2H59: NAD-dependent deacetylase

Sir2 H116A-deacetylated p53 peptide-3'-o-acetyl ADP ribose. Determined by X-ray diffraction at 1.9 Å resolution. Released 5 Sept 2006.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Thermotoga maritima
Chains: 4
Atoms: 4,244
Mol. weight: 60.49 kDa
Ligands: 3OD, APR, ZN
Released: 5 Sept 2006

Explore 2H59 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2H59 contains 36 α-helices and 34 β-strands across 4 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.

Chains A and B: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	16-20	5	1
α-helix	22-24	3
α-helix	26-28	3
α-helix	39-41	3
α-helix	45-48	4
β-strand	49	1	2
α-helix	50-55	6
α-helix	57-67	11
α-helix	69-73	5
α-helix	78-88	11
β-strand	94-97	4	1
α-helix	103-106	4
β-strand	112-114	3	1
β-strand	117-124	8	3
β-strand	130-132	3	3
α-helix	133-139	7
β-strand	147	1	4
β-strand	154	1	4
β-strand	155-159	5	3
α-helix	160-161	2
β-strand	162	1	2
β-strand	165	1	5
α-helix	166-167	2
α-helix	168-180	13
β-strand	183-187	5	1
β-strand	193-194	2	6
α-helix	196-198	3
α-helix	199-206	8
β-strand	209-213	5	1
α-helix	221-223	3
β-strand	226-228	3	1
α-helix	232-241	10

Chains D and E: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	5
β-strand	12-13	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent deacetylase	A, B	protein	246	Thermotoga maritima	Q9WYW0 (AlphaFold model)
Cellular tumor antigen p53	D, E	protein	18		P04637 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2H59_1 NAD-dependent deacetylase (chains A, B)
MKMKEFLDLLNESRLTVTLTGAGISTPSGIPDFRGPNGIYKKYSQNVFDIDFFYSHPEEF
YRFAKEGIFPMLQAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQRAGSKKVIELAGNVE
EYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLIRPNIVFFGENLPQDALREAIGLSSR
ASLMIVLGSSLVVYPAAELPLITVRSGGKLVIVNLGETPFDDIATLKYNMDVVEFARRVM
EEGGIS

Sequence of entity 2 (D, E), FASTA

>2H59_2 Cellular tumor antigen p53 (chains D, E)
KKGQSTSRHKKLMFKTEG

Ligands and cofactors

ID	Name	Formula	Copies
3OD	(2S,3S,4R,5S)-2-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihy…	C17 H25 N5 O15 P2	1
APR	Adenosine-5-diphosphoribose	C15 H23 N5 O14 P2	1
ZN	Zinc ion	Zn	2

Primary citation

Insights into the Sirtuin Mechanism from Ternary Complexes Containing NAD(+) and Acetylated Peptide. Hoff, K.G., Avalos, J.L., Sens, K. et al. Structure (2006) 14:1231-1240. DOI 10.1016/j.str.2006.06.006 · PubMed

Other PDB entries of the same protein (UniProt Q9WYW0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1YC5 1.4 Å, Sir2-p53 peptide-nicotinamide
3JR3 1.5 Å, Sir2 bound to acetylated peptide
2H2G 1.63 Å, The Structural Basis of Sirtuin substrate affinity
2H2D 1.7 Å, The Structural Basis for Sirtuin Substrate Affinity
2H2I 1.8 Å, The Structural basis of Sirtuin Substrate Affinity
3PDH 1.8 Å, Structure of Sir2Tm bound to a propionylated peptide
3D4B 1.9 Å, Crystal structure of Sir2Tm in complex with Acetyl p53 peptide and DADMe-NAD+
4BUZ 1.9 Å, SIR2 complex structure mixture of ex-527 inhibitor and reaction products or of reaction…
2H4H 1.99 Å, Sir2 H116Y mutant-p53 peptide-NAD
2H4F 2.0 Å, Sir2-p53 peptide-NAD+
2H4J 2.1 Å, Sir2-deacetylated peptide (from enzymatic turnover in crystal)
2H2F 2.2 Å, The Structural basis for Sirtuin Substrate affinity

Browse structure collections

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