4TWI: Sir2Af1

The structure of Sir2Af1 bound to a succinylated histone peptide. Determined by X-ray diffraction at 1.79 Å resolution. Released 3 Dec 2014.

Method: X-ray diffraction
Resolution: 1.79 Å
Organisms: Archaeoglobus fulgidus, Saccharomyces cerevisiae
Chains: 2
Atoms: 2,213
Mol. weight: 29.02 kDa
Ligands: ZN
Released: 3 Dec 2014

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

Secondary structure: helices and β-sheets

4TWI contains 18 α-helices and 13 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: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	15-19	5	1
α-helix	21-23	3
α-helix	25-27	3
α-helix	44-46	3
α-helix	50-55	6
α-helix	57-73	17
α-helix	78-88	11
β-strand	92-97	6	1
α-helix	103-106	4
β-strand	112-114	3	1
β-strand	117-124	8	2
β-strand	130-132	3	2
α-helix	136-138	3
α-helix	142-143	2
β-strand	144	1	3
α-helix	150	1
β-strand	151	1	3
β-strand	152-156	5	2
α-helix	157-158	2
α-helix	162-164	3
α-helix	165-177	13
β-strand	180-184	5	1
β-strand	190-191	2	4
α-helix	193-195	3
α-helix	196-202	7
β-strand	206-210	5	1
α-helix	218-220	3
β-strand	223-225	3	1
α-helix	229-244	16

Chain B: 0 helices, 1 β-strand

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacylase 1	A	protein	245	Archaeoglobus fulgidus	O28597 (AlphaFold model)
Succinylated H4 Peptide (aa8-20)	B	protein	14	Saccharomyces cerevisiae	P02309 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4TWI_1 NAD-dependent protein deacylase 1 (chains A)
MDEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKV
WKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNVDDLHERAGSRNVIHLHGSLR
VVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWFGEMLPPDVLDRAMREVERADV
IIVAGTSAVVQPAASLPLIVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHV
RKALS

Sequence of entity 2 (B), FASTA

>4TWI_2 Succinylated H4 Peptide (aa8-20) (chains B)
KGLGKGGAXRHRKW

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (GOL) 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 O28597 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1M2K 1.47 Å, Sir2 homologue F159A mutant-ADP ribose complex
1M2G 1.7 Å, Sir2 homologue-ADP ribose complex
1M2J 1.7 Å, Sir2 homologue H80N mutant-ADP ribose complex
1M2H 1.8 Å, Sir2 homologue S24A mutant-ADP ribose complex
1ICI 2.1 Å, Crystal structure of a SIR2 homolog-NAD complex
1M2N 2.6 Å, Sir2 homologues (D102G/F159A/R170A) mutant-2'-O-acetyl ADP ribose complex

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