2C49

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

Summary for 2C49

• Entry DOI: 10.2210/pdb2c49/pdb
• Related: 2C4E
• Descriptor: SUGAR KINASE MJ0406, ADENOSINE, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: transferase, nucleoside kinase, hyperthermophile, ribokinase family, ribokinase fold
• Biological source: METHANOCOCCUS JANNASCHII
• Total number of polymer chains: 2
• Total formula weight: 69569.32

Authors

Arnfors, L.,Hansen, T.,Meining, W.,Schoenheit, P.,Ladenstein, R. (deposition date: 2005-10-17, release date: 2006-08-30, Last modification date: 2024-05-08)

Primary citation

Arnfors, L.,Hansen, T.,Schoenheit, P.,Ladenstein, R.,Meining, W.
Structure of Methanocaldococcus Jannaschii Nucleoside Kinase: An Archaeal Member of the Ribokinase Family.
Acta Crystallogr.,Sect.D, 62:1085-, 2006

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. 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.

PubMed: 16929110
DOI: 10.1107/S0907444906024826

Experimental method

X-RAY DIFFRACTION (1.92 Å)