2XCE

Structure of YncF in complex with dUpNHpp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The Structure of the Genomic Bacillus Subtilis Dutpase: Novel Features in the Phe-Lid.

Garcia-Nafria, J.Burchell, L.Takezawa, M.Rzechorzek, N.Fogg, M.Wilson, K.S.

(2010) Acta Crystallogr D Biol Crystallogr 66: 953

  • DOI: https://doi.org/10.1107/S0907444910026272
  • Primary Citation of Related Structures:  
    2XCD, 2XCE

  • PubMed Abstract: 

    dUTPases are a ubiquitous family of enzymes that are essential for all organisms and catalyse the breakdown of 2-deoxyuridine triphosphate (dUTP). In Bacillus subtilis there are two homotrimeric dUTPases: a genomic and a prophage form. Here, the structures of the genomic dUTPase and of its complex with the substrate analogue dUpNHpp and calcium are described, both at 1.85 A resolution. The overall fold resembles that of previously solved trimeric dUTPases. The C-terminus, which contains one of the conserved sequence motifs, is disordered in both structures. The crystal of the complex contains six independent protomers which accommodate six dUpNHpp molecules, with three triphosphates in the trans conformation and the other three in the active gauche conformation. The structure of the complex confirms the role of several key residues that are involved in ligand binding and the position of the catalytic water. Asp82, which has previously been proposed to act as a general base, points away from the active site. In the complex Ser64 reorients in order to hydrogen bond the phosphate chain of the substrate. A novel feature has been identified: the position in the sequence of the ;Phe-lid', which packs against the uracil moiety, is adjacent to motif III, whereas in all other dUTPase structures the lid is in a conserved position in motif V of the flexible C-terminal arm. This requires a reconsideration of some aspects of the accepted mechanism.


  • Organizational Affiliation

    Department of Chemistry, University of York, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
A, B, C, D, E
A, B, C, D, E, F
144Bacillus subtilisMutation(s): 0 
EC: 3.6.1.23
UniProt
Find proteins for O31801 (Bacillus subtilis (strain 168))
Explore O31801 
Go to UniProtKB:  O31801
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31801
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DUP
Query on DUP

Download Ideal Coordinates CCD File 
G [auth A]
L [auth B]
N [auth C]
P [auth D]
U [auth E]
G [auth A],
L [auth B],
N [auth C],
P [auth D],
U [auth E],
Y [auth F]
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]
K [auth A]
Q [auth D]
S [auth D]
V [auth E]
I [auth A],
K [auth A],
Q [auth D],
S [auth D],
V [auth E],
Z [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A]
J [auth A]
M [auth B]
O [auth C]
R [auth D]
H [auth A],
J [auth A],
M [auth B],
O [auth C],
R [auth D],
T [auth D],
W [auth E],
X [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.116α = 90
b = 99.345β = 90
c = 99.252γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2012-04-11
    Changes: Database references, Non-polymer description, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description