1p0r

Solution NMR

Solution Structure of UBL5 a human Ubiquitin-Like Protein

Released:
Source organism: Homo sapiens
Primary publication:
Structural analysis of UBL5, a novel ubiquitin-like modifier.
Protein Sci. 12 1562-6 (2003)
PMID: 12824502

Function and Biology Details

Reactions catalysed:
Phosphoenolpyruvate + D-arabinose 5-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
Hydrolysis of terminal, non-reducing branched (1->3)-alpha-D-galactosidic residues, producing free D-galactose
4 sulfur + 4 H(2)O + O(2) = 2 H(2)S + 2 HSO(3)(-) + 2 H(+)
dUTP + H(2)O = dUMP + diphosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Tetrahydropteroyl-(gamma-glutamyl)(n) + (n-1) H(2)O = 5,6,7,8-tetrahydrofolate + (n-1) L-glutamate
Catechol + O(2) = 2-hydroxymuconate-6-semialdehyde
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + a protein = ADP + a phosphoprotein
Prephenate + NADP(+) = 4-hydroxyphenylpyruvate + CO(2) + NADPH
L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H(2)O
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
D-glucose + O(2) = 2-dehydro-D-glucose + H(2)O(2)
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA 
Endonucleolytic cleavage to 5'-phosphomonoester.
H(2) + oxidized coenzyme F420 = reduced coenzyme F420
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.
GTP + H(2)O = GDP + phosphate
A beta-D-glucuronoside + H(2)O = D-glucuronate + an alcohol
4-amino-2-methyl-5-diphosphomethylpyrimidine + 2-((2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate = diphosphate + thiamine phosphate + CO(2)
(S)-2-haloacid + H(2)O = (R)-2-hydroxyacid + halide
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Cleavage of peptide bonds with very broad specificity.
Diphosphate + H(2)O = 2 phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
ATP + adenosine = ADP + AMP
UDP-alpha-D-galactopyranose = UDP-alpha-D-galactofuranose
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
6-phospho-beta-D-glucosyl-(1,4)-D-glucose + H(2)O = D-glucose + D-glucose 6-phosphate
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
Endohydrolysis of (1->4)-beta-D-linkages between D-galactose 4-sulfate and 3,6-anhydro-D-galactose in kappa-carrageenans.
Urea + H(2)O = CO(2) + 2 NH(3)
Propane-1,2-diol = propanal + H(2)O
L-phenylalanine + tetrahydrobiopterin + O(2) = L-tyrosine + 4a-hydroxytetrahydrobiopterin
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
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
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-|-
Sucrose + ((1->6)-alpha-D-glucosyl)(n) = D-fructose + ((1->6)-alpha-D-glucosyl)(n+1)
Thioredoxin + NADP(+) = thioredoxin disulfide + NADPH
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2)
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
(S)-dihydroorotate + fumarate = orotate + succinate
Meso-2,6-diaminoheptanedioate + H(2)O + NADP(+) = L-2-amino-6-oxoheptanedioate + NH(3) + NADPH
5-methyltetrahydrofolate + L-homocysteine = tetrahydrofolate + L-methionine
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
Glutathione + glutathionylspermidine + ATP = N(1),N(8)-bis(glutathionyl)spermidine + 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
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
Maltose = alpha,alpha-trehalose
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
sn-glycerol 3-phosphate + O(2) = glycerone phosphate + H(2)O(2)
A beta-lactam + H(2)O = a substituted beta-amino acid
(S)-dihydroorotate + H(2)O = N-carbamoyl-L-aspartate
5,6-dihydrouracil + H(2)O = 3-ureidopropanoate
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
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
D-glucose 6-phosphate = D-fructose 6-phosphate
L-arginine + H(2)O = L-ornithine + urea
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
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)
ATP + 4-methyl-5-(2-hydroxyethyl)thiazole = ADP + 4-methyl-5-(2-phosphonooxyethyl)thiazole 
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
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
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.
ATP + [I-kappa-B protein] = ADP + [I-kappa-B phosphoprotein]
L-alanine = D-alanine
2 H(2)O(2) = O(2) + 2 H(2)O
Peptidylproline (omega=180) = peptidylproline (omega=0)
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
3-hydroxy-2-methylpropanoate + NAD(+) = 2-methyl-3-oxopropanoate + NADH
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
(1a) 2 farnesyl diphosphate = diphosphate + presqualene diphosphate
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate = ADP + phosphate + (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate
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
N,N-dimethylformamide + H(2)O = dimethylamine + formate
H(2)CO(3) = CO(2) + H(2)O
S-(hydroxymethyl)glutathione + NAD(P)(+) = S-formylglutathione + NAD(P)H
(1a) 2 L-ascorbate + H(2)O(2) + 2 H(+) = 2 monodehydroascorbate + 2 H(2)O
Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends
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
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.
Acetyl-CoA + L-glutamate = CoA + N-acetyl-L-glutamate
ATP + thymidine = ADP + thymidine 5'-phosphate
L-glutamate = 4-aminobutanoate + CO(2)
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).
2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one + NAD(P)(+) = 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + NAD(P)H
D-glucose + NAD(P)(+) = D-glucono-1,5-lactone + NAD(P)H
(S)-malate + NADP(+) = pyruvate + CO(2) + NADPH
Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
(2E,6E)-farnesyl diphosphate + 4 isopentenyl diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
(S)-lactate + NAD(+) = pyruvate + NADH
ATP + (phosphate)(n) = ADP + (phosphate)(n+1)
H(2) + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H(+)
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met)
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
(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.
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O
Sucrose + (6)-beta-D-fructofuranosyl-(2->)(n) alpha-D-glucopyranoside = glucose + (6)-beta-D-fructofuranosyl-(2->)(n+1) alpha-D-glucopyranoside
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr)
Glutathione + (Glu(-Cys))(n)-Gly = Gly + (Glu(-Cys))(n+1)-Gly
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
A pyrimidine nucleoside + H(2)O = D-ribose + a pyrimidine base
D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
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
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
(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
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
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
NADPH + NAD(+) + H(+)(Side 1) = NADP(+) + H(+)(Side 2) + NADH
ATP + L-aspartate = ADP + 4-phospho-L-aspartate
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin-like protein 5 Chain: A
Molecule details ›
Chain: A
Length: 93 amino acids
Theoretical weight: 10.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BZL1 (Residues: 1-73; Coverage: 100%)
Gene name: UBL5
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Refinement method: simulated annealing
Expression system: Escherichia coli BL21(DE3)