5EDD: Deoxyuridine 5'-triphosphate nucleotidohydrolase

Name: PDB 5EDD: Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H145W mutant
Published: 2016-11-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H145W mutant. Determined by X-ray diffraction at 1.97 Å resolution. Released 2 Nov 2016.

Method: X-ray diffraction
Resolution: 1.97 Å
Organism: Mycobacterium tuberculosis
Chains: 1
Atoms: 1,222
Mol. weight: 18.63 kDa
Ligands: MG, DUP
Released: 2 Nov 2016

Explore 5EDD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EDD contains 6 α-helices and 11 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: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	-3--1	3
α-helix	2-4	3
β-strand	7-9	3	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	49-51	3	1
α-helix	53-54	2
β-strand	57-62	6	2
α-helix	65-71	7
β-strand	73-75	3	4
β-strand	80-83	4	2
β-strand	91-96	6	4
β-strand	103-105	3	3
β-strand	110-118	9	2

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

>5EDD_1 Deoxyuridine 5'-triphosphate nucleotidohydrolase (chains A)
MGSSHHHHHHSSGLVPRGSHMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPG
RRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPA
APIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSKGDGGWGSSGGHASL

Ligands and cofactors

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

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

Primary citation

Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases. Nagy, G.N., Suardiaz, R., Lopata, A. et al. J Am Chem Soc (2016) 138:15035-15045. DOI 10.1021/jacs.6b09012 · 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)

Browse structure collections

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