8P8O: Deoxyuridine 5'-triphosphate nucleotidohydrolase

Name: PDB 8P8O: M. tuberculosis dUTPase - Stl1-159 (StlNT) complex structure
Published: 2024-11-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

M. tuberculosis dUTPase - Stl1-159 (StlNT) complex structure. Determined by X-ray diffraction at 3.4 Å resolution. Released 27 Nov 2024.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: Mycobacterium tuberculosis, Staphylococcus aureus
Chains: 12
Atoms: 11,820
Mol. weight: 222.26 kDa
Released: 27 Nov 2024

Explore 8P8O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P8O contains 87 α-helices and 73 β-strands across 12 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: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	15-17	3
β-strand	27-30	4	2
α-helix	31	1
β-strand	35-37	3	3
β-strand	42-46	5	4
β-strand	49-52	4	1
α-helix	53-54	2
β-strand	57-63	7	2
α-helix	65-70	6
β-strand	73-75	3	4
β-strand	80-82	3	2
β-strand	91-96	6	4
β-strand	103-105	3	3
β-strand	110-118	9	2
β-strand	119	1	5
β-strand	123-126	4	6

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	6
α-helix	15-17	3
β-strand	27-30	4	5
α-helix	31	1
β-strand	35-37	3	7
β-strand	42-51	10	6
α-helix	53-54	2
β-strand	57-63	7	5
α-helix	65-70	6
β-strand	73-75	3	6
β-strand	80-82	3	5
β-strand	89-96	8	6
β-strand	103-105	3	7
β-strand	110-118	9	5
β-strand	123-126	4	8

Chain C: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	8
α-helix	15-18	4
β-strand	27-30	4	9
α-helix	31	1
β-strand	35-37	3	10
β-strand	42-46	5	11
β-strand	49-51	3	8
α-helix	53-54	2
β-strand	57-63	7	9
α-helix	64	1
α-helix	65-70	6
β-strand	73-75	3	11
β-strand	80-82	3	9
β-strand	91-96	6	11
β-strand	103-105	3	10
β-strand	110-118	9	9
β-strand	119	1	2
β-strand	123-126	4	1

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	12
α-helix	15-17	3
β-strand	27-30	4	13
β-strand	35-37	3	14
β-strand	42-46	5	15
β-strand	49-52	4	12
α-helix	53-54	2
β-strand	57-63	7	13
α-helix	65-70	6
β-strand	73-75	3	15
β-strand	80-82	3	13
β-strand	91-96	6	15
β-strand	103-105	3	14
β-strand	110-118	9	13
β-strand	123-126	4	16

Chain E: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	16
α-helix	15-17	3
β-strand	27-30	4	17
α-helix	31	1
β-strand	35-37	3	18
α-helix	38	1
β-strand	42-46	5	19
β-strand	49-51	3	16
α-helix	53-54	2
β-strand	57-63	7	17
α-helix	65-70	6
β-strand	73-75	3	19
β-strand	80-82	3	17
β-strand	91-96	6	19
β-strand	103-105	3	18
β-strand	110-118	9	17
β-strand	123-126	4	20

Chain F: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	29-36	8
α-helix	40-48	9
α-helix	55-64	10
α-helix	69-82	14
α-helix	86-89	4
α-helix	91-107	17
α-helix	109-112	4
α-helix	118-131	14
α-helix	141-152	12

Chain G: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	20
α-helix	15-17	3
β-strand	27-30	4	21
α-helix	31	1
β-strand	35-37	3	22
β-strand	42-46	5	23
β-strand	50-51	2	20
α-helix	53-54	2
β-strand	57-63	7	21
α-helix	64	1
α-helix	65-70	6
β-strand	73-75	3	23
β-strand	80-82	3	21
β-strand	91-96	6	23
β-strand	103-105	3	22
β-strand	110-118	9	21
β-strand	123-126	4	12

Chain H: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	29-36	8
α-helix	40-47	8
α-helix	52-54	3
α-helix	57-64	8
α-helix	69-82	14
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

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A, B, C, D, E, G	protein	174	Mycobacterium tuberculosis	P9WNS5 (AlphaFold model)
Orf20	F, H, I, J, K, L	protein	165	Staphylococcus aureus	Q9F0J8 (AlphaFold model)

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

>8P8O_1 Deoxyuridine 5'-triphosphate nucleotidohydrolase (chains A, B, C, D, E, G)
MGSSHHHHHHSSGLVPRGSHMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPG
RRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPA
APIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGGHGSSGGHASL

Sequence of entity 2 (F, H, I, J, K, L), FASTA

>8P8O_2 Orf20 (chains F, H, I, J, K, L)
GSPEFSMEGAGQMAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIG
VNEIEIYGKGLGIPSYILHRISDEFKEKGYSPTLNDFGKFDKMYSYVNKAYYNDGDIYYS
SYDLYDETIKLLELLKESKINVNDIDYDYVLKLYKQILSTDTEKS

Primary citation

The homodimerization domain of the Stl repressor is crucial for efficient inhibition of mycobacterial dUTPase. Toth, Z.S., Leveles, I., Nyiri, K. et al. Sci Rep (2024) 14:27171-27171. DOI 10.1038/s41598-024-76349-2 · PubMed

Other PDB entries of the same protein (UniProt P9WNS5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3HZA 1.2 Å, Crystal structure of dUTPase H145W mutant
3LOJ 1.25 Å, Structure of Mycobacterium tuberculosis dUTPase H145A mutant
1SIX 1.3 Å, Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP
5ECT 1.3 Å, Mycobacterium tuberculosis dUTPase G143STOP mutant
8CGA 1.3 Å, Structure of Mycobacterium tuberculosis dUTPase delta 133A-137S mutant
2PY4 1.49 Å, Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium…
4GCY 1.5 Å, Structure of Mycobacterium tuberculosis dUTPase H21W mutant
1SJN 1.8 Å, Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP
3H6D 1.8 Å, Structure of the mycobacterium tuberculosis DUTPase D28N mutant
3I93 1.8 Å, Crystal structure of Mycobacterium tuberculosis dUTPase STOP138T mutant
1SNF 1.85 Å, Mycobacterium tuberculosis dutpase complexed with magnesium and deoxyuridine…
1MQ7 1.95 Å, Crystal structure of dutpase from mycobacterium tuberculosis (RV2697C)

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