2C49

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.,Sect.D 62: 1085

  • DOI: 10.1107/S0907444906024826
  • Primary Citation of Related Structures:  

  • 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 in ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUGAR KINASE MJ0406
A, B
302Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Find proteins for Q57849 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q57849
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADN
Query on ADN

Download SDF File 
Download CCD File 
A, B
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.006α = 90.00
b = 83.131β = 90.00
c = 146.784γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance