PDBsum entry 2v5x

Hydrolase

PDB id: 2v5x

Contents

Protein chains

363 a.a. *

Ligands

V5X ×2

Metals

_ZN ×2

__K ×4

Waters ×321

* Residue conservation analysis

PDB id:

2v5x

Name:

Hydrolase

Title:

Crystal structure of hdac8-inhibitor complex

Structure:

Histone deacetylase 8. Chain: a, b. Synonym: hdac8, hd8. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.25Å R-factor: 0.198 R-free: 0.240

Authors:

S.Di Marco,A.Vannini,C.Volpari,P.Gallinari,P.Jones,M.Mattu,A.Carfi, R.Defrancesco,C.Steinkuhler

Key ref:

A.Vannini et al. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex. EMBO Rep, 8, 879-884. PubMed id: 17721440 DOI: 10.1038/sj.embor.7401047

Date:

10-Jul-07 Release date: 04-Sep-07

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 1 residue position (black cross)

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: 10.1038/sj.embor.7401047

EMBO Rep 8:879-884 (2007)

PubMed id: 17721440

Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex.

A.Vannini, C.Volpari, P.Gallinari, P.Jones, M.Mattu, A.Carfí, R.De Francesco, C.Steinkühler, S.Di Marco.

ABSTRACT

Histone deacetylases (HDACs)-an enzyme family that deacetylates histones and non-histone proteins-are implicated in human diseases such as cancer, and the first-generation of HDAC inhibitors are now in clinical trials. Here, we report the 2.0 A resolution crystal structure of a catalytically inactive HDAC8 active-site mutant, Tyr306Phe, bound to an acetylated peptidic substrate. The structure clarifies the role of active-site residues in the deacetylation reaction and substrate recognition. Notably, the structure shows the unexpected role of a conserved residue at the active-site rim, Asp 101, in positioning the substrate by directly interacting with the peptidic backbone and imposing a constrained cis-conformation. A similar interaction is observed in a new hydroxamate inhibitor-HDAC8 structure that we also solved. The crucial role of Asp 101 in substrate and inhibitor recognition was confirmed by activity and binding assays of wild-type HDAC8 and Asp101Ala, Tyr306Phe and Asp101Ala/Tyr306Phe mutants.

Selected figure(s)

Figure 1.
Figure 1 Structure of the human HDAC8–substrate complex. (A) Ribbon diagram of the two HDAC8–substrate complexes in the asymmetric unit. The substrate and residues involved in the head-to-head packing are shown in a stick representation. Carbon, oxygen and nitrogen for the substrate are green, red and blue, respectively. Zn^2+ and K^+ ions are represented as purple spheres. (B) Enlarged view of the substrate-binding site in the asymmetric unit with the 1.0 -contoured 2F[o]-F[c] electron density map. (C) HDAC8 monomer with the bound substrate. Atoms are coloured as in (A). (D) Enlarged view of the active site. Polar interactions are shown as dashed yellow lines. HDAC, histone deacetylase.

Figure 3.
Figure 3 Comparison of the structure of HDAC8–substrate with that of the HDAC8–hydroxamate inhibitor. (A) View of the substrate-binding site superimposed with the structure of the HDAC8–inhibitor (r.m.s.d.-C , 0.315 Å). Oxygen, nitrogen and carbon of the inhibitor are red, blue and cyan, respectively. Protein is cyan in the HDAC8–inhibitor structure. (B) Molecular surface of the HDAC8–substrate complex at the active-site entrance. Water molecules are shown as red spheres. (C) Molecular surface of the HDAC8–inhibitor complex. HDAC, histone deacetylase.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO Rep (2007, 8, 879-884) copyright 2007.

Figures were selected by the author.