1cbs

X-ray diffraction
1.8Å resolution

CRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING PROTEINS I AND II IN COMPLEX WITH ALL-TRANS-RETINOIC ACID AND A SYNTHETIC RETINOID

Released:

Function and Biology Details

Reactions catalysed:
An aromatic primary alcohol + O(2) = an aromatic aldehyde + H(2)O(2)
Hydrolysis of terminal, non-reducing branched (1->3)-alpha-D-galactosidic residues, producing free D-galactose
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
dUTP + H(2)O = dUMP + diphosphate
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate 
A beta-D-glucuronoside + H(2)O = D-glucuronate + an alcohol
ATP + D-ribose = ADP + D-ribose 5-phosphate
ATP + a protein = ADP + a phosphoprotein
ATP + (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = ADP + phosphate + NADH
(S)-3-hydroxybutanoyl-CoA + NADP(+) = 3-acetoacetyl-CoA + NADPH
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
Oligoglycosylglucosyl-(1<->1)-ceramide + H(2)O = ceramide + oligoglycosylglucose
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.
A phosphate monoester + H(2)O = an alcohol + phosphate
Formate + NAD(+) = CO(2) + NADH
CoB + CoM + methanophenazine = CoM-S-S-CoB + dihydromethanophenazine
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
An aliphatic amide = a nitrile + H(2)O
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
Urea + H(2)O = CO(2) + 2 NH(3)
L-serine + L-homocysteine = L-cystathionine + H(2)O
Triacylglycerol + H(2)O = diacylglycerol + a carboxylate
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.
Triphosphate + [microsomal-membrane protein] = diphosphate + [microsomal-membrane protein] phosphate
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
Hydrolyzes poly(ADP-D-ribose) at glycosidic (1''-2') linkage of ribose-ribose bond to produce free ADP-D-ribose
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
An acyl-[acyl-carrier protein] + NADP(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADPH
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
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]
Prephenate = phenylpyruvate + H(2)O + CO(2)
NTP + H(2)O = NDP + phosphate
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
L-fucopyranose = L-fuculose
Cleaves proteins of the adenovirus and its host cell at two consensus sites: -Yaa-Xaa-Gly-Gly-|-Xaa- and -Yaa-Xaa-Gly-Xaa-|-Gly- (in which Yaa is Met, Ile or Leu, and Xaa is any amino acid).
6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH
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
dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-alpha-D-glucose
5,10-methylenetetrahydrofolate + dUMP + NADPH = dTMP + tetrahydrofolate + NADP(+)
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.
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
A beta-lactam + H(2)O = a substituted beta-amino acid
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
2 reduced ferredoxin + NADP(+) + H(+) = 2 oxidized ferredoxin + NADPH
GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H(2)O
3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholan-24-oylglycine + H(2)O = 3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholanate + glycine
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
L-aspartate = D-aspartate
D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
Hydrolysis of (1->4)-beta-D-glucosidic linkages in beta-D-glucans containing (1->3)- and (1->4)-bonds
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
L-histidinol + H(2)O + 2 NAD(+) = L-histidine + 2 NADH
UDP-glucose + 2 NAD(+) + H(2)O = UDP-glucuronate + 2 NADH
2 H(2)O(2) = O(2) + 2 H(2)O
A nitroalkane + H(2)O + O(2) = an aldehyde or ketone + nitrite + H(2)O(2)
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]
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
Hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains
Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans
L-aspartate 4-semialdehyde + phosphate + NADP(+) = L-4-aspartyl phosphate + NADPH
Hydrolysis of (1->6)-alpha-D-glucosidic linkages in pullulan, amylopectin and glycogen, and in the alpha- and beta-limit dextrins of amylopectin and glycogen.
(S)-malate = fumarate + H(2)O
N,N-dimethylformamide + H(2)O = dimethylamine + formate
H(2)CO(3) = CO(2) + H(2)O
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
A 4-O-methyl-D-glucopyranuronate ester + H(2)O = 4-O-methyl-D-glucuronic acid + an alcohol
A glutathione-S-conjugate + H(2)O = an (L-cysteinylglycine)-S-conjugate + L-glutamate
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.
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
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 + a 5-hydroxyfurocoumarin = S-adenosyl-L-homocysteine + a 5-methoxyfurocoumarin
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
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.
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
Methyl-CoM + CoB = CoM-S-S-CoB + methane
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]
ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys)
ATP + glycerol = ADP + sn-glycerol 3-phosphate
4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate
Succinate + a quinone = fumarate + a quinol
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
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.
IMP + H(2)O = inosine + phosphate
D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H(2)O
3-dehydroquinate = 3-dehydroshikimate + H(2)O
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
Random hydrolysis of (1->6)-alpha-D-mannosidic linkages in unbranched (1->6)-mannans
A purine nucleoside + H(2)O = D-ribose + a purine base
A primary alcohol + NAD(+) = an aldehyde + NADH
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical
Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucose residues with release of alpha-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
Hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides
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
A (5-L-glutamyl)-peptide + an amino acid = a peptide + a 5-L-glutamyl amino acid
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cellular retinoic acid-binding protein 2 Chain: A
Molecule details ›
Chain: A
Length: 137 amino acids
Theoretical weight: 15.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P29373 (Residues: 2-138; Coverage: 99%)
Gene name: CRABP2
Sequence domains: Lipocalin / cytosolic fatty-acid binding protein family
Structure domains: Lipocalin

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P212121
Unit cell:
a: 45.65Å b: 47.56Å c: 77.61Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.2 0.237
Expression system: Escherichia coli BL21(DE3)