2C4E

Crystal Structure of Methanocaldococcus jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Methanocaldococcus Jannaschii Nucleoside Kinase: An Archaeal Member of the Ribokinase Family.

Arnfors, L.Hansen, T.Schoenheit, P.Ladenstein, R.Meining, W.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1085

  • DOI: 10.1107/S0907444906024826
  • Primary Citation of Related Structures:  
    2C49, 2C4E

  • PubMed Abstract: 
  • Nucleoside kinase from the hyperthermophilic archaeon Methanocaldococcus jannaschii (MjNK) is a member of the ribokinase family. In the presence of ATP and Mg(2+), MjNK is able to catalyze the phosphorylation of a variety of nucleosides, including inosine, cytidine, guanosine and adenosine ...

    Nucleoside kinase from the hyperthermophilic archaeon Methanocaldococcus jannaschii (MjNK) is a member of the ribokinase family. In the presence of ATP and Mg(2+), MjNK is able to catalyze the phosphorylation of a variety of nucleosides, including inosine, cytidine, guanosine and adenosine. Here, the crystal structure of MjNK, the first structure of an archaeal representative of the ribokinase family, is presented. The structure was solved using the multiple-wavelength anomalous dispersion technique. Three-dimensional structures of the unliganded enzyme and a complex of MjNK, an ATP analogue and adenosine were determined to 1.7 and 1.9 A resolution, respectively. Each subunit comprises an alpha/beta-domain and a smaller lid domain and has an overall fold characteristic of the ribokinase superfamily. MjNK shares highest structural similarity to the ribokinases from Escherichia coli and Thermotoga maritima. Similar to ribokinase and other superfamily members, the lid domain of MjNK undergoes a significant conformational change upon substrate binding. In the crystal structure of the MjNK complex, subunit A adopts a closed conformation and subunit B an open conformation. In subunit A all substrates and Mg(2+) were observed, whereas in subunit B only the ATP analogue could be clearly identified in the electron density. The structures of MjNK and E. coli ribokinase (EcRK) were compared with respect to putative determinants of thermal stability. Relative to EcRK, MjNK shows an increased charged and a decreased hydrophobic accessible surface area, as well as a higher fraction of charged residues, ionic networks and large aromatic clusters, characteristics that are frequently observed in enzymes from hyperthermophiles.


    Organizational Affiliation

    Karolinska Institutet, Department of Biosciences at Novum, Center for Structural Biochemistry, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUGAR KINASE MJ0406A302Methanocaldococcus jannaschiiMutation(s): 0 
EC: 2.7.1.213 (UniProt), 2.7.1 (UniProt), 2.7.1.73 (UniProt)
UniProt
Find proteins for Q57849 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57849 
Go to UniProtKB:  Q57849
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.123α = 90
b = 148.081β = 90
c = 41.122γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-17
    Changes: Data collection