
Tetradecanoyl-CoA + an N-terminal-glycyl-[protein] = CoA + an N-terminal-N-tetradecanoylglycyl-[protein]
NTP + H(2)O = NDP + phosphate
H(2) + 2 ferricytochrome c3 = 2 H(+) + 2 ferrocytochrome c3
A (3R)-3-hydroxyacyl-[acyl-carrier protein] = a trans-2-enoyl-[acyl-carrier protein] + H(2)O
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
L-fucopyranose = L-fuculose
6-phospho-beta-D-glucosyl-(1,4)-D-glucose + H(2)O = D-glucose + D-glucose 6-phosphate
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
Oxalyl-CoA = formyl-CoA + CO(2)
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
Benzoylformate = benzaldehyde + CO(2)
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
UTP + N-acetyl-alpha-D-glucosamine 1-phosphate = diphosphate + UDP-N-acetyl-alpha-D-glucosamine
Carbamoyl phosphate + N(2)-succinyl-L-ornithine = phosphate + N-succinyl-L-citrulline
Citrate = acetate + oxaloacetate
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
Aceneneuramate = N-acetyl-D-mannosamine + pyruvate
A beta-lactam + H(2)O = a substituted beta-amino acid
3'-phosphoadenylyl sulfate + a phenol = adenosine 3',5'-bisphosphate + an aryl sulfate
3-deoxy-D-manno-octulosonate 8-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
dTDP-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H(2)O
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
D-glyceraldehyde 3-phosphate = glycerone phosphate
UTP + alpha-D-glucose 1-phosphate = diphosphate + UDP-glucose
(1a) L-methionine = methanethiol + 2-aminobut-2-enoate
D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
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'.
Acetyl-CoA + L-2,4-diaminobutanoate = CoA + N(4)-acetyl-L-2,4-diaminobutanoate
L-glutamate 5-semialdehyde + NAD(+) + H(2)O = L-glutamate + NADH
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-.
Maltose = alpha,alpha-trehalose
L-histidinol + H(2)O + 2 NAD(+) = L-histidine + 2 NADH
2 H(2)O(2) = O(2) + 2 H(2)O
Peptidylproline (omega=180) = peptidylproline (omega=0)
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
CO + H(2)O + 2 oxidized ferredoxin = CO(2) + 2 reduced ferredoxin + 2 H(+)
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH
L-aspartate 4-semialdehyde + phosphate + NADP(+) = L-4-aspartyl phosphate + NADPH
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
Succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + NAD(P)H
H(2)CO(3) = CO(2) + H(2)O
ADP-alpha-D-glucose + D-glucose 6-phosphate = ADP + alpha,alpha-trehalose 6-phosphate
ATP + L-citrulline + L-aspartate = AMP + diphosphate + N(omega)-(L-arginino)succinate
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.
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
ATP + thymidine = ADP + thymidine 5'-phosphate
ATP + adenylyl sulfate = ADP + 3'-phosphoadenylyl sulfate
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
UDP-N-acetyl-alpha-D-mannosamine + N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = UDP + N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
(1a) 2 geranylgeranyl diphosphate = diphosphate + prephytoene diphosphate
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
(1a) Man(9)GlcNAc(2)-[protein] + H(2)O = Man(8)GlcNAc(2)-[protein] (isomer 8A(1,2,3)B(1,2)) + beta-D-mannopyranose
(S)-lactate + NAD(+) = pyruvate + NADH
ATP + AMP = 2 ADP
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(36) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(36)
Methyl-CoM + CoB = CoM-S-S-CoB + methane
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec)
ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met)
5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
An aliphatic amide = a nitrile + H(2)O
Betaine aldehyde + NAD(+) + H(2)O = betaine + NADH
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
O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate
ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys)
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Propanoyl-CoA + phosphate = CoA + propanoyl phosphate
A pyrimidine nucleoside + H(2)O = D-ribose + a pyrimidine base
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
O-phospho-L-homoserine + H(2)O = L-threonine + phosphate
ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe)
Glycerone phosphate = methylglyoxal + phosphate
ATP + H(2)O = ADP + phosphate
L-proline + NAD(P)(+) = 1-pyrroline-5-carboxylate + NAD(P)H
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O
ATP + pyruvate + HCO(3)(-) = ADP + phosphate + oxaloacetate
(S)-acetoin + NAD(+) = diacetyl + NADH
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Krueppel-like factor 4 Chain: A
Molecule details ›
Chain: A
Length: 93 amino acids
Theoretical weight: 10.81 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q60793 (Residues: 396-483; Coverage: 18%)
Gene names: Ezf, Gklf, Klf4, Zie
Sequence domains: Zinc finger, C2H2 type
DNA (5'-D(*GP*AP*GP*GP*TP*GP*TP*GP*GP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.14 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*CP*AP*CP*AP*CP*CP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 2.95 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P43212
Unit cell:
a: 51.44Å b: 51.44Å c: 130.594Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.214 0.272
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided