2PY4: Deoxyuridine 5'-triphosphate nucleotidohydrolase

Name: PDB 2PY4: Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.
Published: 2007-05-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP. Determined by X-ray diffraction at 1.49 Å resolution. Released 22 May 2007.

Method: X-ray diffraction
Resolution: 1.49 Å
Organism: Mycobacterium tuberculosis
Chains: 1
Atoms: 1,250
Mol. weight: 18.61 kDa
Ligands: DUP, MG
Released: 22 May 2007

Explore 2PY4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PY4 contains 5 α-helices and 10 β-strands across 1 chain. 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	1
α-helix	15-17	3
β-strand	27-30	4	2
α-helix	31	1
β-strand	35-37	3	3
β-strand	42-52	11	1
α-helix	53-54	2
β-strand	57-62	6	2
α-helix	65-71	7
β-strand	73-75	3	1
β-strand	80-82	3	2
β-strand	89-96	8	1
β-strand	103-105	3	3
β-strand	110-118	9	2
α-helix	135-137	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A	protein	174	Mycobacterium tuberculosis	P9WNS5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2PY4_1 Deoxyuridine 5'-triphosphate nucleotidohydrolase (chains A)
MGSSHHHHHHSSGLVPRGSHMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPG
RRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPA
APIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGGHGSSGGHASL

Ligands and cofactors

ID	Name	Formula	Copies
DUP	2'-deoxyuridine 5'-alpha,beta-imido-triphosphate	C9 H16 N3 O13 P3	1
MG	Magnesium ion	Mg	1

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

Primary citation

Active site of mycobacterial dUTPase: structural characteristics and a built-in sensor. Varga, B., Barabas, O., Takacs, E. et al. Biochem Biophys Res Commun (2008) 373:8-13. DOI 10.1016/j.bbrc.2008.05.130 · 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
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)
5EDD 1.97 Å, Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H145W mutant

Browse structure collections

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