› 2d4n

X-ray diffraction
1.53Å resolution

Crystal Structure of M-PMV dUTPase complexed with dUPNPP, substrate analogue

Released:
DOI: 10.2210/pdb2d4n/pdb
PDB entry 2d4n coloured by chain, front view.
PDB entry 2d4n coloured by chain, side view.
PDB entry 2d4n coloured by chain, top view.
Source organism: Mason-Pfizer monkey virus
Primary publication:
Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins.
Németh-Pongrácz V, Barabás O, Fuxreiter M, Simon I, Pichová I, Rumlová M, Zábranská H, Svergun D, Petoukhov M, Harmat V, Klement E, Hunyadi-Gulyás E, Medzihradszky KF, Kónya E, Vértessy BG
Nucleic Acids Res 35 495-505 (2007)
PMID: 17169987

Function and Biology Details

Reaction catalysed: 
dUTP + H(2)O = dUMP + diphosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139635 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleocapsid protein-dUTPase Chain: A
Molecule details ›
Chain: A
Length: 152 amino acids
Theoretical weight: 16.16 KDa
Source organism: Mason-Pfizer monkey virus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P07570 (Residues: 608-759; Coverage: 17%)
Gene name: gag-pro
Sequence domains: dUTPase
Structure domains: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand DUP 1 x DUP
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P63
Unit cell:
a: 61.071Å b: 61.071Å c: 64.357Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.166 0.164 0.187
Expression system: Escherichia coli BL21

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Citations

4 review citations

X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
Putnam et al. (2007)
3 more

2 mentions without citation

Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins.
Németh-Pongrácz et al. (2007)
1 more