X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with dUDP

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.

Jeudy, S.Lartigue, A.Claverie, J.M.Abergel, C.

(2009) J Virol 83: 7142-7150

  • DOI: https://doi.org/10.1128/JVI.00511-09
  • Primary Citation of Related Structures:  
    2B8P, 2B8Q, 3B6B, 3DDI, 3DKD, 3EE3, 3EIC, 3EJM, 3ELH, 3EM1, 3EMT, 3ENA, 3ETM, 3EVM, 3EVO, 3EVW, 3FBB, 3FBC, 3FBE, 3FBF, 3FC9, 3FCV, 3FCW, 3G2X, 3GP9, 3GPA

  • PubMed Abstract: 

    The analysis of the Acanthamoeba polyphaga mimivirus genome revealed the first virus-encoded nucleoside diphosphate kinase (NDK), an enzyme that is central to the synthesis of RNA and DNA, ubiquitous in cellular organisms, and well conserved among the three domains of life. In contrast with the broad specificity of cellular NDKs for all types of ribo- and deoxyribonucleotides, the mimivirus enzyme exhibits a strongly preferential affinity for deoxypyrimidines. In order to elucidate the molecular basis of this unique substrate specificity, we determined the three-dimensional (3D) structure of the Acanthamoeba polyphaga mimivirus NDK alone and in complex with various nucleotides. As predicted from a sequence comparison with cellular NDKs, the 3D structure of the mimivirus enzyme exhibits a shorter Kpn loop, previously recognized as a main feature of the NDK active site. The structure of the viral enzyme in complex with various nucleotides also pinpointed two residue changes, both located near the active site and specific to the viral NDK, which could explain its stronger affinity for deoxynucleotides and pyrimidine nucleotides. The role of these residues was explored by building a set of viral NDK variants, assaying their enzymatic activities, and determining their 3D structures in complex with various nucleotides. A total of 26 crystallographic structures were determined at resolutions ranging from 2.8 A to 1.5 A. Our results suggest that the mimivirus enzyme progressively evolved from an ancestral NDK under the constraints of optimizing its efficiency for the replication of an AT-rich (73%) viral genome in a thymidine-limited host environment.

  • Organizational Affiliation

    Structural and Genomic Information Laboratory, CNRS-UPR2589, IFR88, Marseille Cedex 9, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase
A, B, C, D, E
A, B, C, D, E, F
142Acanthamoeba polyphaga mimivirusMutation(s): 0 
Gene Names: MIMI_R418NDK
Find proteins for Q5UQL3 (Acanthamoeba polyphaga mimivirus)
Explore Q5UQL3 
Go to UniProtKB:  Q5UQL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5UQL3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DUD

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
C9 H14 N2 O11 P2
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.717α = 90
b = 153.576β = 90
c = 185.795γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 

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: Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description