1dsz

X-ray diffraction
1.7Å resolution

STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1

Released:

Function and Biology Details

Reactions catalysed:
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
S-adenosyl-L-methionine + uridine(2552) in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methyluridine(2552) in 23S rRNA
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
ATP + AMP = 2 ADP
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
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
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).
(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
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
NAD(P)H + a quinone = NAD(P)(+) + a hydroquinone
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.
5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H(2)O
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
Beta-D-ribopyranose = beta-D-ribofuranose
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
Release of N-terminal proline from a peptide.
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
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.
Naphthalene + NADH + O(2) = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD(+)
Geranyl diphosphate = gamma-terpinene + diphosphate
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
Choline = trimethylamine + acetaldehyde
ATP + a protein = ADP + a phosphoprotein
(R)-10-hydroxystearate = oleate + H(2)O
NTP + H(2)O = NDP + phosphate
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.
L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
Geranyl diphosphate = alpha-terpinene + diphosphate
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]
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
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.
ATP + thymidine = ADP + thymidine 5'-phosphate
Succinate + a quinone = fumarate + a quinol
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.
ATP + H(2)O = ADP + phosphate
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
Geranylgeranyl diphosphate = (+)-copalyl diphosphate
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
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
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction)
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
(S)-lactate + NAD(+) = pyruvate + NADH
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'.
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.
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 H(2)O
Phosphoenolpyruvate + D-erythrose 4-phosphate + H(2)O = 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate + phosphate
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]
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
L-histidinol phosphate + H(2)O = L-histidinol + phosphate
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
2 H(2)O(2) = O(2) + 2 H(2)O
A phosphate monoester + H(2)O = an alcohol + phosphate
Pectin + n H(2)O = n methanol + pectate
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
Diphosphate + H(2)O = 2 phosphate
Blasticidin S + H(2)O = deaminohydroxyblasticidin S + NH(3)
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
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).
A beta-lactam + H(2)O = a substituted beta-amino acid
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
An alpha-L-fucoside + H(2)O = L-fucose + an alcohol
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
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:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Retinoic acid receptor alpha Chain: A
Molecule details ›
Chain: A
Length: 86 amino acids
Theoretical weight: 10.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P10276 (Residues: 82-167; Coverage: 19%)
Gene names: NR1B1, RARA
Sequence domains: Zinc finger, C4 type (two domains)
Structure domains: Erythroid Transcription Factor GATA-1, subunit A
Retinoic acid receptor RXR-alpha Chain: B
Molecule details ›
Chain: B
Length: 85 amino acids
Theoretical weight: 9.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P19793 (Residues: 129-212; Coverage: 18%)
Gene names: NR2B1, RXRA
Sequence domains: Zinc finger, C4 type (two domains)
Structure domains: Erythroid Transcription Factor GATA-1, subunit A
DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.64 KDa
DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.54 KDa

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 80.66Å b: 33.9Å c: 101.86Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.198 0.267
Expression system: Escherichia coli