4WRK: DUTPase

The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion. Determined by X-ray diffraction at 2.9 Å resolution. Released 23 Dec 2015.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Staphylococcus phage phi11
Chains: 6
Atoms: 7,158
Mol. weight: 113.27 kDa
Ligands: MG, DUP
Released: 23 Dec 2015

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

Secondary structure: helices and β-sheets

4WRK contains 28 α-helices and 90 β-strands across 6 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: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
β-strand	18	1	2
β-strand	27-30	4	2
β-strand	35-37	3	3
β-strand	42-46	5	4
β-strand	49-51	3	1
α-helix	53-54	2
β-strand	57-63	7	2
α-helix	65-70	6
β-strand	73-75	3	4
α-helix	76-77	2
β-strand	78-80	3	2
α-helix	81	1
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
α-helix	153-155	3

Chain B: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	6
β-strand	18	1	7
β-strand	27-30	4	7
β-strand	35-37	3	8
β-strand	42-46	5	9
β-strand	49-52	4	6
α-helix	53-54	2
β-strand	57-63	7	7
α-helix	65-70	6
β-strand	73-75	3	9
α-helix	76-77	2
β-strand	78-80	3	7
β-strand	89-94	6	9
α-helix	97-98	2
β-strand	103-108	6	8
β-strand	114-122	9	8
β-strand	126-128	3	8
α-helix	129	1
β-strand	133-141	9	7
β-strand	146-149	4	1

Chain C: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	5
β-strand	18	1	10
β-strand	26-30	5	10
β-strand	35-37	3	11
β-strand	42-46	5	12
β-strand	49-52	4	5
α-helix	53-54	2
β-strand	57-63	7	10
α-helix	65-70	6
β-strand	73-75	3	12
α-helix	76-77	2
β-strand	78-80	3	10
β-strand	89-94	6	12
α-helix	96-99	4
β-strand	103-108	6	11
β-strand	114-122	9	11
β-strand	126-128	3	11
α-helix	129	1
β-strand	133-141	9	10
β-strand	146-150	5	6

Chain D: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	13
β-strand	18	1	14
β-strand	27-30	4	14
β-strand	35-37	3	15
β-strand	42-46	5	16
β-strand	49-52	4	13
α-helix	53-54	2
β-strand	57-62	6	14
α-helix	65-70	6
β-strand	73-75	3	16
α-helix	76-77	2
β-strand	78-80	3	14
β-strand	89-94	6	16
β-strand	103-108	6	15
β-strand	114-122	9	15
β-strand	126-128	3	15
α-helix	129	1
β-strand	133-141	9	14
β-strand	146-149	4	17

Chain E: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	18
β-strand	18	1	19
β-strand	27-30	4	19
β-strand	35-37	3	20
β-strand	42-46	5	21
β-strand	49-52	4	18
α-helix	53-54	2
β-strand	57-63	7	19
α-helix	65-70	6
β-strand	73-75	3	21
α-helix	76-77	2
β-strand	78-80	3	19
β-strand	89-94	6	21
α-helix	99-101	3
β-strand	103-108	6	20
β-strand	114-122	9	20
β-strand	126-128	3	20
α-helix	129	1
β-strand	133-141	9	19
β-strand	146-149	4	13

Chain F: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	17
β-strand	18	1	22
β-strand	27-30	4	22
β-strand	35-37	3	23
β-strand	42-46	5	24
β-strand	49-52	4	17
α-helix	53-54	2
β-strand	57-62	6	22
α-helix	65-70	6
β-strand	73-75	3	24
β-strand	78-80	3	22
β-strand	89-94	6	24
α-helix	96-98	3
β-strand	103-108	6	23
β-strand	114-122	9	23
β-strand	126-128	3	23
β-strand	133-141	9	22
β-strand	146-149	4	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DUTPase	A, B, C, D, E, F	protein	169	Staphylococcus phage phi11	Q8SDV3

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>4WRK_1 DUTPase (chains A, B, C, D, E, F)
MTNTLQVRLLSENARMPERNHKTDAGYDIFSAETVVLEPQEKAVIKTDVAVSIPEGYVGL
LTSRSGVSSKTHLVIETGKIDAGYHGNLGINIKNNAIASNGYITPGVFDIKGEIDLSDAI
RQYGTYQINEGDKLAQLVIVPIWTPELKQVEEFESVSERGEKGFGSSGV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	6
DUP	2'-deoxyuridine 5'-alpha,beta-imido-triphosphate	C9 H16 N3 O13 P3	6

Primary citation

The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion. Bendes, A.A., Leveles, I., Vertessy, B.G. To be published.

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
6H4C 2.52 Å, A polyamorous repressor: deciphering the evolutionary strategy used by the…

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