2ld5

Solution NMR

Solution NMR-derived complex structure of Hoxa13 DNA binding domain bound to DNA

Released:

Function and Biology Details

Reactions catalysed:
Phosphoenolpyruvate + N-acetyl-D-mannosamine + H(2)O = phosphate + N-acetylneuraminate
Phosphoenolpyruvate + D-erythrose 4-phosphate + H(2)O = 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate + phosphate
Diphosphate + D-fructose 6-phosphate = phosphate + D-fructose 1,6-bisphosphate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
4-coumarate = 4-vinylphenol + CO(2)
D-glucose 6-phosphate = D-fructose 6-phosphate
Nitrite + acceptor = nitrate + reduced acceptor
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
(8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate
D-glucuronate = D-fructuronate
ATP + D-ribose = ADP + D-ribose 5-phosphate
ATP + a protein = ADP + a phosphoprotein
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
(1a) glutaryl-CoA + electron-transfer flavoprotein = (E)-glutaconyl-CoA + reduced electron-transfer flavoprotein
(1a) [acetyl-CoA C-acyltransferase]-S-acyl-L-cyteine + acetyl-CoA = 3-oxoacyl-CoA + [acetyl-CoA C-acyltransferase]-L-cyteine
Chloride + O(2) = chlorite
(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
Penicillin + H(2)O = a carboxylate + 6-aminopenicillanate
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
6-hydroxymethyl-7,8-dihydropterin diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
S-adenosyl-L-methionine = S-adenosyl 3-(methylthio)propylamine + CO(2)
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
L-threonine = glycine + acetaldehyde
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
2-deoxy-D-gluconate + NAD(+) = 3-dehydro-2-deoxy-D-gluconate + NADH
UDP-alpha-D-galactopyranose = UDP-alpha-D-galactofuranose
An aliphatic amide = a nitrile + H(2)O
(1a) L-tyrosine + 1/2 O(2) = L-dopa
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
Urea + H(2)O = CO(2) + 2 NH(3)
Triacylglycerol + H(2)O = diacylglycerol + a carboxylate
L-alanine = D-alanine
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
Endohydrolysis of (1->6)-alpha-D-glucosidic linkages in dextran
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
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
Hydrolysis of Xaa-|-Pro dipeptides. Also acts on aminoacyl-hydroxyproline analogs. No action on Pro-|-Pro.
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
L-erythro-3,5-diaminohexanoate + H(2)O + NAD(+) = (S)-5-amino-3-oxohexanoate + NH(3) + NADH
Tetradecanoyl-CoA + an N-terminal-glycyl-[protein] = CoA + an N-terminal-N-tetradecanoylglycyl-[protein]
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
ATP + H(2)O = ADP + phosphate
NTP + H(2)O = NDP + phosphate
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
A (3R)-3-hydroxyacyl-[acyl-carrier protein] = a trans-2-enoyl-[acyl-carrier protein] + H(2)O
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
L-methionine + thioredoxin disulfide + H(2)O = L-methionine (S)-S-oxide + thioredoxin
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
UTP + N-acetyl-alpha-D-glucosamine 1-phosphate = diphosphate + UDP-N-acetyl-alpha-D-glucosamine
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.
Isocitrate = succinate + glyoxylate
ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO(2)
A chalcone = a flavanone
A beta-lactam + H(2)O = a substituted beta-amino acid
5,6-dihydrouracil + H(2)O = 3-ureidopropanoate
Hydrolysis of (1->4)-beta-D-galactosidic linkages in agarose, giving the tetramer as the predominant product
2 reduced ferredoxin + NADP(+) + H(+) = 2 oxidized ferredoxin + NADPH
5,6,7,8-tetrahydrobiopterin + 2 NADP(+) = biopterin + 2 NADPH
Chorismate + L-glutamine = anthranilate + pyruvate + L-glutamate
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
GTP = 3',5'-cyclic GMP + diphosphate
ATP = 3',5'-cyclic AMP + diphosphate
(1a) 2 cob(II)alamin + 2 [corrinoid adenosyltransferase] = 2 [corrinoid adenosyltransferase]-cob(II)alamin
L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
L-arabinose = L-ribulose
D-xylopyranose = D-xylulose
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).
