3pua

X-ray diffraction
1.89Å resolution

PHF2 Jumonji-NOG-Ni(II)

Released:
Source organism: Homo sapiens

Function and Biology Details

Reactions catalysed:
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
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'.
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
D-ribose 5-phosphate = D-ribulose 5-phosphate
ADP-D-ribose 1''-phosphate + H(2)O = ADP-D-ribose + phosphate
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.
Chorismate = prephenate
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.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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
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-.
ATP + RNA(n) = diphosphate + RNA(n+1)
Succinate + a quinone = fumarate + a quinol
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinose
4a-hydroxytetrahydrobiopterin = 6,7-dihydrobiopterin + H(2)O
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
(S)-dihydroorotate + fumarate = orotate + succinate
NTP + H(2)O = NDP + phosphate
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
A 5'-phosphopolynucleotide + H(2)O = a polynucleotide + phosphate
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
(S)-malate = fumarate + H(2)O
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
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.
ADP-alpha-D-glucose + D-glucose 6-phosphate = ADP + alpha,alpha-trehalose 6-phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
ATP + H(2)O = ADP + phosphate
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
S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
A chalcone = a flavanone
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
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
L-asparagine + H(2)O = L-aspartate + NH(3)
UDP-alpha-D-glucuronate + NAD(+) = UDP-beta-L-threo-pentapyranos-4-ulose + CO(2) + NADH
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
S-formylglutathione + H(2)O = glutathione + formate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase PHF2 Chain: A
Molecule details ›
Chain: A
Length: 392 amino acids
Theoretical weight: 44.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75151 (Residues: 60-451; Coverage: 36%)
Gene names: CENP-35, KIAA0662, PHF2
Sequence domains:
Structure domains:

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 109.575Å b: 65.767Å c: 66.612Å
α: 90° β: 102.09° γ: 90°
R-values:
R R work R free
0.167 0.164 0.21
Expression system: Escherichia coli