4TWJ: Sir2Af2

The structure of Sir2Af2 bound to a myristoylated histone peptide. Determined by X-ray diffraction at 1.65 Å resolution. Released 3 Dec 2014.

Method: X-ray diffraction
Resolution: 1.65 Å
Organisms: Archaeoglobus fulgidus, Saccharomyces cerevisiae
Chains: 2
Atoms: 2,139
Mol. weight: 30.88 kDa
Ligands: ZN
Released: 3 Dec 2014

Explore 4TWJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4TWJ contains 15 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: 15 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
β-strand	18-22	5	1
α-helix	24-26	3
β-strand	28	1	2
α-helix	48-51	4
β-strand	52	1	3
α-helix	53-58	6
α-helix	60-73	14
β-strand	74	1	2
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	4
β-strand	132-134	3	4
α-helix	135-137	3
α-helix	139-143	5
α-helix	146-148	3
β-strand	158-162	5	4
β-strand	165	1	3
β-strand	168	1	5
α-helix	169-170	2
α-helix	171-182	12
β-strand	186-190	5	1
β-strand	196-197	2	6
α-helix	201-208	8
β-strand	212-217	6	1
α-helix	224-226	3
β-strand	229-232	4	1
α-helix	235-249	15

Chain B: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
β-strand	6-7	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacylase 2	A	protein	253	Archaeoglobus fulgidus	O30124 (AlphaFold model)
Histone H4 peptide	B	protein	14	Saccharomyces cerevisiae	P02309 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4TWJ_1 NAD-dependent protein deacylase 2 (chains A)
MEDEIRKAAEILAKSKHAVVFTGAGISAESGIPTFRGEDGLWRKYDPEEVASISGFKRNP
RAFWEFSMEMKDKLFAEPNPAHYAIAELERMGIVKAVITQNIDMLHQRAGSRRVLELHGS
MDKLDCLDCHETYDWSEFVEDFNKGEIPRCRKCGSYYVKPRVVLFGEPLPQRTLFEAIEE
AKHCDAFMVVGSSLVVYPAAELPYIAKKAGAKMIIVNAEPTMADPIFDVKIIGKAGEVLP
KIVEEVKRLRSEK

Sequence of entity 2 (B), FASTA

>4TWJ_2 Histone H4 peptide (chains B)
KGLGKGGAXRHRKW

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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

Primary citation

Alternate deacylating specificities of the archaeal sirtuins Sir2Af1 and Sir2Af2. Ringel, A.E., Roman, C., Wolberger, C. Protein Sci (2014) 23:1686-1697. DOI 10.1002/pro.2546 · PubMed

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

1MA3 2.0 Å, Structure of a Sir2 enzyme bound to an acetylated p53 peptide
1S7G 2.3 Å, Structural Basis for the Mechanism and Regulation of Sir2 Enzymes
1YC2 2.4 Å, Sir2Af2-NAD-ADPribose-nicotinamide

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