1DUD | pdb_00001dud

DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE (D-UTPASE) COMPLEXED WITH THE SUBSTRATE ANALOGUE DEOXYURIDINE 5'-DIPHOSPHATE (D-UDP)

• PDB DOI: https://doi.org/10.2210/pdb1DUD/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1996-04-30 Released: 1996-11-08 
• Deposition Author(s): Larsson, G., Svensson, L.A., Nyman, P.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 
  0.200 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUDP).

Larsson, G., Svensson, L.A., Nyman, P.O.

(1996) Nat Struct Biol 3: 532-538

• PubMed: 8646539 
• DOI: https://doi.org/10.1038/nsb0696-532
• Primary Citation Related Structures: 
  1DUD


• PubMed Abstract: 
  

  We have determined the structure of the homotrimeric dUTPase from Escherichia coli, completed with an inhibitor and substrate analogue, dUDP. Three molecules of dUDP are found symmetrically bound per trimer, each in a shallow cleft between adjacent subunits, interacting with evolutionary conserved residues. The interactions of the uracil ring and the deoxypentose with the protein are consistent with the high specificity of the enzyme with respect to these groups. The positions of the two phosphate groups and adjacent water molecules are discussed in relation to the mechanism and kinetics of catalysis. The role that dUTPase plays in DNA metabolism makes the enzyme a potential target for chemotherapeutic drugs: the results presented here will aid in the design and development of inhibitory compounds.

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Organizational Affiliation: 
• Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Sweden.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 16.69 kDa 
• Atom Count: 1,145 
• Modeled Residue Count: 136 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE	A	152	Escherichia coli	Mutation(s): 0  EC: 3.6.1.23
UniProt
Find proteins for P06968 (Escherichia coli (strain K12)) Explore P06968  Go to UniProtKB:  P06968

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUD	B [auth A]	DEOXYURIDINE-5'-DIPHOSPHATE C9 H14 N2 O11 P2 QHWZTVCCBMIIKE-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work:  0.200 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.64	α = 90
b = 86.64	β = 90
c = 62.23	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-11-08 
Deposition Author(s): Larsson, G., Svensson, L.A., Nyman, P.O.

Revision History  

• Version 1.0: 1996-11-08
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations