3HHQ

Crystal structure of apo dUT1p from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and activity of the Saccharomyces cerevisiae dUTP pyrophosphatase DUT1, an essential housekeeping enzyme.

Tchigvintsev, A.Singer, A.U.Flick, R.Petit, P.Brown, G.Evdokimova, E.Savchenko, A.Yakunin, A.F.

(2011) Biochem J 437: 243-253

  • DOI: 10.1042/BJ20110304
  • Primary Citation of Related Structures:  
    3P48, 3HHQ, 3F4F

  • PubMed Abstract: 
  • Genomes of all free-living organisms encode the enzyme dUTPase (dUTP pyrophosphatase), which plays a key role in preventing uracil incorporation into DNA. In the present paper, we describe the biochemical and structural characterization of DUT1 (Saccharomyces cerevisiae dUTPase) ...

    Genomes of all free-living organisms encode the enzyme dUTPase (dUTP pyrophosphatase), which plays a key role in preventing uracil incorporation into DNA. In the present paper, we describe the biochemical and structural characterization of DUT1 (Saccharomyces cerevisiae dUTPase). The hydrolysis of dUTP by DUT1 was strictly dependent on a bivalent metal cation with significant activity observed in the presence of Mg2+, Co2+, Mn2+, Ni2+ or Zn2+. In addition, DUT1 showed a significant activity against another potentially mutagenic nucleotide: dITP. With both substrates, DUT1 demonstrated a sigmoidal saturation curve, suggesting a positive co-operativity between the subunits. The crystal structure of DUT1 was solved at 2 Å resolution (1 Å=0.1 nm) in an apo state and in complex with the non-hydrolysable substrate α,β-imido dUTP or dUMP product. Alanine-replacement mutagenesis of the active-site residues revealed seven residues important for activity including the conserved triad Asp87/Arg137/Asp85. The Y88A mutant protein was equally active against both dUTP and UTP, indicating that this conserved tyrosine residue is responsible for discrimination against ribonucleotides. The structure of DUT1 and site-directed mutagenesis support a role of the conserved Phe142 in the interaction with the uracil base. Our work provides further insight into the molecular mechanisms of substrate selectivity and catalysis of dUTPases.


    Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, Centre for Structural Proteomics in Toronto, University of Toronto, Toronto, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
167Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DUT1dUT1pYBR1705YBR252W
EC: 3.6.1.23
UniProt
Find proteins for P33317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33317 
Go to UniProtKB:  P33317
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AE [auth X], BE [auth X], GB [auth J], HB [auth J], NB [auth K], YB [auth M], ZA [auth H]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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AB [auth I] , AC [auth N] , AD [auth S] , BA [auth B] , CA [auth B] , CB [auth J] , DD [auth T] , FC [auth O] , 
AB [auth I],  AC [auth N],  AD [auth S],  BA [auth B],  CA [auth B],  CB [auth J],  DD [auth T],  FC [auth O],  GA [auth D],  IB [auth K],  JB [auth K],  KD [auth U],  LA [auth E],  LC [auth P],  MC [auth P],  OA [auth F],  OD [auth V],  PA [auth F],  PC [auth Q],  PD [auth V],  QA [auth F],  QD [auth V],  RB [auth M],  SB [auth M],  UA [auth G],  VA [auth G],  VC [auth R],  WA [auth G],  XD [auth W],  Y [auth A],  YA [auth H],  YD [auth W],  Z [auth A],  ZB [auth N],  ZC [auth S]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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ND [auth U]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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CD [auth S] , EB [auth J] , EC [auth N] , FB [auth J] , HC [auth O] , HD [auth T] , ID [auth T] , JA [auth D] , 
CD [auth S],  EB [auth J],  EC [auth N],  FB [auth J],  HC [auth O],  HD [auth T],  ID [auth T],  JA [auth D],  JC [auth O],  JD [auth T],  KA [auth D],  KB [auth K],  KC [auth O],  LB [auth K],  MB [auth K],  MD [auth U],  NA [auth E],  OC [auth P],  RC [auth Q],  SC [auth Q],  SD [auth V],  TA [auth F],  TC [auth Q],  TD [auth V],  UB [auth M],  UC [auth Q],  VB [auth M],  WB [auth M],  WD [auth V],  XA [auth G],  XB [auth M],  XC [auth R],  YC [auth R],  ZD [auth W]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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BB [auth I] , CC [auth N] , DA [auth B] , DB [auth J] , DC [auth N] , EA [auth C] , GD [auth T] , HA [auth D] , 
BB [auth I],  CC [auth N],  DA [auth B],  DB [auth J],  DC [auth N],  EA [auth C],  GD [auth T],  HA [auth D],  IA [auth D],  LD [auth U],  MA [auth E],  OB [auth L],  QB [auth L],  QC [auth Q],  RA [auth F],  VD [auth V],  WC [auth R]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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AA [auth A] , BC [auth N] , BD [auth S] , ED [auth T] , FA [auth C] , FD [auth T] , GC [auth O] , IC [auth O] , 
AA [auth A],  BC [auth N],  BD [auth S],  ED [auth T],  FA [auth C],  FD [auth T],  GC [auth O],  IC [auth O],  NC [auth P],  PB [auth L],  RD [auth V],  SA [auth F],  TB [auth M],  UD [auth V]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.461α = 98.79
b = 95.466β = 97.42
c = 97.594γ = 107.13
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2012-10-10
    Changes: Database references