PDBsum entry 5d1c

Hydrolase

PDB id: 5d1c

Contents

Protein chains

364 a.a.

Ligands

ACE-ARG-HIS-ALY-ALY-MCM ×2

GOL

Metals

_ZN ×2

__K ×4

Waters ×819

PDB id:

5d1c

Name:

Hydrolase

Title:

Crystal structure of d233g-y306f hdac8 in complex with a tetrapeptide substrate

Structure:

Histone deacetylase 8. Chain: a, b. Synonym: hd8. Engineered: yes. Mutation: yes. Hdac8 fluor de lys tetrapeptide 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. Unidentified. Organism_taxid: 32644

Resolution:

1.42Å R-factor: 0.147 R-free: 0.167

Authors:

C.Decroos,N.H.Christianson,L.E.Gullett,C.M.Bowman,K.E.Christianson, M.A.Deardorff,D.W.Christianson

Key ref:

C.Decroos et al. (2015). Biochemical and structural characterization of HDAC8 mutants associated with Cornelia de Lange syndrome spectrum disorders. Biochemistry, 54, 6501-6513. PubMed id: 26463496 DOI: 10.1021/acs.biochem.5b00881

Date:

04-Aug-15 Release date: 21-Oct-15

Protein chains

Q9BY41  (HDAC8_HUMAN) -  Histone deacetylase 8 from Homo sapiens

Seq: 377 a.a.

Struc: 364 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.5b00881

Biochemistry 54:6501-6513 (2015)

PubMed id: 26463496

Biochemical and structural characterization of HDAC8 mutants associated with Cornelia de Lange syndrome spectrum disorders.

C.Decroos, N.H.Christianson, L.E.Gullett, C.M.Bowman, K.E.Christianson, M.A.Deardorff, D.W.Christianson.

ABSTRACT

Cornelia de Lange Syndrome (CdLS) spectrum disorders are characterized by multiple organ system congenital anomalies that result from mutations in genes encoding core cohesin proteins SMC1A, SMC3, and RAD21, or proteins that regulate cohesin function such as NIPBL and HDAC8. HDAC8 is the Zn(2+)-dependent SMC3 deacetylase required for cohesin recycling during the cell cycle, and 17 different HDAC8 mutants have been identified to date in children diagnosed with CdLS. As part of our continuing studies focusing on aberrant HDAC8 function in CdLS, we now report the preparation and biophysical evaluation of five human HDAC8 mutants: P91L, G117E, H180R, D233G, and G304R. Additionally, the double mutants D233G-Y306F and P91L-Y306F were prepared to enable cocrystallization of intact enzyme-substrate complexes. X-ray crystal structures of G117E, P91L-Y306F, and D233G-Y306F HDAC8 mutants reveal that each CdLS mutation causes structural changes that compromise catalysis and/or thermostability. For example, the D233G mutation disrupts the D233-K202-S276 hydrogen bond network, which stabilizes key tertiary structure interactions, thereby significantly compromising thermostability. Molecular dynamics simulations of H180R and G304R HDAC8 mutants suggest that the bulky arginine side chain of each mutant protrudes into the substrate binding site and also causes active site residue Y306 to fluctuate away from the position required for substrate activation and catalysis. Significantly, the catalytic activities of most mutants can be partially or fully rescued by the activator N-(phenylcarbamothioyl)-benzamide, suggesting that HDAC8 activators may serve as possible leads in the therapeutic management of CdLS.