5THT: Crystal Structure of G303A HDAC8 in complex with M344

Citation:
Abstract
Histone deacetylase 8 (HDAC8) catalyzes the hydrolysis of acetyl-l-lysine to yield products l-lysine and acetate through a mechanism in which a nucleophilic water molecule is activated by a histidine general base and a catalytic metal ion (Zn(2+) or Fe(2+)). Acetyl-l-lysine also requires activation by metal coordination and a hydrogen bond with catalytic tyrosine Y306, which also functions in transition state stabilization. Interestingly, Y306 is located in the conserved glycine-rich loop G(302)GGGY. The potential flexibility afforded by the tetraglycine segment may facilitate induced-fit conformational changes in Y306 between "in" and "out" positions, as observed in related deacetylases. To probe the catalytic importance of the glycine-rich loop in HDAC8, we rigidified this loop by preparing the G302A, G303A, G304A, and G305A mutants and measured their steady state kinetics and determined their X-ray crystal structures. Substantial losses of catalytic efficiency are observed (10-500-fold based on kcat/KM), particularly for G304A HDAC8 and G305A HDAC8. These mutants also exhibit the greatest structural changes for catalytic tyrosine Y306 (1.3-1.7 A shifts of the phenolic hydroxyl group). Molecular dynamics simulations further indicate that G304 and G305 undergo pronounced structural changes as residue 306 undergoes a transition between "in" and "out" conformations. Thus, the G304A and G305A substitutions likely compromise the position and conformational changes of Y306 required for substrate activation and transition state stabilization. The G302A and G303A substitutions have less severe catalytic consequences, and these substitutions may influence an internal channel through which product acetate is believed to exit.
PDB ID: 5THTDownload
MMDB ID: 145886
PDB Deposition Date: 2016/9/30
Updated in MMDB: 2016/12
Experimental Method:
x-ray diffraction
Resolution: 2.407  Å
Source Organism:
Similar Structures:
Biological Unit for 5THT: monomeric; determined by author and by software (PISA)
Molecular Components in 5THT
Label Count Molecule
Protein (1 molecule)
1
Histone Deacetylase 8(Gene symbol: HDAC8)
Molecule annotation
Chemicals (11 molecules)
1
2
2
1
3
2
4
6
* Click molecule labels to explore molecular sequence information.

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