PDBsum entry 2c4e

Transferase

PDB id: 2c4e

Contents

Protein chain

299 a.a. *

Metals

_MG

Waters ×113

* Residue conservation analysis

PDB id:

2c4e

Name:

Transferase

Title:

Crystal structure of methanocaldococcus jannaschii nucleoside kinase - an archaeal member of the ribokinase family

Structure:

Sugar kinase mj0406. Chain: a. Synonym: nucleoside kinase. Engineered: yes

Source:

Methanococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: methanocaldococcus jannaschii

Biol. unit:

Dimer (from PDB file)

Resolution:

1.70Å R-factor: 0.235 R-free: 0.253

Authors:

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

Key ref:

L.Arnfors et al. (2006). Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family. Acta Crystallogr D Biol Crystallogr, 62, 1085-1097. PubMed id: 16929110 DOI: 10.1107/S0907444906024826

Date:

18-Oct-05 Release date: 30-Aug-06

Protein chain

Q57849  (NK_METJA) -  Nucleoside kinase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 302 a.a.

Struc: 299 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.7.1.213 - cytidine kinase.
• Reaction: cytidine + ATP = CMP + ADP + H⁺
• Enzyme class 2: E.C.2.7.1.73 - inosine kinase.
• Reaction: inosine + ATP = IMP + ADP + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444906024826

Acta Crystallogr D Biol Crystallogr 62:1085-1097 (2006)

PubMed id: 16929110

Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family.

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

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.

Selected figure(s)

Figure 3.
Figure 3 Ribbon representation of MjNK. (a) Crystallographic dimer of the apo form (subunit A, purple; subunit A', pink) and (b) in complex with adenosine (red) and AMP-PNP (yellow). Subunit A (dark blue) is in the closed conformation with the lid domain closer to the / -domain and contains the strongly bound adenosine, whereas subunit B (light blue) is in the open conformation and contains an adenosine that is bound with low occupancy. Mg atoms and surrounding waters are shown as green and red spheres, respectively.

Figure 7.
Figure 7 Schematic overview of contacts between adenosine (red), AMP-PNP (green), the solvated magnesium ion (blue) and the protein environment (black). Dashed lines indicate atomic distances between non-C atoms of less than 3.5 Å. The imidazole ring of adenosine is sandwiched between the aromatic ring of Phe113 and the amid group of Gln163.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 1085-1097) copyright 2006.

Figures were selected by an automated process.