2cph

Solution NMR

Solution structure of the C-terminal RNA recognition motif of hypothetical RNA-binding protein RBM19

Released:
Source organism: Mus musculus
Entry authors: Nagata T, Muto Y, Inoue M, Kigawa T, Terada T, Shirouzu M, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reactions catalysed:
Hydrolysis of proteins in presence of ATP.
ATP + kanamycin = ADP + kanamycin 3'-phosphate
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
dUTP + H(2)O = dUMP + diphosphate
Acts on substrates that are at least partially unfolded. The cleavage site P1 residue is normally between a pair of hydrophobic residues, such as Val-|-Val
(8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate
Tetrahydropteroyl-(gamma-glutamyl)(n) + (n-1) H(2)O = 5,6,7,8-tetrahydrofolate + (n-1) L-glutamate
L-glutaminyl-peptide = 5-oxoprolyl-peptide + NH(3)
A beta-D-glucuronoside + H(2)O = D-glucuronate + an alcohol
Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + a protein = ADP + a phosphoprotein
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
N(6)-(Delta(2)-isopentenyl)-adenosine 5'-phosphate + H(2)O = N(6)-(dimethylallyl)adenine + D-ribose 5'-phosphate
D-glucose + O(2) = 2-dehydro-D-glucose + H(2)O(2)
6-phospho-D-glucono-1,5-lactone + H(2)O = 6-phospho-D-gluconate
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
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(79) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(79)
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.
1-haloalkane + H(2)O = a primary alcohol + halide
A phosphate monoester + H(2)O = an alcohol + phosphate
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)(+) + H(2)O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H
Formate + NAD(+) = CO(2) + NADH
Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
Diphosphate + H(2)O = 2 phosphate
3 malonyl-CoA + benzoyl-CoA = 4 CoA + 3,5-dihydroxybiphenyl + 4 CO(2)
2 pyruvate = 2-acetolactate + CO(2)
(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
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
Chorismate = prephenate
L-asparagine + H(2)O = L-aspartate + NH(3)
Urea + H(2)O = CO(2) + 2 NH(3)
A carboxylic ester + H(2)O = an alcohol + a carboxylate
Propane-1,2-diol = propanal + H(2)O
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.
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
4-phosphonooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + L-glutamate
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.
L-proline + a quinone = (S)-1-pyrroline-5-carboxylate + a quinol
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO(3)(-) = ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
(1,4-alpha-D-galacturonosyl)(n+m) + H(2)O = (1,4-alpha-D-galacturonosyl)(n) + (1,4-alpha-D-galacturonosyl)(m)
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and 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(+)
An acyl-[acyl-carrier protein] + NADP(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADPH
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
7,8-dihydroneopterin 3'-triphosphate = 6-pyruvoyl-5,6,7,8-tetrahydropterin + triphosphate
Thioredoxin + NADP(+) = thioredoxin disulfide + NADPH
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
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.
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
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
4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate
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
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
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
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
(+)-muconolactone = 5-oxo-4,5-dihydrofuran-2-acetate
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
ATP + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine = ADP + phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole
L-threonine + NAD(+) = L-2-amino-3-oxobutanoate + NADH
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
Aceneneuramate = N-acetyl-D-mannosamine + pyruvate
A beta-lactam + H(2)O = a substituted beta-amino acid
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
2-carboxy-2,5-dihydro-5-oxofuran-2-acetate = cis,cis-butadiene-1,2,4-tricarboxylate
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
2 reduced ferredoxin + NADP(+) + H(+) = 2 oxidized ferredoxin + NADPH
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
GTP = 3',5'-cyclic GMP + diphosphate
(1a) 2 cob(II)alamin + 2 [corrinoid adenosyltransferase] = 2 [corrinoid adenosyltransferase]-cob(II)alamin
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
6-hydroxymethyl-7,8-dihydropterin diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate
2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
