2ypb

X-ray diffraction
2.87Å resolution

Function and Biology Details

Reactions catalysed:
Glutarate + 2-oxoglutarate + O(2) = (S)-2-hydroxyglutarate + succinate + CO(2)
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = (S)-allantoin + CO(2)
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
ATP = 3',5'-cyclic AMP + diphosphate
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
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.
Phosphoenolpyruvate + D-erythrose 4-phosphate + H(2)O = 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate + 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).
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(27) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(27)
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
Peptidylproline (omega=180) = peptidylproline (omega=0)
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'.
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(+)
ATP + a protein = ADP + a phosphoprotein
2 nitric oxide + 2 O(2) + NAD(P)H = 2 nitrate + NAD(P)(+) + H(+)
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + H(2)O = 4-O-(beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 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.
Acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an N-acetyldiamine
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Blasticidin S + H(2)O = deaminohydroxyblasticidin S + NH(3)
NTP + H(2)O = NDP + phosphate
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Random hydrolysis of (1->6)-alpha-D-mannosidic linkages in unbranched (1->6)-mannans
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
2-iminobutanoate + H(2)O = 2-oxobutanoate + NH(3)
17-alpha-hydroxypregnenolone + [reduced NADPH--hemoprotein reductase] + O(2) = 3-beta-hydroxyandrost-5-en-17-one + acetate + [oxidized NADPH--hemoprotein reductase] + H(2)O
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
A C(21)-steroid + [reduced NADPH--hemoprotein reductase] + O(2) = a 17-alpha-hydroxy-C(21)-steroid + [oxidized NADPH--hemoprotein reductase] + H(2)O
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
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 (1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
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
5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
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.
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
1-haloalkane + H(2)O = a primary alcohol + halide
(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
ATP + H(2)O = ADP + phosphate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
(S)-lactate + NAD(+) = pyruvate + NADH
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-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
Thioredoxin + ROOH = thioredoxin disulfide + H(2)O + ROH
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
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.
7,8-dihydroneopterin 3'-triphosphate + H(2)O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + triphosphate
Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO(2)
Diphosphate + H(2)O = 2 phosphate
AMP + H(2)O = D-ribose 5-phosphate + adenine
Cleavage of peptide bonds with very broad specificity.
(S)-dihydroorotate + fumarate = orotate + succinate
ATP + thymidine = ADP + thymidine 5'-phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
Aceneneuramate = N-acetyl-D-mannosamine + pyruvate
ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamate 5-phosphate
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
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
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):
T-cell acute lymphocytic leukemia protein 1 Chain: A
Molecule details ›
Chain: A
Length: 91 amino acids
Theoretical weight: 10.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P17542 (Residues: 180-253; Coverage: 22%)
Gene names: BHLHA17, SCL, TAL1, TCL5
Sequence domains: Helix-loop-helix DNA-binding domain
Structure domains: Helix-loop-helix DNA-binding domain
Transcription factor E2-alpha Chain: B
Molecule details ›
Chain: B
Length: 82 amino acids
Theoretical weight: 9.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P15923 (Residues: 538-616; Coverage: 12%)
  • Best match: P15923-2 (Residues: 535-613)
Gene names: BHLHB21, E2A, ITF1, TCF3
Sequence domains: Helix-loop-helix DNA-binding domain
Structure domains: Helix-loop-helix DNA-binding domain
EBOX FORWARD Chain: E
Molecule details ›
Chain: E
Length: 11 nucleotides
Theoretical weight: 3.28 KDa
EBOX REVERSE Chain: F
Molecule details ›
Chain: F
Length: 11 nucleotides
Theoretical weight: 3.42 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: C2221
Unit cell:
a: 73.193Å b: 152.882Å c: 55.412Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.255 0.254 0.288
Expression system: Escherichia coli