1DEL

DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP AND AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.186 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.

Teplyakov, A.Sebastiao, P.Obmolova, G.Perrakis, A.Brush, G.S.Bessman, M.J.Wilson, K.S.

(1996) EMBO J 15: 3487-3497

  • Primary Citation of Related Structures:  
    1DEK, 1DEL

  • PubMed Abstract: 

    NMP kinases catalyse the phosphorylation of the canonical nucleotides to the corresponding diphosphates using ATP as a phosphate donor. Bacteriophage T4 deoxynucleotide kinase (DNK) is the only member of this family of enzymes that recognizes three structurally dissimilar nucleotides: dGMP, dTMP and 5-hydroxymethyl-dCMP while excluding dCMP and dAMP. The crystal structure of DNK with its substrate dGMP has been determined at 2.0 A resolution by single isomorphous replacement. The structure of the ternary complex with dGMP and ATP has been determined at 2.2 A resolution. The polypeptide chain of DNK is folded into two domains of equal size, one of which resembles the mononucleotide binding motif with the glycine-rich P-loop. The second domain, consisting of five alpha-helices, forms the NMP binding pocket. A hinge connection between the domains allows for large movements upon substrate binding which are not restricted by dimerization of the enzyme. The mechanism of active centre formation via domain closure is described. Comparison with other P-loop-containing proteins indicates an induced-fit mode of NTP binding. Protein-substrate interactions observed at the NMP and NTP sites provide the basis for understanding the principles of nucleotide discrimination.


  • Organizational Affiliation

    European Molecular Biology Laboratory, DESY, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE
A, B
241Tequatrovirus T4Mutation(s): 0 
Gene Names: 1
EC: 2.7.4.13
UniProt
Find proteins for P04531 (Enterobacteria phage T4)
Explore P04531 
Go to UniProtKB:  P04531
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04531
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.2α = 90
b = 58.5β = 108.1
c = 75.7γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other