PDBsum entry 1kof

Transferase

PDB id: 1kof

Contents

Protein chains

171 a.a. *

Ligands

ACP ×2

Metals

_MG ×2

Waters ×67

* Residue conservation analysis

PDB id:

1kof

Name:

Transferase

Title:

Crystal structure of gluconate kinase

Structure:

Gluconate kinase. Chain: a, b. Synonym: thermoresistant gluconokinase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: gntk. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.80Å R-factor: 0.255 R-free: 0.315

Authors:

L.Kraft,G.A.Sprenger,Y.Lindqvist

Key ref:

L.Kraft et al. (2002). Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography. J Mol Biol, 318, 1057-1069. PubMed id: 12054802 DOI: 10.1016/S0022-2836(02)00215-2

Date:

20-Dec-01 Release date: 29-May-02

Protein chains

P46859  (GNTK_ECOLI) -  Thermoresistant gluconokinase from Escherichia coli (strain K12)

Seq: 175 a.a.

Struc: 171 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.12 - gluconokinase.
• Reaction: D-gluconate + ATP = 6-phospho-D-gluconate + ADP + H⁺

D-gluconate + ATP = 6-phospho-D-gluconate + ADP (Bound ligand (Het Group name = ACP) matches with 81.25% similarity) + H(+)

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

reference

DOI no: 10.1016/S0022-2836(02)00215-2

J Mol Biol 318:1057-1069 (2002)

PubMed id: 12054802

Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography.

L.Kraft, G.A.Sprenger, Y.Lindqvist.

ABSTRACT

The crystal structure of gluconate kinase from Escherichia coli has been determined to 2.0 A resolution by X-ray crystallography. The three-dimensional structure was solved by multi-wavelength anomalous dispersion, using a crystal of selenomethionine-substituted enzyme. Gluconate kinase is an alpha/beta structure consisting of a twisted parallel beta-sheet surrounded by alpha-helices with overall topology similar to nucleoside monophosphate (NMP) kinases, such as adenylate kinase. In order to identify residues involved in substrate binding and catalysis, structures of binary complexes with ATP, the ATP analogue adenosine 5'-(beta,gamma-methylene) triphosphate and the product, gluconate-6-phosphate have been determined. Significant conformational changes are induced upon binding of ATP to the enzyme. The largest changes involve a hinge-bending motion of the NMP(bind) part and a motion of the LID with adjacent helices, which opens the cavity to the second substrate, gluconate. Opening of the active site cleft upon ATP binding is the opposite of what has been observed in the NMP kinase family so far, which usually close their active site to prevent fortuitous hydrolysis of ATP. The conformational change positions the side-chain of Arg120 to stack with the purine ring of ATP and the side-chain of Arg124 is shifted to interact with the alpha-phosphate in ATP, at the same time protecting ATP from solvent water. The beta and gamma-phosphate groups of ATP bind in the predicted P-loop. A conserved lysine side-chain interacts with the gamma-phosphate group, and might promote phosphoryl transfer. Gluconate-6-phosphate binds with its phosphate group in a similar position as the gamma-phosphate of ATP, consistent with inline phosphoryl transfer. The gluconate binding-pocket in GntK is located in a different position than the nucleoside binding-site usually found in NMP kinases.

Selected figure(s)

Figure 1.
Figure 1. Schematic view of the homodimer of gluconate kinase. The colouring is by B-factor, from 10 Å2 (blue) via grey to 50 Å2 (red). Two chloride ions bound in apo-enzyme mark the binding sites for the phosphate and carboxyl-group of gluconate-6-phosphate. This and all other Figures were generated using BOBSCRIPT[46.] and Raster3D [47.] if not otherwise specified.

Figure 4.
Figure 4. Stereo picture of the superimposed C^a-traces of (a) adenylate kinase (ligated with Ap[5]A, a bisubstrate analogue) (yellow) and GntK (red) and of (b) adenosine-5-phosphosulphate kinase (green) and GntK (red), showing the differences in the NMP[bind] region and the LID.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 1057-1069) copyright 2002.

Figures were selected by an automated process.