1SZD: NAD-dependent deacetylase HST2

Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases. Determined by X-ray diffraction at 1.5 Å resolution. Released 15 Jun 2004.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 2,773
Mol. weight: 35.61 kDa
Ligands: APR, ZN
Released: 15 Jun 2004

Explore 1SZD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1SZD contains 17 α-helices and 17 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	9-21	13
β-strand	27-31	5	1
α-helix	33-39	7
α-helix	50-57	8
α-helix	63-67	5
β-strand	68	1	2
α-helix	69-74	6
α-helix	77-86	10
α-helix	95-105	11
β-strand	109-114	6	1
α-helix	120-123	4
α-helix	128-130	3
β-strand	131-133	3	1
β-strand	136-143	8	3
β-strand	149-150	2	3
α-helix	153-158	6
β-strand	169	1	4
β-strand	176	1	4
β-strand	177-181	5	3
α-helix	182-183	2
β-strand	184	1	2
β-strand	187	1	5
α-helix	188-189	2
α-helix	190-207	18
β-strand	218-222	5	1
β-strand	228-229	2	6
α-helix	231-233	3
β-strand	244-247	4	1
α-helix	254-257	4
β-strand	264-266	3	1
α-helix	270-281	12
α-helix	284-292	9

Chain B: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	5
β-strand	17-18	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent deacetylase HST2	A	protein	297	Saccharomyces cerevisiae	P53686 (AlphaFold model)
Histone H4 peptide	B	protein	10		P02309 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1SZD_1 NAD-dependent deacetylase HST2 (chains A)
MASMSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLAR
LKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNI
DTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELV
KPAIVFFGEDLPDSFSETWLNDSEWLREKITTSGKHPQQPLVIVVGTSLAVYPFASLPEE
IPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTAQ

Sequence of entity 2 (B), FASTA

>1SZD_2 Histone H4 peptide (chains B)
KGGAKRHRKI

Ligands and cofactors

ID	Name	Formula	Copies
APR	Adenosine-5-diphosphoribose	C15 H23 N5 O14 P2	1
ZN	Zinc ion	Zn	1

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD(+)-dependent Sir2 histone/protein deacetylases. Zhao, K., Harshaw, R., Chai, X. et al. Proc Natl Acad Sci U S A (2004) 101:8563-8568. DOI 10.1073/pnas.0401057101 · PubMed

Other PDB entries of the same protein (UniProt P53686 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Q1A 1.5 Å, Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP…
1SZC 1.75 Å, Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent…
7F4E 1.78 Å, Crystal structure of Hst2 in complex with H3K9bz peptide
7F51 1.98 Å, Crystal structure of Hst2 in complex with 2'-O-Benzoyl ADP Ribose
2OD2 2.0 Å, Crystal Structure of yHst2 I117F mutant bound to carba-NAD+ and an acetylated H4 peptide
2OD7 2.0 Å, Crystal Structure of yHst2 bound to the intermediate analogue ADP-HPD, and and aceylated…
2QQF 2.0 Å, Hst2 bound to ADP-HPD and Acetylated histone H4
2OD9 2.05 Å, Structural Basis for Nicotinamide Inhibition and Base Exchange in Sir2 Enzymes
2QQG 2.05 Å, Hst2 bound to ADP-HPD, acetyllated histone H4 and nicotinamide
1Q14 2.5 Å, Structure and autoregulation of the yeast Hst2 homolog of Sir2
1Q17 2.7 Å, Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP…

Browse structure collections

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