PDBsum entry 1v1s

Transferase

PDB id: 1v1s

Contents

Protein chains

(+ 0 more) 302 a.a. *

* Residue conservation analysis

PDB id:

1v1s

Name:

Transferase

Title:

2-keto-3-deoxygluconate kinase from thermus thermophilus (crystal form 2)

Structure:

2-keto-3-deoxygluconate kinase. Chain: a, b, c, d, e, f. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PDB file)

Resolution:

3.20Å R-factor: 0.239 R-free: 0.278

Authors:

T.H.Tahirov,E.Inagaki

Key ref:

N.Ohshima et al. (2004). Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate. J Mol Biol, 340, 477-489. PubMed id: 15210349 DOI: 10.1016/j.jmb.2004.04.074

Date:

23-Apr-04 Release date: 26-Apr-04

Protein chains

Q53W83  (KDGK_THET8) -  2-dehydro-3-deoxygluconokinase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 309 a.a.

Struc: 302 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.45 - 2-dehydro-3-deoxygluconokinase.
• Reaction: 2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D- gluconate + ADP + H⁺

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

reference

DOI no: 10.1016/j.jmb.2004.04.074

J Mol Biol 340:477-489 (2004)

PubMed id: 15210349

Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.

N.Ohshima, E.Inagaki, K.Yasuike, K.Takio, T.H.Tahirov.

ABSTRACT

2-Keto-3-deoxygluconate kinase (KDGK) catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate (KDGP). The genome sequence of Thermus thermophilus HB8 contains an open reading frame that has a 30% identity to Escherichia coli KDGK. The KDGK activity of T.thermophilus protein (TtKDGK) has been confirmed, and its crystal structure has been determined by the molecular replacement method and refined with two crystal forms to 2.3 angstroms and 3.2 angstroms, respectively. The enzyme is a hexamer organized as a trimer of dimers. Each subunit is composed of two domains, a larger alpha/beta domain and a smaller beta-sheet domain, similar to that of ribokinase and adenosine kinase, members of the PfkB family of carbohydrate kinases. Furthermore, the TtKDGK structure with its KDG and ATP analogue was determined and refined at 2.1 angstroms. The bound KDG was observed predominantly as an open chain structure. The positioning of ligands and the conservation of important catalytic residues suggest that the reaction mechanism is likely to be similar to that of other members of the PfkB family, including ribokinase. In particular, the Asp251 is postulated to have a role in transferring the gamma-phosphate of ATP to the 5'-hydroxyl group of KDG.

Selected figure(s)

Figure 2.
Figure 2. The overall view of (a) TtKDGK and (b) EcRK dimers. The view is parallel to the pseudo 2-fold axis in (a) and crystallographic 2-fold axis in (b). Subunits are represented by ribbons and are colored green and cyan. The bound ligands are drawn by balls and sticks. The figure was prepared using Molscript[30.] and Raster3D. [30.]

Figure 5.
Figure 5. The KDG binding. (a) 2F[o] -F[c] Fourier maps of bound KDG in the A subunit of TtKDGK. The open chain keto form of KDG and side-chain of Arg167 colored by atom colors: carbon atoms in yellow, nitrogen atoms in cyan and oxygen atoms in red. The modeled a-furanose form of KDG is in cyan. (b) and (c) The hydrogen bonds between the KDG and (b) A and (c) B subunits of TtKDGK. (a) Was prepared using TURBO-FRODO and the (b) and (c) were prepared using Molscript[30.] and Raster3D. [31.]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 340, 477-489) copyright 2004.

Figures were selected by an automated process.