(R)-mandelonitrile = cyanide + benzaldehyde
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
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'.
Hydrolysis of (1->6)-alpha-D-glucosidic linkages in (1->6)-alpha-D-glucans and derived oligosaccharides
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-.
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
Acetyl-CoA + glycine = CoA + 2-amino-3-oxobutanoate
L-alanine = D-alanine
2 H(2)O(2) = O(2) + 2 H(2)O
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 H(2)O
Peptidylproline (omega=180) = peptidylproline (omega=0)
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
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
L-histidinol phosphate + H(2)O = L-histidinol + phosphate
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
(S)-malate + NAD(+) = oxaloacetate + NADH
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine(34) in tRNA(Leu) = S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine(34) in tRNA(Leu)
D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
N,N-dimethylformamide + H(2)O = dimethylamine + formate
H(2)CO(3) = CO(2) + H(2)O
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
(1a) 2 L-ascorbate + H(2)O(2) + 2 H(+) = 2 monodehydroascorbate + 2 H(2)O
1D-chiro-inositol + NAD(+) = 2D-2,3,5/4,6-pentahydroxycyclohexanone + NADH
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 + thymidine = ADP + thymidine 5'-phosphate
A glutathione-S-conjugate + H(2)O = an (L-cysteinylglycine)-S-conjugate + L-glutamate
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).
Hydrolysis of proteins and small molecule substrates at -Asn-|-Xaa- bonds.
Formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin
(S)-malate + NADP(+) = pyruvate + CO(2) + NADPH
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
UDP-glucose + 2 NAD(+) + H(2)O = UDP-glucuronate + 2 NADH
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
ATP-dependent breakage, passage and rejoining of double-stranded DNA
ATP + AMP = 2 ADP
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
ATP + 6-hydroxymethyl-7,8-dihydropterin = AMP + 6-hydroxymethyl-7,8-dihydropterin diphosphate
ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met)
ATP + glycerol = ADP + sn-glycerol 3-phosphate
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
NAD(+) + protein-L-arginine = nicotinamide + N(omega)-(ADP-D-ribosyl)-protein-L-arginine
4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate
Release of N-terminal proline from a peptide.
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H(2)O
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.
ATP + acetate = ADP + acetyl phosphate
Myo-inositol + NAD(+) = 2,4,6/3,5-pentahydroxycyclohexanone + NADH
3-dehydroquinate = 3-dehydroshikimate + H(2)O
Produces alpha-D-fructofuranose beta-D-fructofuranose 1,2':2,1'-dianhydride (DFA I) by successively eliminating the diminishing (2->1)-beta-D-fructan (inulin) chain from the terminal D-fructosyl-D-fructosyl disaccharide.
ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophyl-tRNA(Trp)
ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
D-fructose 6-phosphate + phosphate = acetyl phosphate + D-erythrose 4-phosphate + H(2)O
A purine nucleoside + H(2)O = D-ribose + a purine base
A primary alcohol + NAD(+) = an aldehyde + NADH
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Leu is conserved at position P1 for all four cleavage sites. Alanine is found at position P1' of the NS4A-NS4B cleavage site, whereas serine is found at position P1' of the NS3-NS4A, NS4B-NS5A and NS5A-NS5B cleavage sites
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 + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His)
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
NADPH + NAD(+) + H(+)(Side 1) = NADP(+) + H(+)(Side 2) + NADH
(1a) 2 farnesyl diphosphate = diphosphate + presqualene diphosphate
4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O
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
ATP + propanoyl-CoA + HCO(3)(-) = ADP + phosphate + (S)-methylmalonyl-CoA
ATP + pyruvate + HCO(3)(-) = ADP + phosphate + oxaloacetate
A (5-L-glutamyl)-peptide + an amino acid = a peptide + a 5-L-glutamyl amino acid
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable RNA-binding protein 19 Chain: A
Molecule details ›
Chain: A
Length: 107 amino acids
Theoretical weight: 11.77 KDa
Source organism: Mus musculus
Expression system: Not provided
UniProt:
  • Canonical: Q8R3C6 (Residues: 816-909; Coverage: 10%)
Gene name: Rbm19
Sequence domains: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
Structure domains: Alpha-Beta Plaits

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Refinement method: torsion angle dyanamics, simulated annealing
Expression system: Not provided