PDBsum entry: 1gqt

Transferase

PDB id: 1gqt

Contents

Protein chains

305 a.a. *

Ligands

ACP ×3

RIB ×4

Metals

_CS ×4

Waters ×242

* Residue conservation analysis

PDB id:

1gqt

Name:

Transferase

Title:

Activation of ribokinase by monovalent cations

Structure:

Ribokinase. Chain: a, b, c, d. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.34Å R-factor: 0.196 R-free: 0.257

Authors:

C.E.Andersson,S.L.Mowbray

Key ref:

C.E.Andersson and S.L.Mowbray (2002). Activation of ribokinase by monovalent cations. J Mol Biol, 315, 409-419. PubMed id: 11786021 DOI: 10.1006/jmbi.2001.5248

Date:

05-Dec-01 Release date: 28-Jan-02

Protein chains

P0A9J6  (RBSK_ECOLI) -  Ribokinase

Seq: 309 a.a.

Struc: 305 a.a.

Enzyme reactions

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

ATP + D-ribose (Bound ligand (Het Group name = RIB) corresponds exactly) = ADP (Bound ligand (Het Group name = ACP) matches with 81.00% similarity) + D-ribose 5-phosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: carbohydrate metabolic process (3 terms)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1006/jmbi.2001.5248

J Mol Biol 315:409-419 (2002)

PubMed id: 11786021

Activation of ribokinase by monovalent cations.

C.E.Andersson, S.L.Mowbray.

ABSTRACT

Carbohydrate kinases frequently require a monovalent cation for their activity. The physical basis of this phenomenon is, however, usually unclear. We report here that Escherichia coli ribokinase is activated by potassium with an apparent K(d) of 5 mM; the enzyme should therefore be fully activated under physiological conditions. Cesium can be used as an alternative ion, with an apparent K(d) of 17 mM. An X-ray structure of ribokinase in the presence of cesium was solved and refined at 2.34 A resolution. The cesium ion was bound between two loops immediately adjacent to the anion hole of the active site. The buried location of the site suggests that conformational changes will accompany ion binding, thus providing a direct mechanism for activation. Comparison with structures of a related enzyme, the adenosine kinase of Toxoplasma gondii, support this proposal. This is apparently the first instance in which conformational activation of a carbohydrate kinase by a monovalent cation has been assigned a clear structural basis. The mechanism is probably general to ribokinases, to some adenosine kinases, and to other members of the larger family. A careful re-evaluation of the biochemical and structural data is suggested for other enzyme systems.

Selected figure(s)

Figure 1.
Figure 1. The dimer of RK, and location of various features. RK is shown as ribbon drawings in two views 90° apart ((a) and (b)). One subunit is colored lilac and the other blue-green, with the a/b domain in a lighter shade than the respective b-sheet lids. The anion hole of the active site lies near the N-terminal end of helix a8, which is colored slightly darker than the rest of the a/b domain. Ribose and AMP-PCP are shown as stick representations colored red in both subunits. Residues 249-251 and 285-294, the two loops of the monovalent cation-binding sites, are gold, while the ions themselves are indicated by red spheres.

Figure 2.
Figure 2. The ion-binding site. The residues that define the ion-binding site of RK are shown with atomic colors in a ball-and-stick representation. Most side-chains are removed for simplicity, but the C^a atoms are indicated with slightly larger spheres. Interacting residues are labeled, and the most relevant hydrogen-bonding interactions are indicated by green bubbled lines. The view is similar to that of the left-hand subunit in Figure 1(a); ribose and nucleotide are shown to assist in that comparison.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 315, 409-419) copyright 2002.

Figures were selected by an automated process.