PDBsum entry 5dc6

Hydrolase

PDB id: 5dc6

Contents

Protein chains

363 a.a.

Ligands

ACE-ARG-HIS-ALY-ALY-MCM ×2

GOL ×3

Metals

_ZN ×2

__K ×2

Waters ×610

PDB id:

5dc6

Name:

Hydrolase

Title:

Crystal structure of d176n-y306f hdac8 in complex with a tetrapeptide substrate

Structure:

Histone deacetylase 8. Chain: a, b. Synonym: hd8. Engineered: yes. Mutation: yes. Fluor-de-lys tetrapeptide assay substrate. Chain: c, d. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hdac8, hdacl1, cda07. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

1.55Å R-factor: 0.148 R-free: 0.166

Authors:

C.Decroos,M.S.Lee,D.W.Christianson

Key ref:

S.M.Gantt et al. (2016). General Base-General Acid Catalysis in Human Histone Deacetylase 8. Biochemistry, 55, 820-832. PubMed id: 26806311 DOI: 10.1021/acs.biochem.5b01327

Date:

23-Aug-15 Release date: 03-Feb-16

Protein chains

Q9BY41  (HDAC8_HUMAN) -  Histone deacetylase 8 from Homo sapiens

Seq: 377 a.a.

Struc: 363 a.a.*

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

Enzyme reactions

• Enzyme class 1: E.C.3.5.1.- - ?????
• Enzyme class 2: E.C.3.5.1.98 - histone deacetylase.
• Reaction: N₆-acetyl-L-lysyl-[histone] + H2O = L-lysyl-[histone] + acetate

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

Key reference

DOI no: 10.1021/acs.biochem.5b01327

Biochemistry 55:820-832 (2016)

PubMed id: 26806311

General Base-General Acid Catalysis in Human Histone Deacetylase 8.

S.M.Gantt, C.Decroos, M.S.Lee, L.E.Gullett, C.M.Bowman, D.W.Christianson, C.A.Fierke.

ABSTRACT

No abstract given.