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'.
L-glutamate 5-semialdehyde + NAD(+) + H(2)O = L-glutamate + NADH
Alditol + NAD(P)(+) = aldose + NAD(P)H
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Dolichyl diphosphooligosaccharide + [protein]-L-asparagine = dolichyl diphosphate + a glycoprotein with the oligosaccharide chain attached by N-beta-D-glycosyl linkage to a protein L-asparagine
D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
Succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + NAD(P)H
N,N-dimethylformamide + H(2)O = dimethylamine + formate
D-glucosyl-N-acylsphingosine + H(2)O = D-glucose + N-acylsphingosine
ATP + H(2)O + vitamin B12-[cobalamin-binding protein](Side 1) = ADP + phosphate + vitamin B12(Side 2) + [cobalamin-binding protein](Side 1)
Sarcosine + H(2)O + O(2) = glycine + formaldehyde + H(2)O(2)
GTP + IMP + L-aspartate = GDP + phosphate + N(6)-(1,2-dicarboxyethyl)-AMP
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-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.
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-adenosyl-L-homocysteine + H(2)O = L-homocysteine + adenosine
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
ATP + formate + tetrahydrofolate = ADP + phosphate + 10-formyltetrahydrofolate
Methylamine + H(2)O + 2 oxidized [amicyanin] = formaldehyde + NH(3) + 2 reduced [amicyanin]
L-glutamate = 4-aminobutanoate + CO(2)
N(6)-prenyladenine + acceptor + H(2)O = adenine + 3-methylbut-2-enal + reduced acceptor
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
A primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L) + 2 H(+)
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
S-adenosyl-L-methionine + cytidine(1402) in 16S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine(1402) in 16S rRNA 
ATP + phenylacetate + CoA = AMP + diphosphate + phenylacetyl-CoA
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
ATP + 6-hydroxymethyl-7,8-dihydropterin = AMP + 6-hydroxymethyl-7,8-dihydropterin diphosphate
ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met)
4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate
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.
An aldehyde + NAD(+) + H(2)O = a carboxylate + NADH
Hydroxymethylbilane = uroporphyrinogen III + H(2)O
UDP-glucose + (1,4-beta-D-glucosyl)(n) = UDP + (1,4-beta-D-glucosyl)(n+1)
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
ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr)
(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
n ATP + n H(2)O + a microtubule = n ADP + n phosphate + (n+1) alpha/beta tubulin heterodimers
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
Hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides
L-proline + NAD(P)(+) = 1-pyrroline-5-carboxylate + NAD(P)H
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
L-ornithine = L-proline + NH(3)
ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamate 5-phosphate
4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O
2-hydroxy-2H-chromene-2-carboxylate = (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate
2-iminobutanoate + H(2)O = 2-oxobutanoate + NH(3)
ATP + 3-phospho-D-glycerate = ADP + 3-phospho-D-glyceroyl phosphate
L-glutaminyl-peptide = 5-oxoprolyl-peptide + NH(3)
ATP + acetate = ADP + acetyl phosphate
Biochemical function:
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):
Homeobox protein Hox-A13 Chain: A
Molecule details ›
Chain: A
Length: 71 amino acids
Theoretical weight: 8.67 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q62424 (Residues: 320-386; Coverage: 17%)
Gene names: Hox-1.10, Hoxa13
Sequence domains: Homeodomain
Structure domains: Homeodomain-like
DNA (5'-D(*CP*AP*AP*AP*TP*AP*AP*AP*AP*TP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.33 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(P*GP*AP*TP*TP*TP*TP*AP*TP*TP*TP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Chemical shift assignment: 27%
Refinement method: simulated annealing
Chemical shifts: BMR16577  
Expression systems:
  • Escherichia coli
  • Not provided