3D81: Sir2-S-alkylamidate complex crystal structure

Sir2-S-alkylamidate complex crystal structure. Determined by X-ray diffraction at 2.5 Å resolution. Released 30 Sept 2008.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Thermotoga maritima
Chains: 2
Atoms: 1,983
Mol. weight: 29.28 kDa
Ligands: ZN
Released: 30 Sept 2008

Explore 3D81 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D81 contains 16 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: 16 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
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	103-107	5
β-strand	112-114	3	1
β-strand	117-124	8	3
β-strand	130-132	3	3
α-helix	133-139	7
α-helix	140-142	3
β-strand	147	1	4
α-helix	153	1
β-strand	154	1	4
β-strand	155-159	5	3
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	199-205	7
β-strand	209-213	5	1
β-strand	226-228	3	1
α-helix	232-243	12

Chain C: 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	protein	246	Thermotoga maritima	Q9WYW0 (AlphaFold model)
S-alkylamidate intermediate	C	protein	8

Sequence of entity 1 (A), FASTA

>3D81_1 NAD-dependent deacetylase (chains A)
MKMKEFLDLLNESRLTVTLTGAGISTPSGIPDFRGPNGIYKKYSQNVFDIDFFYSHPEEF
YRFAKEGIFPMLQAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQRAGSKKVIELHGNVE
EYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLIRPNIVFFGENLPQDALREAIGLSSR
ASLMIVLGSSLVVYPAAELPLITVRSGGKLVIVNLGETPFDDIATLKYNMDVVEFARRVM
EEGGIS

Sequence of entity 2 (C), FASTA

>3D81_2 S-alkylamidate intermediate (chains C)
SRHKKLMF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structural insights into intermediate steps in the Sir2 deacetylation reaction. Hawse, W.F., Hoff, K.G., Fatkins, D.G. et al. Structure (2008) 16:1368-1377. DOI 10.1016/j.str.2008.05.015 · 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
2H59 1.9 Å, Sir2 H116A-deacetylated p53 peptide-3'-o-acetyl ADP ribose
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)

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