PDBsum entry: 2yu2

Oxidoreductase

PDB id

2yu2

Contents

			Protein chain

					387 a.a. *

			Metals

					FE2

			Waters ×117

* Residue conservation analysis

PDB id:

2yu2

Links

Name:

Oxidoreductase

Title:

Crystal structure of hjhdm1a without a-ketoglutarate

Structure:

Jmjc domain-containing histone demethylation protein 1a. Chain: a. Fragment: residues 1-383, residues 450-517. Synonym: [histone-h3]-lysine-36 demethylase 1a, f-box/lrr- repeat protein 11, f-box and leucine-rich repeat protein 11, f-box protein fbl7, f-box protein lilina. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hjhdm1a. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.70Å

R-factor:

0.248

R-free:

0.287

Authors:

Z.Han

Key ref:

Z.Han et al. Structural basis for histone demethylation by jhdm1. To be published,

Date:

05-Apr-07

Release date:

24-Apr-07

PROCHECK

	Headers

	References

Protein chain

Q9Y2K7 (KDM2A_HUMAN) - Lysine-specific demethylase 2A

Seq: Struc:

Seq: Struc:

Seq: Struc:					1162 a.a. 387 a.a.*

Key:

PfamA domain

Secondary structure

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



		Enzyme reactions

Enzyme class:

E.C.1.14.11.27 - [Histone H3]-lysine-36 demethylase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

1.	Protein N₆,N₆-dimethyl-L-lysine + 2-oxoglutarate + O₂ = protein N₆-methyl-L-lysine + succinate + formaldehyde + CO₂
2.	Protein N₆-methyl-L-lysine + 2-oxoglutarate + O₂ = protein L-lysine + succinate + formaldehyde + CO₂

Protein N(6),N(6)-dimethyl-L-lysine	+	2-oxoglutarate	+	O(2)	=	protein N(6)-methyl-L-lysine	+	succinate	+	formaldehyde	+	CO(2)

Protein N(6)-methyl-L-lysine	+	2-oxoglutarate	+	O(2)	=	protein L-lysine	+	succinate	+	formaldehyde	+	CO(2)

Cofactor:

Fe(2+)

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