PDBsum entry 5c11

Hydrolase

PDB id: 5c11

Contents

Protein chain

52 a.a.

Ligands

ALA-ARG-THR-4WQ-GLN-THR-ALA

Metals

_ZN ×2

PDB id:

5c11

Name:

Hydrolase

Title:

Crystal structure of jarid1a phd finger bound to histone h3c4me3 peptide

Structure:

Lysine-specific demethylase 5a. Chain: a. Fragment: phd finger domain, unp residues 1609-1659. Synonym: histone demethylase jarid1a,jumonji/arid domain-containing protein 1a,retinoblastoma-binding protein 2,rbbp-2. Engineered: yes. H3 peptide. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: kdm5a, jarid1a, rbbp2, rbp2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.80Å R-factor: 0.248 R-free: 0.279

Authors:

J.Huang,H.Li

Key ref:

J.Huang and h.li Crystal structure of jarid1a phd finger bound to hist h3c4me3 peptide. Nat commun, .

Date:

12-Jun-15 Release date: 25-Nov-15

Protein chain

P29375  (KDM5A_HUMAN) -  Lysine-specific demethylase 5A from Homo sapiens

Seq: 1690 a.a.

Struc: 52 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.14.11.67 - [histone H3]-trimethyl-L-lysine(4) demethylase.
• Reaction: N₆,N₆,N₆-trimethyl-L-lysyl₄-[histone H3] + 3 2-oxoglutarate + 3 O2 = L-lysyl₄-[histone H3] + 3 formaldehyde + 3 succinate + 3 CO2

N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] (Bound ligand (Het Group name = GLN) matches with 58.33% similarity) + 3 × 2-oxoglutarate + 3 × O2 = L-lysyl(4)-[histone H3] + 3 × formaldehyde (Bound ligand (Het Group name = ALA) matches with 40.00% similarity) + 3 × succinate + 3 × CO2 (Bound ligand (Het Group name = THR) matches with 50.00% similarity)

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