6H4C: DUTPase

A polyamorous repressor: deciphering the evolutionary strategy used by the phage-inducible chromosomal islands to spread in nature. Determined by X-ray diffraction at 2.52 Å resolution. Released 28 Aug 2019.

Method: X-ray diffraction
Resolution: 2.52 Å
Organisms: Staphylococcus phage phi11, Staphylococcus aureus
Chains: 8
Atoms: 9,321
Mol. weight: 157.5 kDa
Ligands: NI, MG
Released: 28 Aug 2019

Explore 6H4C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H4C contains 64 α-helices and 63 β-strands across 8 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: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
β-strand	18	1	2
β-strand	26-30	5	2
β-strand	35-37	3	3
β-strand	42-46	5	4
β-strand	49-51	3	1
β-strand	57-62	6	2
α-helix	65-70	6
β-strand	73-76	4	4
α-helix	77	1
β-strand	78-81	4	2
β-strand	89-94	6	4
β-strand	103-108	6	3
β-strand	114-122	9	3
β-strand	126-128	3	3
α-helix	129	1
β-strand	133-141	9	2
β-strand	146-149	4	5

Chain B: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	6
α-helix	10-11	2
α-helix	14-24	11
α-helix	29-36	8
α-helix	40-48	9
α-helix	52-53	2
β-strand	54	1	6
α-helix	55-65	11
α-helix	70-82	13
α-helix	86-89	4
α-helix	91-107	17
α-helix	109-112	4
α-helix	118-131	14
α-helix	136-138	3
α-helix	141-152	12

Chain C: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	7
β-strand	18	1	8
β-strand	27-30	4	8
β-strand	35-37	3	9
β-strand	42-46	5	10
β-strand	49-51	3	7
α-helix	53-54	2
β-strand	57-62	6	8
α-helix	65-70	6
β-strand	73-75	3	10
α-helix	76-77	2
β-strand	78-80	3	8
β-strand	89-94	6	10
β-strand	103-108	6	9
β-strand	114-122	9	9
β-strand	126-128	3	9
α-helix	129	1
β-strand	133-141	9	8
α-helix	145	1
β-strand	146-149	4	1

Chain D: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	11
α-helix	14-24	11
α-helix	29-36	8
α-helix	40-48	9
α-helix	52-53	2
β-strand	54	1	11
α-helix	55-65	11
α-helix	69-82	14
α-helix	86-89	4
α-helix	91-105	15
α-helix	109-112	4
α-helix	118-131	14
α-helix	136-138	3
α-helix	141-151	11

Chain E: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	5
β-strand	18	1	12
β-strand	27-30	4	12
β-strand	35-37	3	13
β-strand	42-46	5	14
β-strand	49-51	3	5
α-helix	53-54	2
β-strand	57-62	6	12
α-helix	65-70	6
β-strand	73-76	4	14
α-helix	77	1
β-strand	78-80	3	12
β-strand	89-94	6	14
α-helix	96-98	3
β-strand	103-108	6	13
β-strand	114-122	9	13
β-strand	126-128	3	13
β-strand	133-141	9	12
β-strand	146-149	4	7

Chain F: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	29-36	8
α-helix	40-48	9
α-helix	55-65	11
α-helix	70-82	13
α-helix	86-89	4
α-helix	91-107	17
α-helix	109-112	4
α-helix	118-131	14
α-helix	136-138	3
α-helix	141-151	11

Chain G: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	15
β-strand	18	1	16
β-strand	27-30	4	16
β-strand	35-37	3	17
β-strand	42-46	5	18
β-strand	49-51	3	15
α-helix	53-54	2
β-strand	57-62	6	16
α-helix	65-70	6
β-strand	73-75	3	18
β-strand	78-80	3	16
β-strand	89-94	6	18
α-helix	96-98	3
β-strand	103-108	6	17
β-strand	114-122	9	17
β-strand	126-128	3	17
α-helix	129	1
β-strand	133-141	9	16
α-helix	145-147	3

Chain H: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	29-36	8
α-helix	40-48	9
α-helix	55-65	11
α-helix	69-81	13
α-helix	86-89	4
α-helix	91-105	15
α-helix	109-112	4
α-helix	118-131	14
α-helix	136-138	3
α-helix	141-151	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
dUTPase	A, C, E, G	protein	191	Staphylococcus phage phi11	Q8SDV3
Orf20	B, D, F, H	protein	157	Staphylococcus aureus	Q9F0J8 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>6H4C_1 dUTPase (chains A, C, E, G)
MHHHHHHSSGVDLGTENLYFQSMTNTLQVRLLSENARMPERNHKTDAGYDIFSAETVVLE
PQEKAVIKTDVAVSIPEGYVGLLTSRSGVSSKTHLVIETGKIDAGYHGNLGINIKNDAIA
SNGYITPGVFDIKGEIDLSDAIRQYGTYQINEGDKLAQLVIVPIWTPELKQVEEFESVSE
RGEKGFGSSGV

Sequence of entity 2 (B, D, F, H), FASTA

>6H4C_2 Orf20 (chains B, D, F, H)
GMEGAGQMAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIE
IYGKGLGIPSYILHRISDEFKEKGYSPTLNDFGKFDKMYSYVNKAYYNDGDIYYSSYDLY
DETIKLLELLKESKINVNDIDYDYVLKLYKQILSTDT

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	5
MG	Magnesium ion	Mg	2

Water and common crystallization additives (PEG) are not listed.

Primary citation

The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature. Rafael Ciges-Tomas, J., Alite, C., Humphrey, S. et al. Nat Commun (2019) 10:3676-3676. DOI 10.1038/s41467-019-11504-2 · PubMed

Other PDB entries of the same protein (UniProt Q8SDV3), best resolution first:

4GV8 2.1 Å, DUTPase from phage phi11 of S.aureus: visualization of the species-specific insert
4WRK 2.9 Å, The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the…

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