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Catalytic Site Atlas

CSA LITERATURE entry for 1szd

E.C. namehistone/protein deacetylase
SpeciesSaccharomyces cerevisiae (Baker's yeast)
E.C. Number (IntEnz) 3.5.1.-
CSA Homologues of 1szd
CSA Entries With UniProtID P53686
CSA Entries With EC Number 3.5.1.-
PDBe Entry 1szd
PDBSum Entry 1szd
MACiE Entry M0240

Literature Report

IntroductionhST2, isolated from Saccharomyces cerevisiae, is a class III histone deacetylase (HDAC), though it also deacetylates other proteins. It belongs to the sirtuin (Sir2) family and catalyses the deacetylation of lysine residues from proteins using NAD+ as a co-substrate. The reaction produces a deacetylated lysine, nicotinamide and 2'-O-acetyl ADP-ribose. hST2 play roles in gene silencing and mediating life span extension. hST2 is of interest because its homologues in humans are potential drug targets for diseases associated with ageing, such as type-II diabetes, and Alzheimer's and Parkinson's diseases.
MechansimAided by lone pair donation of the acetylated lysine nitrogen, the acetyl oxygen acts as the nucleophile for associative, Sn2 attack on the C1' position of the nicotinamide-ribose of NAD+. The leaving group is nicotinamide and the reaction produces a 1'-O-alkylamidate intermediate. His135 deprotonates the 3'-hydroxyl, which then goes on to deprotonate the 2'-hydroxyl. The 2'-hydroxyl is then the nucleophile for attack on the acetyl carbon, forming a 1',2'-cyclic intermediate. The nitrogen of the lysine is protonated by His135 and then dissociates from the intermediate to form a cyclic acyl-oxonium ion. Water attacks the positively-charged carbon (stabilised by the two oxygens of the intermediate) with the lysine of the product deprotonating the positively-charged oxygen. The ring is opened when the exocyclic oxygen forms a carbonyl, with proton transfer to the 1' endocyclic oxygen. This produces 2'-O-acetyl ADP-ribose.

Catalytic Sites for 1szd

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA118118macie:sideChainAsp118 forms a hydrogen bond to the carboxamide nitrogen of NAD+. This interaction causes the carboxamide to rotate by 150 degrees and so disrupts the electronic resonance between the carboxamide and the pyridine ring. This weakens the glycosidic bond and destabilises the ground state. Asp118 also interacts with the the 2'-hydroxyl group of the ribose, which may aid NAD+ cleavage by inductive polarisation.
PheA4444macie:sideChainPhe44 protects the substrate during the formation of the 1'-O-alkylamidate intermediate, preventing hydrolysis. It may also play a part in stabilising the transition state of this reaction. Phe44 can then move between the intermediate and nicotinamide, preventing the nicotinamide exchange reaction. It also forms a hydrogen bond to the nitrogen of nicotinamide, holding it in the non-reactive conformation and preventing nicotinamide exchange.
PheA4444macie:mainChainAmidePhe44 protects the substrate during the formation of the 1'-O-alkylamidate intermediate, preventing hydrolysis. It may also play a part in stabilising the transition state of this reaction. Phe44 can then move between the intermediate and nicotinamide, preventing the nicotinamide exchange reaction. It also forms a hydrogen bond to the nitrogen of nicotinamide, holding it in the non-reactive conformation and preventing nicotinamide exchange.
ProA4242macie:mainChainCarbonylPro42 is part of a flexible loop that occludes the nicotinamide binding pocket after NAD+ cleavage. This prevents nicotinamide exchange. Pro42 also forms a hydrogen bond to the nicotinamide nitrogen after NAD+ cleavage. This holds the nicotinamide in a non-reactive position, thus preventing nicotinamide exchange.
HisA135135macie:sideChainHis135 deprotonates the 3'-hydroxyl of the 1'-O-alkylamidate intermediate. It protonates the nitrogen of the lysine in the 1',2'-cyclic intermediate, making it a better leaving group.
AspA4343macie:mainChainAmideAsp43 is part of a flexible loop that occludes the nicotinamide binding pocket after NAD+ cleavage. This prevents nicotinamide exchange. Asp43 also forms a hydrogen bond to the nicotinamide nitrogen after NAD+ cleavage. This holds the nicotinamide in a non-reactive position, thus preventing nicotinamide exchange.
ArgA4545macie:sideChainArg45 is thought to interact with the O4' of ribose in the 1'-O-alkylamidate intermediate. This is thought to stabilise the high-energy intermediate.
AsnA116116macie:sideChainAsn116 forms a water-mediated hydrogen bond to the ribose oxygen of NAD+. This may stabilise the transition state of NAD+ cleavage. The residue also interacts with the the 2'-hydroxyl group of the ribose, which may aid NAD+ cleavage by inductive polarisation. Asn116 also positions, and possibly activates, a water molecule for attack on the cyclic acyl-oxonium intermediate.

Literature References

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