1Q17: HST2 protein

Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide. Determined by X-ray diffraction at 2.7 Å resolution. Released 18 Nov 2003.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 7,261
Mol. weight: 103.45 kDa
Ligands: APR, ZN
Released: 18 Nov 2003

Explore 1Q17 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Q17 contains 57 α-helices and 46 β-strands across 3 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: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
α-helix	8-21	14
β-strand	27-31	5	2
α-helix	33-36	4
α-helix	51-53	3
α-helix	56-58	3
α-helix	63-67	5
β-strand	68	1	3
α-helix	69-74	6
α-helix	77-86	10
α-helix	95-105	11
β-strand	109-114	6	2
α-helix	120-123	4
α-helix	128-130	3
β-strand	131-133	3	2
β-strand	136-143	8	4
β-strand	149-150	2	4
α-helix	153-160	8
α-helix	167-168	2
β-strand	169	1	5
β-strand	176	1	5
β-strand	177-181	5	4
β-strand	184	1	3
α-helix	187-189	3
α-helix	190-205	16
β-strand	218-222	5	2
β-strand	228-229	2	6
α-helix	231-233	3
α-helix	235-237	3
β-strand	243-247	5	2
α-helix	253-255	3
β-strand	264-266	3	2
α-helix	270-280	11
α-helix	284-293	10

Chain B: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	6
β-strand	5	1	7
α-helix	8-21	14
β-strand	27-31	5	7
α-helix	33-39	7
α-helix	51-53	3
α-helix	56-58	3
α-helix	63-67	5
β-strand	68	1	8
α-helix	69-74	6
α-helix	77-86	10
α-helix	95-105	11
β-strand	109-114	6	7
α-helix	120-123	4
α-helix	128-130	3
β-strand	131-133	3	7
β-strand	136-143	8	9
β-strand	149-150	2	9
α-helix	152-160	9
α-helix	167-168	2
β-strand	169	1	10
β-strand	176	1	10
β-strand	177-181	5	9
β-strand	184	1	8
α-helix	187-189	3
α-helix	190-206	17
β-strand	218-222	5	7
β-strand	228-229	2	11
α-helix	231-233	3
α-helix	235-237	3
β-strand	244-247	4	7
α-helix	253-257	5
β-strand	264-266	3	7
α-helix	270-281	12
α-helix	284-292	9

Chain C: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	11
α-helix	8-20	13
β-strand	27-31	5	12
α-helix	33-39	7
α-helix	51-53	3
α-helix	56-58	3
α-helix	63-67	5
β-strand	68	1	13
α-helix	69-74	6
α-helix	77-83	7
α-helix	84-86	3
α-helix	95-105	11
β-strand	109-114	6	12
α-helix	120-123	4
α-helix	128-130	3
β-strand	131-133	3	12
β-strand	136-143	8	14
β-strand	149-150	2	14
α-helix	153-157	5
β-strand	169	1	15
β-strand	176	1	15
β-strand	177-181	5	14
β-strand	184	1	13
α-helix	187-189	3
α-helix	190-204	15
α-helix	214-216	3
β-strand	219-222	4	12
β-strand	228-229	2	1
α-helix	231-233	3
β-strand	244-247	4	12
α-helix	253-256	4
β-strand	264-266	3	12
α-helix	270-281	12
α-helix	284-292	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HST2 protein	A, B, C	protein	300	Saccharomyces cerevisiae	P53686 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>1Q17_1 HST2 protein (chains A, B, C)
HHGMASMSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHN
LARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYT
QNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCG
ELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITTSGKHPQQPLVIVVGTSLAVYPFASL
PEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTAQ

Ligands and cofactors

ID	Name	Formula	Copies
APR	Adenosine-5-diphosphoribose	C15 H23 N5 O14 P2	3
ZN	Zinc ion	Zn	3

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

Primary citation

Structure of the Yeast Hst2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl ADP Ribose and Histone Peptide. Zhao, K., Chai, X., Marmorstein, R. Structure (2003) 11:1403-1411. DOI 10.1016/j.str.2003.09.016 · 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…
1SZD 1.5 Å, Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent…
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

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