PDBsum entry 1rka

Transferase

PDB id: 1rka

Contents

Protein chain

305 a.a. *

Waters ×123

* Residue conservation analysis

PDB id:

1rka

Name:

Transferase

Title:

The apo form of e. Coli ribokinase

Structure:

Protein (ribokinase). Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: mri240. Cellular_location: cytoplasm. Gene: rbsk. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the rbsk gene was cloned behind aurce 11 trp- promoter, forming the plasmid pjgk10

Biol. unit:

Dimer (from PDB file)

Resolution:

2.30Å R-factor: 0.210 R-free: 0.253

Authors:

J.A.Sigrell,A.D.Cameron,S.L.Mowbray

Key ref:

J.A.Sigrell et al. (1999). Induced fit on sugar binding activates ribokinase. J Mol Biol, 290, 1009-1018. PubMed id: 10438599 DOI: 10.1006/jmbi.1999.2938

Date:

22-Mar-99 Release date: 31-Aug-99

Protein chain

P0A9J6  (RBSK_ECOLI) -  Ribokinase from Escherichia coli (strain K12)

Seq: 309 a.a.

Struc: 305 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.15 - ribokinase.
• Reaction: D-ribose + ATP = D-ribose 5-phosphate + ADP + H⁺

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

reference

DOI no: 10.1006/jmbi.1999.2938

J Mol Biol 290:1009-1018 (1999)

PubMed id: 10438599

Induced fit on sugar binding activates ribokinase.

J.A.Sigrell, A.D.Cameron, S.L.Mowbray.

ABSTRACT

The enzyme ribokinase phosphorylates ribose at O5* as the first step in its metabolism. The original X-ray structure of Escherichia coli ribokinase represented the ternary complex including ribose and ADP. Structures are presented here for the apo enzyme, as well as the ribose-bound state and four new ternary complex forms. Combined, the structures suggest that large and small conformational changes play critical roles in the function of this kinase. An initially open apo form can allow entry of the ribose substrate. After ribose binding, the active site lid is observed in a closed conformation, with the sugar trapped underneath. This closure and associated changes in the protein appear to assist ribokinase in recognition of the co-substrate ATP as the next step. Binding of the nucleotide brings about further, less dramatic adjustments in the enzyme structure. Additional small movements are almost certainly required during the phosphoryltransfer reaction. Evidence is presented that some types of movements of the lid are allowed in the ternary complex, which may be critical to the creation and breakdown of the transition state. Similar events are likely to take place during catalysis by other related carbohydrate kinases, including adenosine kinase.

Selected figure(s)

Figure 6.
Figure 6. Stereo plot of the original ternary complex (dark blue) and the most different lid conformation found among the new ternary complex structures (chain A, cyan). Ribose, ADP, phosphate and two nearby water molecules are shown; the phosphate molecule is absent in the latter structure. The apo protein is also shown (red). The struc- tural alignments were done using residues 116-192.

The above figure is reprinted by permission from Elsevier: J Mol Biol (1999, 290, 1009-1018) copyright 1999.

Figure was selected by an automated process.