PDBsum entry 4e4h

Oxidoreductase

PDB id: 4e4h

Contents

Protein chains

455 a.a.

Ligands

ACT

GOL

PEG

Metals

_FE ×4

Waters ×589

PDB id:

4e4h

Name:

Oxidoreductase

Title:

Crystal structure of histone demethylase no66

Structure:

Lysine-specific demethylase no66. Chain: a, b, c, d. Fragment: unp residues 183-641. Synonym: nucleolar protein 66, hsno66. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: c14orf169, no66. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.28Å R-factor: 0.204 R-free: 0.252

Authors:

M.Wu,Y.Tao,J.Zang

Key ref:

Y.Tao et al. Tructural basis for tetramerization-Dependent gene repression by histone demethylase no66. To be published, .

Date:

13-Mar-12 Release date: 30-Jan-13

Protein chains

Q9H6W3  (RIOX1_HUMAN) -  Ribosomal oxygenase 1 from Homo sapiens

Seq: 641 a.a.

Struc: 455 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.1.14.11.27 - [histone H3]-dimethyl-L-lysine(36) demethylase.
• Reaction: N₆,N₆-dimethyl-L-lysyl₃₆-[histone H3] + 2 2-oxoglutarate + 2 O2 = L-lysyl₃₆-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2

N(6),N(6)-dimethyl-L-lysyl(36)-[histone H3] (Bound ligand (Het Group name = GOL) matches with 45.45% similarity) + 2 × 2-oxoglutarate + 2 × O2 = L-lysyl(36)-[histone H3] (Bound ligand (Het Group name = ACT) matches with 75.00% similarity) + 2 × formaldehyde + 2 × succinate + 2 × CO2

• Cofactor: Fe(2+)
• Enzyme class 3: E.C.1.14.11.79 - protein-L-histidine (3S)-3-hydroxylase.
• Reaction: L-histidyl-[protein] + 2-oxoglutarate + O2 = (3S)-3-hydroxy-L-histidyl- [protein] + succinate + CO2

L-histidyl-[protein] (Bound ligand (Het Group name = GOL) matches with 45.45% similarity) + 2 × 2-oxoglutarate + 2 × O2 = (3S)-3-hydroxy-L-histidyl- [protein] + 2 × succinate (Bound ligand (Het Group name = ACT) matches with 75.00% similarity) + 2 × CO2

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site