1S7G: The Mechanism and Regulation of Sir2 Enzymes

Structural Basis for the Mechanism and Regulation of Sir2 Enzymes. Determined by X-ray diffraction at 2.3 Å resolution. Released 23 Mar 2004.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Archaeoglobus fulgidus
Chains: 5
Atoms: 10,187
Mol. weight: 148.49 kDa
Ligands: 2PE, NAD, ZN, APR
Released: 23 Mar 2004

Explore 1S7G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1S7G contains 77 α-helices and 55 β-strands across 5 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: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	18-22	5	1
α-helix	24-30	7
α-helix	41-44	4
α-helix	47-51	5
β-strand	52	1	2
α-helix	53-58	6
α-helix	60-69	10
α-helix	80-90	11
β-strand	94-99	6	1
α-helix	105-108	4
β-strand	114-116	3	1
β-strand	119-126	8	3
β-strand	132-134	3	3
α-helix	135-137	3
α-helix	139-143	5
β-strand	158-162	5	3
β-strand	165	1	2
α-helix	171-183	13
β-strand	186-190	5	1
α-helix	202-209	8
β-strand	212-217	6	1
α-helix	224-226	3
β-strand	229-232	4	1
α-helix	235-250	16

Chain B: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	18-22	5	4
α-helix	24-26	3
α-helix	28-30	3
α-helix	37-42	6
α-helix	47-50	4
β-strand	52	1	5
α-helix	53-58	6
α-helix	60-67	8
α-helix	80-90	11
β-strand	94-99	6	4
α-helix	105-109	5
β-strand	114-116	3	4
β-strand	119-126	8	6
β-strand	132-134	3	6
α-helix	135-138	4
α-helix	139-143	5
β-strand	158-162	5	6
β-strand	165	1	5
α-helix	168-170	3
α-helix	171-183	13
β-strand	186-190	5	4
α-helix	202-208	7
β-strand	212-217	6	4
α-helix	224-226	3
β-strand	229-232	4	4
α-helix	235-250	16

Chain C: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-13	12
β-strand	18-22	5	7
α-helix	24-30	7
α-helix	37-42	6
α-helix	47-50	4
β-strand	52	1	8
α-helix	53-58	6
α-helix	60-68	9
α-helix	80-90	11
β-strand	94-99	6	7
α-helix	105-108	4
β-strand	114-116	3	7
β-strand	119-126	8	9
β-strand	132-134	3	9
α-helix	135-138	4
α-helix	139-143	5
α-helix	146-148	3
β-strand	158-162	5	9
β-strand	165	1	8
α-helix	171-183	13
β-strand	186-190	5	7
α-helix	202-208	7
β-strand	212-217	6	7
α-helix	224-226	3
β-strand	229-232	4	7
α-helix	235-251	17

Chain D: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
β-strand	18-22	5	10
α-helix	24-26	3
α-helix	41-44	4
α-helix	47-50	4
β-strand	52	1	11
α-helix	53-58	6
α-helix	60-69	10
α-helix	80-90	11
β-strand	94-99	6	10
α-helix	105-109	5
β-strand	114-116	3	10
β-strand	119-126	8	12
β-strand	132-134	3	12
α-helix	135-137	3
α-helix	139-143	5
α-helix	146-148	3
β-strand	158-162	5	12
α-helix	163-164	2
β-strand	165	1	11
α-helix	171-183	13
β-strand	186-190	5	10
α-helix	202-209	8
β-strand	212-217	6	10
α-helix	224-226	3
β-strand	229-232	4	10
α-helix	235-251	17

Chain E: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
β-strand	18-22	5	13
α-helix	24-30	7
α-helix	41-43	3
α-helix	47-50	4
β-strand	52	1	14
α-helix	53-58	6
α-helix	60-69	10
α-helix	80-90	11
β-strand	94-99	6	13
α-helix	105-108	4
β-strand	114-116	3	13
β-strand	119-126	8	15
β-strand	132-134	3	15
α-helix	135-137	3
α-helix	139-143	5
α-helix	146-148	3
β-strand	158-162	5	15
β-strand	165	1	14
α-helix	168-170	3
α-helix	171-182	12
β-strand	186-190	5	13
α-helix	201-207	7
β-strand	212-217	6	13
α-helix	224-226	3
β-strand	229-232	4	13
α-helix	235-249	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent deacetylase 2	A, B, C, D, E	protein	253	Archaeoglobus fulgidus	O30124 (AlphaFold model)

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

>1S7G_1 NAD-dependent deacetylase 2 (chains A, B, C, D, E)
MEDEIRKAAEILAKSKHAVVFTGAGISAESGIPTFRGEDGLWRKYDPEEVASISGFKRNP
RAFWEFSMEMKDKLFAEPNPAHYAIAELERMGIVKAVITQNIDMLHQRAGSRRVLELHGS
MDKLDCLDCHETYDWSEFVEDFNKGEIPRCRKCGSYYVKPRVVLFGEPLPQRTLFEAIEE
AKHCDAFMVVGSSLVVYPAAELPYIAKKAGAKMIIVNAEPTMADPIFDVKIIGKAGEVLP
KIVEEVKRLRSEK

Ligands and cofactors

ID	Name	Formula	Copies
2PE	Nonaethylene glycol	C18 H38 O10	1
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	3
ZN	Zinc ion	Zn	9
APR	Adenosine-5-diphosphoribose	C15 H23 N5 O14 P2	1

Water and common crystallization additives (PG4, P6G, EDO, 1PE, SO4) are not listed.

Primary citation

Structural basis for the mechanism and regulation of sir2 enzymes. Avalos, J.L., Boeke, J.D., Wolberger, C. Mol Cell (2004) 13:639-648. DOI 10.1016/S1097-2765(04)00082-6 · PubMed

Other PDB entries of the same protein (UniProt O30124 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4TWJ 1.65 Å, The structure of Sir2Af2 bound to a myristoylated histone peptide
1MA3 2.0 Å, Structure of a Sir2 enzyme bound to an acetylated p53 peptide
1YC2 2.4 Å, Sir2Af2-NAD-ADPribose-nicotinamide

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