4GV8: DUTPase

DUTPase from phage phi11 of S.aureus: visualization of the species-specific insert. Determined by X-ray diffraction at 2.1 Å resolution. Released 11 Sept 2013.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Staphylococcus phage 11
Chains: 6
Atoms: 7,352
Mol. weight: 113.32 kDa
Ligands: DUP, MG
Released: 11 Sept 2013

Explore 4GV8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GV8 contains 32 α-helices and 94 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: 5 helices, 16 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	78-81	4	2
β-strand	89-94	6	4
α-helix	97-98	2
β-strand	103-108	6	3
β-strand	114-122	9	3
β-strand	126-128	3	3
β-strand	133-141	9	2
β-strand	143	1	5
α-helix	145	1
β-strand	146-149	4	6

Chain B: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	7
β-strand	18-19	2	8
β-strand	26-30	5	8
β-strand	35-37	3	9
β-strand	42-46	5	10
β-strand	49-52	4	7
α-helix	53-54	2
β-strand	57-63	7	8
α-helix	65-70	6
β-strand	73-75	3	10
α-helix	76-77	2
β-strand	78-80	3	8
α-helix	87-88	2
β-strand	89-94	6	10
α-helix	97-98	2
β-strand	103-108	6	9
β-strand	114-122	9	9
β-strand	126-128	3	9
β-strand	133-141	9	8
β-strand	143	1	2
α-helix	145	1
β-strand	146-149	4	1

Chain C: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	6
β-strand	18	1	5
β-strand	26-30	5	5
β-strand	35-37	3	11
β-strand	42-46	5	12
β-strand	49-51	3	6
α-helix	53-54	2
β-strand	57-63	7	5
α-helix	65-70	6
β-strand	73-75	3	12
α-helix	76-77	2
β-strand	78-81	4	5
β-strand	89-94	6	12
α-helix	97-98	2
β-strand	103-108	6	11
β-strand	114-122	9	11
β-strand	126-128	3	11
β-strand	133-141	9	5
β-strand	143	1	8
α-helix	145	1
β-strand	146-149	4	7

Chain D: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	13
β-strand	18	1	14
β-strand	27-29	3	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	57-63	7	14
α-helix	65-70	6
β-strand	73-75	3	16
α-helix	76-77	2
β-strand	78-80	3	14
α-helix	87-88	2
β-strand	89-94	6	16
α-helix	97-98	2
β-strand	103-108	6	15
β-strand	114-122	9	15
β-strand	126-128	3	15
α-helix	129	1
β-strand	135-141	7	14
α-helix	145	1
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	18-19	2	19
β-strand	26-30	5	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	57-62	6	19
α-helix	65-70	6
β-strand	73-76	4	21
α-helix	77	1
β-strand	78-81	4	19
β-strand	89-94	6	21
α-helix	96-98	3
β-strand	103-108	6	20
β-strand	114-122	9	20
β-strand	126-128	3	20
β-strand	133-141	9	19
α-helix	145	1
β-strand	146-149	4	13

Chain F: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	17
β-strand	18	1	22
β-strand	26-30	5	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	57-63	7	22
α-helix	65-70	6
β-strand	73-75	3	24
α-helix	76-77	2
β-strand	78-80	3	22
β-strand	89-94	6	24
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	143	1	19
α-helix	145	1
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 11	Q8SDV3

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

>4GV8_1 DUTPase (chains A, B, C, D, E, F)
MTNTLQVRLLSENARMPERNHKTDAGYDIFSAETVVLEPQEKAVIKTDVAVSIPEGYVGL
LTSRSGVSSKTHLVIETGKIDAGYHGNLGINIKNDAIASNGYITPGVFDIKGEIDLSDAI
RQYGTYQINEGDKLAQLVIVPIWTPELKQVEEFESVSERGEKGFGSSGV

Ligands and cofactors

ID	Name	Formula	Copies
DUP	2'-deoxyuridine 5'-alpha,beta-imido-triphosphate	C9 H16 N3 O13 P3	6
MG	Magnesium ion	Mg	8

Primary citation

Structure and enzymatic mechanism of a moonlighting dUTPase. Leveles, I., Nemeth, V., Szabo, J.E. et al. Acta Crystallogr D Biol Crystallogr (2013) 69:2298-2308. DOI 10.1107/S0907444913021136 · PubMed

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

6H4C 2.52 Å, A polyamorous repressor: deciphering the evolutionary strategy used by the…
4WRK 2.9 Å, The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the…

Browse structure collections

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