3pus

X-ray diffraction
2.08Å resolution

PHF2 Jumonji-NOG-Ni(II)

Released:
Source organism: Homo sapiens

Function and Biology Details

Reactions catalysed:
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
dUTP + H(2)O = dUMP + diphosphate
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
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.
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.
2 nitric oxide + 2 O(2) + NAD(P)H = 2 nitrate + NAD(P)(+) + H(+)
ATP + acetate + CoA = ADP + phosphate + acetyl-CoA
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Beta-D-ribopyranose = beta-D-ribofuranose
ATP + glycerol = ADP + sn-glycerol 3-phosphate
3-dehydroquinate = 3-dehydroshikimate + H(2)O
(1a) [acetyl-CoA C-acyltransferase]-S-acyl-L-cyteine + acetyl-CoA = 3-oxoacyl-CoA + [acetyl-CoA C-acyltransferase]-L-cyteine
ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate = ADP + 1D-myo-inositol hexakisphosphate
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
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.
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
RH + [reduced NADPH--hemoprotein reductase] + O(2) = ROH + [oxidized NADPH--hemoprotein reductase] + H(2)O
NTP + H(2)O = NDP + phosphate
D-mannose = D-fructose
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
Diphosphate + H(2)O = 2 phosphate
ATP + a protein = ADP + a phosphoprotein
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 + [biotin carboxyl-carrier protein]-biotin-N(6)-L-lysine + hydrogencarbonate- = ADP + phosphate + [biotin carboxyl-carrier protein]-carboxybiotin-N(6)-L-lysine
Cleaves -Ala-|-Ser- and -Ala-|-Ala- bonds in the scaffold protein.
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
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
A beta-lactam + H(2)O = a substituted beta-amino acid
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
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).
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Chorismate = prephenate
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
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 Chains: A, B
Molecule details ›
Chains: A, B
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 24-ID-C
Spacegroup: P21
Unit cell:
a: 65.353Å b: 96.979Å c: 66.194Å
α: 90° β: 89.78° γ: 90°
R-values:
R R work R free
0.177 0.175 0.232
Expression system: Escherichia coli