PDBsum entry 2o1x

Transferase

PDB id: 2o1x

Contents

Protein chains

578 a.a. *

538 a.a. *

Ligands

TPP ×4

Metals

_MG ×4

* Residue conservation analysis

PDB id:

2o1x

Name:

Transferase

Title:

1-deoxy-d-xylulose 5-phosphate synthase (dxs) from deinococcus radiodurans

Structure:

1-deoxy-d-xylulose-5-phosphate synthase. Chain: a, b, c, d. Synonym: 1-deoxyxylulose-5-phosphate synthase, dxp synthase, dxps. Engineered: yes

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Gene: dxs. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.90Å R-factor: 0.212 R-free: 0.272

Authors:

S.Xiang,G.Usunow,G.Lange,M.Busch,L.Tong

Key ref:

S.Xiang et al. (2007). Crystal structure of 1-deoxy-D-xylulose 5-phosphate synthase, a crucial enzyme for isoprenoids biosynthesis. J Biol Chem, 282, 2676-2682. PubMed id: 17135236 DOI: 10.1074/jbc.M610235200

Date:

29-Nov-06 Release date: 26-Dec-06

Protein chains

Q9RUB5  (DXS_DEIRA) -  1-deoxy-D-xylulose-5-phosphate synthase from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 629 a.a.

Struc: 578 a.a.*

Protein chains

Q9RUB5  (DXS_DEIRA) -  1-deoxy-D-xylulose-5-phosphate synthase from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 629 a.a.

Struc: 538 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.2.2.1.7 - 1-deoxy-D-xylulose-5-phosphate synthase.
• Pathway: Non-Mevalonate Terpenoid biosynthesis
• Reaction: D-glyceraldehyde 3-phosphate + pyruvate + H⁺ = 1-deoxy-D-xylulose 5-phosphate + CO2
• Cofactor: Thiamine diphosphate

Thiamine diphosphate (Bound ligand (Het Group name = TPP) corresponds exactly)

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

reference

DOI no: 10.1074/jbc.M610235200

J Biol Chem 282:2676-2682 (2007)

PubMed id: 17135236

Crystal structure of 1-deoxy-D-xylulose 5-phosphate synthase, a crucial enzyme for isoprenoids biosynthesis.

S.Xiang, G.Usunow, G.Lange, M.Busch, L.Tong.

ABSTRACT

Isopentenyl pyrophosphate (IPP) is a common precursor for the synthesis of all isoprenoids, which have important functions in living organisms. IPP is produced by the mevalonate pathway in archaea, fungi, and animals. In contrast, IPP is synthesized by a mevalonate-independent pathway in most bacteria, algae, and plant plastids. 1-Deoxy-D-xylulose 5-phosphate synthase (DXS) catalyzes the first and the rate-limiting step of the mevalonate-independent pathway and is an attractive target for the development of novel antibiotics, antimalarials, and herbicides. We report here the first structural information on DXS, from Escherichia coli and Deinococcus radiodurans, in complex with the coenzyme thiamine pyrophosphate (TPP). The structure contains three domains (I, II, and III), each of which bears homology to the equivalent domains in transketolase and the E1 subunit of pyruvate dehydrogenase. However, DXS has a novel arrangement of these domains as compared with the other enzymes, such that the active site of DXS is located at the interface of domains I and II in the same monomer, whereas that of transketolase is located at the interface of the dimer. The coenzyme TPP is mostly buried in the complex, but the C-2 atom of its thiazolium ring is exposed to a pocket that is the substrate-binding site. The structures identify residues that may have important roles in catalysis, which have been confirmed by our mutagenesis studies.

Selected figure(s)

Figure 3.
FIGURE 3. Crystal structures of DXS. A, schematic drawing in stereo of the structure of the D. radiodurans DXS dimer. The three domains of one monomer are colored cyan, green, and yellow, respectively, and the linker between domains I and II is colored red. The other monomer is colored gray. TPP is shown as a stick model in magenta. The 2-fold axis of the dimer is vertical. B, structure of E. coli DXS dimer, in the same orientation and color scheme as A. The images were produced with PyMol (44).

Figure 4.
FIGURE 4. Crystal structures of transketolase and pyruvate dehydrogenase E1 subunit. A, schematic drawing of the structure of yeast transketolase dimer (35). B, structure of E. coli pyruvate dehydrogenase E1 subunit dimer (36). The structures are viewed in the same orientation as that for DXS in Fig. 3. The images were produced with PyMol (44).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 2676-2682) copyright 2007.

Figures were selected by an automated process.